File: test_align.py

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# Copyright 2000-2001 by Brad Chapman.  All rights reserved.
# Revisions copyright 2007-2003 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.


"""Test alignment stuff.

Right now we've got tests for:

- Reading and Writing clustal format
- Reading and Writing fasta format
- Converting between formats

"""

# standard library
import os
import unittest
import warnings
from io import StringIO

from Bio import Align
from Bio import AlignIO

# biopython
from Bio import BiopythonDeprecationWarning
from Bio import motifs
from Bio.Align import AlignInfo
from Bio.Align import Alignment
from Bio.Align import MultipleSeqAlignment
from Bio.Align import PairwiseAligner
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import numpy as np


class TestBasics(unittest.TestCase):
    def test_empty_alignment(self):
        """Very simple tests on an empty alignment."""
        alignment = MultipleSeqAlignment([])
        self.assertEqual(alignment.get_alignment_length(), 0)
        self.assertEqual(len(alignment), 0)
        alignment = alignment.alignment  # new-style Alignment object
        self.assertEqual(alignment.length, 0)
        self.assertEqual(len(alignment), 0)

    def test_basic_alignment(self):
        """Basic tests on a simple alignment of three sequences."""
        msa = MultipleSeqAlignment([])
        letters = "AbcDefGhiJklMnoPqrStuVwxYz"
        msa.append(SeqRecord(Seq(letters), id="mixed"))
        msa.append(SeqRecord(Seq(letters.lower()), id="lower"))
        msa.append(SeqRecord(Seq(letters.upper()), id="upper"))
        msa.append(SeqRecord(Seq(letters), id="duplicate"))
        del msa[3]
        self.assertEqual(msa.get_alignment_length(), 26)
        self.assertEqual(len(msa), 3)
        self.assertEqual(msa[0].seq, letters)
        self.assertEqual(msa[1].seq, letters.lower())
        self.assertEqual(msa[2].seq, letters.upper())
        self.assertEqual(msa[0].id, "mixed")
        self.assertEqual(msa[1].id, "lower")
        self.assertEqual(msa[2].id, "upper")
        for col, letter in enumerate(letters):
            self.assertEqual(msa[:, col], letter + letter.lower() + letter.upper())
        # Check row extractions:
        self.assertEqual(msa[0].id, "mixed")
        self.assertEqual(msa[-1].id, "upper")
        # Check sub-alignment extraction by row slicing:
        self.assertIsInstance(msa[::-1], MultipleSeqAlignment)
        self.assertEqual(msa[::-1][0].id, "upper")
        self.assertEqual(msa[::-1][2].id, "mixed")
        # create a new-style Alignment object
        alignment = msa.alignment
        self.assertEqual(alignment.shape, (3, 26))
        self.assertEqual(len(alignment), 3)
        self.assertEqual(alignment.sequences[0].seq, letters)
        self.assertEqual(alignment.sequences[1].seq, letters.lower())
        self.assertEqual(alignment.sequences[2].seq, letters.upper())
        self.assertEqual(alignment.sequences[0].id, "mixed")
        self.assertEqual(alignment.sequences[1].id, "lower")
        self.assertEqual(alignment.sequences[2].id, "upper")
        for col, letter in enumerate(letters):
            self.assertEqual(
                alignment[:, col], letter + letter.lower() + letter.upper()
            )
        # Check row extractions:
        self.assertEqual(alignment[0], letters)
        self.assertEqual(alignment[-1], letters.upper())
        # Check sub-alignment extraction by row slicing:
        self.assertIsInstance(alignment[::-1], Alignment)
        self.assertEqual(alignment[::-1].sequences[0].id, "upper")
        self.assertEqual(alignment[::-1].sequences[2].id, "mixed")


class TestReading(unittest.TestCase):
    def test_read_clustal1(self):
        """Parse an alignment file and get an alignment object."""
        opuntia_clustal_header = """\
CLUSTAL X (1.81) multiple sequence alignment


"""
        opuntia_clustal_body = """\
gi|6273285|gb|AF191659.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273284|gb|AF191658.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273287|gb|AF191661.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273286|gb|AF191660.1|AF191      TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273290|gb|AF191664.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273289|gb|AF191663.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273291|gb|AF191665.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
                                    ******* **** *************************************

gi|6273285|gb|AF191659.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273284|gb|AF191658.1|AF191      TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273287|gb|AF191661.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA
gi|6273286|gb|AF191660.1|AF191      TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA
gi|6273290|gb|AF191664.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273289|gb|AF191663.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273291|gb|AF191665.1|AF191      TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA
                                    ******          ********  **** ********* *********

gi|6273285|gb|AF191659.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT
gi|6273284|gb|AF191658.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273287|gb|AF191661.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273286|gb|AF191660.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273290|gb|AF191664.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273289|gb|AF191663.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT
gi|6273291|gb|AF191665.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
                                    ************************************ *********** *

gi|6273285|gb|AF191659.1|AF191      ACCAGA
gi|6273284|gb|AF191658.1|AF191      ACCAGA
gi|6273287|gb|AF191661.1|AF191      ACCAGA
gi|6273286|gb|AF191660.1|AF191      ACCAGA
gi|6273290|gb|AF191664.1|AF191      ACCAGA
gi|6273289|gb|AF191663.1|AF191      ACCAGA
gi|6273291|gb|AF191665.1|AF191      ACCAGA
                                    ******


"""  # noqa : W291
        opuntia_fasta = """\
>gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----
------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCCATTGATTTAGTGTACCAGA
>gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--
------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273287|gb|AF191661.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----
------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273286|gb|AF191660.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----
------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA
------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA
------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCTATTGATTTAGTATACCAGA
>gi|6273291|gb|AF191665.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA
TATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
"""
        opuntia_fasta_oneline = """\
>gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA
>gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273287|gb|AF191661.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273286|gb|AF191660.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA
>gi|6273291|gb|AF191665.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
"""
        opuntia_fasta_oneline_with_description = """\
>gi|6273285|gb|AF191659.1|AF191 gi|6273285|gb|AF191659.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA
>gi|6273284|gb|AF191658.1|AF191 gi|6273284|gb|AF191658.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273287|gb|AF191661.1|AF191 gi|6273287|gb|AF191661.1|AF191
TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273286|gb|AF191660.1|AF191 gi|6273286|gb|AF191660.1|AF191
TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273290|gb|AF191664.1|AF191 gi|6273290|gb|AF191664.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
>gi|6273289|gb|AF191663.1|AF191 gi|6273289|gb|AF191663.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA
>gi|6273291|gb|AF191665.1|AF191 gi|6273291|gb|AF191665.1|AF191
TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
"""
        path = os.path.join(os.getcwd(), "Clustalw", "opuntia.aln")
        msa = AlignIO.read(path, "clustal")
        opuntia_clustal = opuntia_clustal_header + opuntia_clustal_body
        self.assertEqual(format(msa, "clustal"), opuntia_clustal)
        self.assertEqual(format(msa, "fasta"), opuntia_fasta)
        # create a new-style Alignment object
        alignment = msa.alignment
        self.assertEqual(format(alignment, "clustal"), opuntia_clustal_body)
        # New-style Alignment objects generate FASTA format with the sequence
        # on one line. Also, the clustal parser in Bio.AlignIO generates
        # SeqRecords with an (identical) ID and a description; the clustal
        # parser in Bio.Align generates SeqRecords with an ID only.
        self.assertEqual(
            format(alignment, "fasta"), opuntia_fasta_oneline_with_description
        )
        alignment = Align.read(path, "clustal")
        self.assertEqual(format(alignment, "fasta"), opuntia_fasta_oneline)

    def test_read_clustal2(self):
        """Parse an alignment file and get an alignment object."""
        clustalw_clustal_header = """\
CLUSTAL X (1.81) multiple sequence alignment


"""
        clustalw_clustal_body = """\
gi|4959044|gb|AAD34209.1|AF069      MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNN
gi|671626|emb|CAA85685.1|           ---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFR
                                              * *: ::    :.   :*  :  :. : . :*  ::   .

gi|4959044|gb|AAD34209.1|AF069      LLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW
gi|671626|emb|CAA85685.1|           VTPQPG-----------------VPPEEAGAAVAAESSTGT---------
                                    :   **                  **:...   *.*** ..         

gi|4959044|gb|AAD34209.1|AF069      LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQT
gi|671626|emb|CAA85685.1|           WTTVWTDGLTSLDRYKG-----RCYHIEPVPG------------------
                                     .:*   * *: .* :*        : :* .*                  

gi|4959044|gb|AAD34209.1|AF069      SENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE
gi|671626|emb|CAA85685.1|           -EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIP
                                     *::.  .    .:: :*..*  :* .*   .. .  :    .  :    

gi|4959044|gb|AAD34209.1|AF069      VPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRRAPTLEQSSEN
gi|671626|emb|CAA85685.1|           VAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGLSAKNYGRAVYE
                                    *. .:: : .      .* .  :  *.:     ..::   * .  ::  :

gi|4959044|gb|AAD34209.1|AF069      EPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS
gi|671626|emb|CAA85685.1|           CLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYLN
                                      .*.    :.    :. .  .  .* **.*..  :..  *.. .    .

gi|4959044|gb|AAD34209.1|AF069      ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYE
gi|671626|emb|CAA85685.1|           ATAG-----------------------TCEEMIKRAIFARELGVPIVMHD
                                     ::*                         :.: .*:    :     * ::

gi|4959044|gb|AAD34209.1|AF069      SERGGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLR
gi|671626|emb|CAA85685.1|           YLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQKNHGMHFRVLAKAL
                                       ***  . * :. .  .  :  *: .:: :::   ..   . : :   

gi|4959044|gb|AAD34209.1|AF069      QIMTGFGELSYFMYSDSDSEPSASVSSRNVERVESRNGRGSSGGGNSSGS
gi|671626|emb|CAA85685.1|           RLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSRGIYFTQDW
                                    ::  *    *  : .. :.* . ::.  :: * :  :   * *   :.. 

gi|4959044|gb|AAD34209.1|AF069      SSSSSPSPSSSGESSESSSKMFEGSSEGGSSGPSRKDGRHRAPVTFDESG
gi|671626|emb|CAA85685.1|           VSLPGVIPVASG-----------------------------GIHVWHMPA
                                     * ..  * :**                             .  .:. ..

gi|4959044|gb|AAD34209.1|AF069      SLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKTCSVCI
gi|671626|emb|CAA85685.1|           LTEIFGDDSVLQFGGGTLGHPWGNAPGAVANRVA-----------VEACV
                                       :*.  ..: :. .  .:* * :   : * .             ..*:

gi|4959044|gb|AAD34209.1|AF069      TEYTEGDKLRKLPCSHEFHVHCIDRWLSE-NSTCPICRRAVLSSGNRESV
gi|671626|emb|CAA85685.1|           KARNEG---RDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD--
                                    .  .**   *.*... :  ::   :* .*  ::* : :.  :.    :  

gi|4959044|gb|AAD34209.1|AF069      V
gi|671626|emb|CAA85685.1|           -
                                     


"""  # noqa : W291

        path = os.path.join(os.curdir, "Clustalw", "clustalw.aln")
        msa = AlignIO.read(path, "clustal")
        clustalw_clustal = clustalw_clustal_header + clustalw_clustal_body
        self.assertEqual(format(msa, "clustal"), clustalw_clustal)
        # create a new-style Alignment object
        alignment = msa.alignment
        self.assertEqual(format(alignment, "clustal"), clustalw_clustal_body)

    def test_read_write_clustal(self):
        """Test the base alignment stuff."""
        path = os.path.join(os.getcwd(), "Clustalw", "opuntia.aln")
        msa = AlignIO.read(path, "clustal")
        self.assertEqual(len(msa), 7)
        seq_record = msa[0]
        self.assertEqual(seq_record.description, "gi|6273285|gb|AF191659.1|AF191")
        self.assertEqual(
            seq_record.seq,
            Seq(
                "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA"
            ),
        )
        seq_record = msa[1]
        self.assertEqual(seq_record.description, "gi|6273284|gb|AF191658.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = msa[2]
        self.assertEqual(seq_record.description, "gi|6273287|gb|AF191661.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = msa[3]
        self.assertEqual(seq_record.description, "gi|6273286|gb|AF191660.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = msa[4]
        self.assertEqual(seq_record.description, "gi|6273290|gb|AF191664.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = msa[5]
        self.assertEqual(seq_record.description, "gi|6273289|gb|AF191663.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA",
        )
        seq_record = msa[6]
        self.assertEqual(seq_record.description, "gi|6273291|gb|AF191665.1|AF191")
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(msa.get_alignment_length(), 156)
        alignment = msa.alignment
        dictionary = alignment.substitutions
        self.assertEqual(len(dictionary), 4)
        self.assertEqual(dictionary.shape, (4, 4))
        self.assertEqual(len(dictionary.keys()), 16)
        self.assertAlmostEqual(dictionary[("A", "A")], 1395)
        self.assertAlmostEqual(dictionary[("A", "C")], 3)
        self.assertAlmostEqual(dictionary[("A", "G")], 13)
        self.assertAlmostEqual(dictionary[("A", "T")], 6)
        self.assertAlmostEqual(dictionary[("C", "A")], 3)
        self.assertAlmostEqual(dictionary[("C", "C")], 271)
        self.assertAlmostEqual(dictionary[("C", "G")], 0)
        self.assertAlmostEqual(dictionary[("C", "T")], 16)
        self.assertAlmostEqual(dictionary[("G", "A")], 5)
        self.assertAlmostEqual(dictionary[("G", "C")], 0)
        self.assertAlmostEqual(dictionary[("G", "G")], 480)
        self.assertAlmostEqual(dictionary[("G", "T")], 0)
        self.assertAlmostEqual(dictionary[("T", "A")], 6)
        self.assertAlmostEqual(dictionary[("T", "C")], 12)
        self.assertAlmostEqual(dictionary[("T", "G")], 0)
        self.assertAlmostEqual(dictionary[("T", "T")], 874)

        motif = motifs.Motif("ACGT", alignment)
        counts = motif.counts
        self.assertEqual(
            counts.calculate_consensus(identity=0.7),
            "TATACATTAAAGNAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTNCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            str(counts),
            """\
        0      1      2      3      4      5      6      7      8      9     10     11     12     13     14     15     16     17     18     19     20     21     22     23     24     25     26     27     28     29     30     31     32     33     34     35     36     37     38     39     40     41     42     43     44     45     46     47     48     49     50     51     52     53     54     55     56     57     58     59     60     61     62     63     64     65     66     67     68     69     70     71     72     73     74     75     76     77     78     79     80     81     82     83     84     85     86     87     88     89     90     91     92     93     94     95     96     97     98     99    100    101    102    103    104    105    106    107    108    109    110    111    112    113    114    115    116    117    118    119    120    121    122    123    124    125    126    127    128    129    130    131    132    133    134    135    136    137    138    139    140    141    142    143    144    145    146    147    148    149    150    151    152    153    154    155
A:   0.00   7.00   0.00   7.00   0.00   7.00   0.00   1.00   7.00   7.00   7.00   0.00   4.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   1.00   6.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   1.00   0.00   7.00   0.00   0.00   7.00   0.00   7.00
C:   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   3.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   2.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00
G:   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   3.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00
T:   7.00   0.00   7.00   0.00   0.00   0.00   7.00   6.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   1.00   0.00   0.00   7.00   7.00   4.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   5.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   7.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00
""",
        )

        alignment = msa.alignment
        motif = motifs.Motif("ACGT", alignment)
        counts = motif.counts
        self.assertEqual(
            str(counts),
            """\
        0      1      2      3      4      5      6      7      8      9     10     11     12     13     14     15     16     17     18     19     20     21     22     23     24     25     26     27     28     29     30     31     32     33     34     35     36     37     38     39     40     41     42     43     44     45     46     47     48     49     50     51     52     53     54     55     56     57     58     59     60     61     62     63     64     65     66     67     68     69     70     71     72     73     74     75     76     77     78     79     80     81     82     83     84     85     86     87     88     89     90     91     92     93     94     95     96     97     98     99    100    101    102    103    104    105    106    107    108    109    110    111    112    113    114    115    116    117    118    119    120    121    122    123    124    125    126    127    128    129    130    131    132    133    134    135    136    137    138    139    140    141    142    143    144    145    146    147    148    149    150    151    152    153    154    155
A:   0.00   7.00   0.00   7.00   0.00   7.00   0.00   1.00   7.00   7.00   7.00   0.00   4.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   1.00   6.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   1.00   0.00   7.00   0.00   0.00   7.00   0.00   7.00
C:   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   3.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   2.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00
G:   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   3.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00
T:   7.00   0.00   7.00   0.00   0.00   0.00   7.00   6.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   1.00   0.00   0.00   7.00   7.00   4.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   5.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   7.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00
""",
        )

        with self.assertWarns(BiopythonDeprecationWarning):
            align_info = AlignInfo.SummaryInfo(msa)
        self.assertEqual(align_info.get_column(1), "AAAAAAA")
        self.assertEqual(align_info.get_column(7), "TTTATTT")

        alignment = msa.alignment
        motif = motifs.Motif("ACGT", alignment)
        counts = motif.counts
        self.assertEqual(
            str(counts),
            """\
        0      1      2      3      4      5      6      7      8      9     10     11     12     13     14     15     16     17     18     19     20     21     22     23     24     25     26     27     28     29     30     31     32     33     34     35     36     37     38     39     40     41     42     43     44     45     46     47     48     49     50     51     52     53     54     55     56     57     58     59     60     61     62     63     64     65     66     67     68     69     70     71     72     73     74     75     76     77     78     79     80     81     82     83     84     85     86     87     88     89     90     91     92     93     94     95     96     97     98     99    100    101    102    103    104    105    106    107    108    109    110    111    112    113    114    115    116    117    118    119    120    121    122    123    124    125    126    127    128    129    130    131    132    133    134    135    136    137    138    139    140    141    142    143    144    145    146    147    148    149    150    151    152    153    154    155
A:   0.00   7.00   0.00   7.00   0.00   7.00   0.00   1.00   7.00   7.00   7.00   0.00   4.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   1.00   6.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   1.00   0.00   7.00   0.00   0.00   7.00   0.00   7.00
C:   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   3.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   2.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00
G:   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   3.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00
T:   7.00   0.00   7.00   0.00   0.00   0.00   7.00   6.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   1.00   0.00   0.00   7.00   7.00   4.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   5.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   7.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00
""",
        )
        value = sum(motif[5:50].relative_entropy)
        self.assertAlmostEqual(value, 88.42309908538343)  # Alignment
        relative_entropy = motif.relative_entropy
        value = sum(relative_entropy)
        self.assertAlmostEqual(value, 306.2080592664532)  # Alignment
        self.assertAlmostEqual(relative_entropy[0], 2.0)
        self.assertAlmostEqual(relative_entropy[1], 2.0)
        self.assertAlmostEqual(relative_entropy[2], 2.0)
        self.assertAlmostEqual(relative_entropy[3], 2.0)
        self.assertAlmostEqual(relative_entropy[4], 2.0)
        self.assertAlmostEqual(relative_entropy[5], 2.0)
        self.assertAlmostEqual(relative_entropy[6], 2.0)
        self.assertAlmostEqual(relative_entropy[7], 1.4083272214176723)
        self.assertAlmostEqual(relative_entropy[8], 2.0)
        self.assertAlmostEqual(relative_entropy[9], 2.0)
        self.assertAlmostEqual(relative_entropy[10], 2.0)
        self.assertAlmostEqual(relative_entropy[11], 2.0)
        self.assertAlmostEqual(relative_entropy[12], 1.0147718639657484)
        self.assertAlmostEqual(relative_entropy[13], 2.0)
        self.assertAlmostEqual(relative_entropy[14], 2.0)
        self.assertAlmostEqual(relative_entropy[15], 2.0)
        self.assertAlmostEqual(relative_entropy[16], 2.0)
        self.assertAlmostEqual(relative_entropy[17], 2.0)
        self.assertAlmostEqual(relative_entropy[18], 2.0)
        self.assertAlmostEqual(relative_entropy[19], 2.0)
        self.assertAlmostEqual(relative_entropy[20], 2.0)
        self.assertAlmostEqual(relative_entropy[21], 2.0)
        self.assertAlmostEqual(relative_entropy[22], 2.0)
        self.assertAlmostEqual(relative_entropy[23], 2.0)
        self.assertAlmostEqual(relative_entropy[24], 2.0)
        self.assertAlmostEqual(relative_entropy[25], 2.0)
        self.assertAlmostEqual(relative_entropy[26], 2.0)
        self.assertAlmostEqual(relative_entropy[27], 2.0)
        self.assertAlmostEqual(relative_entropy[28], 2.0)
        self.assertAlmostEqual(relative_entropy[29], 2.0)
        self.assertAlmostEqual(relative_entropy[30], 2.0)
        self.assertAlmostEqual(relative_entropy[31], 2.0)
        self.assertAlmostEqual(relative_entropy[32], 2.0)
        self.assertAlmostEqual(relative_entropy[33], 2.0)
        self.assertAlmostEqual(relative_entropy[34], 2.0)
        self.assertAlmostEqual(relative_entropy[35], 2.0)
        self.assertAlmostEqual(relative_entropy[36], 2.0)
        self.assertAlmostEqual(relative_entropy[37], 2.0)
        self.assertAlmostEqual(relative_entropy[38], 2.0)
        self.assertAlmostEqual(relative_entropy[39], 2.0)
        self.assertAlmostEqual(relative_entropy[40], 2.0)
        self.assertAlmostEqual(relative_entropy[41], 2.0)
        self.assertAlmostEqual(relative_entropy[42], 2.0)
        self.assertAlmostEqual(relative_entropy[43], 2.0)
        self.assertAlmostEqual(relative_entropy[44], 2.0)
        self.assertAlmostEqual(relative_entropy[45], 2.0)
        self.assertAlmostEqual(relative_entropy[46], 2.0)
        self.assertAlmostEqual(relative_entropy[47], 2.0)
        self.assertAlmostEqual(relative_entropy[48], 2.0)
        self.assertAlmostEqual(relative_entropy[49], 2.0)
        self.assertAlmostEqual(relative_entropy[50], 2.0)
        self.assertAlmostEqual(relative_entropy[51], 2.0)
        self.assertAlmostEqual(relative_entropy[52], 2.0)
        self.assertAlmostEqual(relative_entropy[53], 2.0)
        self.assertAlmostEqual(relative_entropy[54], 2.0)
        self.assertAlmostEqual(relative_entropy[55], 2.0)
        self.assertAlmostEqual(relative_entropy[56], 2.0)
        self.assertAlmostEqual(relative_entropy[57], 2.0)
        self.assertAlmostEqual(relative_entropy[58], 2.0)
        self.assertAlmostEqual(relative_entropy[59], 2.0)
        self.assertAlmostEqual(relative_entropy[60], 2.0)
        self.assertAlmostEqual(relative_entropy[61], 2.0)
        self.assertAlmostEqual(relative_entropy[62], 2.0)
        self.assertAlmostEqual(relative_entropy[63], 2.0)
        self.assertAlmostEqual(relative_entropy[64], 2.0)
        self.assertAlmostEqual(relative_entropy[65], 2.0)
        self.assertAlmostEqual(relative_entropy[66], 2.0)
        self.assertAlmostEqual(relative_entropy[67], 2.0)
        self.assertAlmostEqual(relative_entropy[68], 2.0)
        self.assertAlmostEqual(relative_entropy[69], 2.0)
        self.assertAlmostEqual(relative_entropy[70], 2.0)
        self.assertAlmostEqual(relative_entropy[71], 2.0)
        self.assertAlmostEqual(relative_entropy[72], 2.0)
        self.assertAlmostEqual(relative_entropy[73], 2.0)
        self.assertAlmostEqual(relative_entropy[74], 1.4083272214176723)
        self.assertAlmostEqual(relative_entropy[75], 1.4083272214176723)
        self.assertAlmostEqual(relative_entropy[76], 2.0)
        self.assertAlmostEqual(relative_entropy[77], 2.0)
        self.assertAlmostEqual(relative_entropy[78], 2.0)
        self.assertAlmostEqual(relative_entropy[79], 2.0)
        self.assertAlmostEqual(relative_entropy[80], 1.0147718639657484)
        self.assertAlmostEqual(relative_entropy[81], 2.0)
        self.assertAlmostEqual(relative_entropy[82], 2.0)
        self.assertAlmostEqual(relative_entropy[83], 2.0)
        self.assertAlmostEqual(relative_entropy[84], 2.0)
        self.assertAlmostEqual(relative_entropy[85], 2.0)
        self.assertAlmostEqual(relative_entropy[86], 2.0)
        self.assertAlmostEqual(relative_entropy[87], 2.0)
        self.assertAlmostEqual(relative_entropy[88], 2.0)
        self.assertAlmostEqual(relative_entropy[89], 2.0)
        self.assertAlmostEqual(relative_entropy[90], 1.136879431433369)
        self.assertAlmostEqual(relative_entropy[91], 2.0)
        self.assertAlmostEqual(relative_entropy[92], 2.0)
        self.assertAlmostEqual(relative_entropy[93], 2.0)
        self.assertAlmostEqual(relative_entropy[94], 2.0)
        self.assertAlmostEqual(relative_entropy[95], 2.0)
        self.assertAlmostEqual(relative_entropy[96], 2.0)
        self.assertAlmostEqual(relative_entropy[97], 2.0)
        self.assertAlmostEqual(relative_entropy[98], 2.0)
        self.assertAlmostEqual(relative_entropy[99], 2.0)
        self.assertAlmostEqual(relative_entropy[100], 2.0)
        self.assertAlmostEqual(relative_entropy[101], 2.0)
        self.assertAlmostEqual(relative_entropy[102], 2.0)
        self.assertAlmostEqual(relative_entropy[103], 2.0)
        self.assertAlmostEqual(relative_entropy[104], 2.0)
        self.assertAlmostEqual(relative_entropy[105], 2.0)
        self.assertAlmostEqual(relative_entropy[106], 2.0)
        self.assertAlmostEqual(relative_entropy[107], 2.0)
        self.assertAlmostEqual(relative_entropy[108], 2.0)
        self.assertAlmostEqual(relative_entropy[109], 2.0)
        self.assertAlmostEqual(relative_entropy[110], 2.0)
        self.assertAlmostEqual(relative_entropy[111], 2.0)
        self.assertAlmostEqual(relative_entropy[112], 2.0)
        self.assertAlmostEqual(relative_entropy[113], 2.0)
        self.assertAlmostEqual(relative_entropy[114], 2.0)
        self.assertAlmostEqual(relative_entropy[115], 2.0)
        self.assertAlmostEqual(relative_entropy[116], 2.0)
        self.assertAlmostEqual(relative_entropy[117], 2.0)
        self.assertAlmostEqual(relative_entropy[118], 2.0)
        self.assertAlmostEqual(relative_entropy[119], 2.0)
        self.assertAlmostEqual(relative_entropy[120], 2.0)
        self.assertAlmostEqual(relative_entropy[121], 2.0)
        self.assertAlmostEqual(relative_entropy[122], 2.0)
        self.assertAlmostEqual(relative_entropy[123], 2.0)
        self.assertAlmostEqual(relative_entropy[124], 2.0)
        self.assertAlmostEqual(relative_entropy[125], 2.0)
        self.assertAlmostEqual(relative_entropy[126], 2.0)
        self.assertAlmostEqual(relative_entropy[127], 2.0)
        self.assertAlmostEqual(relative_entropy[128], 2.0)
        self.assertAlmostEqual(relative_entropy[129], 2.0)
        self.assertAlmostEqual(relative_entropy[130], 2.0)
        self.assertAlmostEqual(relative_entropy[131], 2.0)
        self.assertAlmostEqual(relative_entropy[132], 2.0)
        self.assertAlmostEqual(relative_entropy[133], 2.0)
        self.assertAlmostEqual(relative_entropy[134], 2.0)
        self.assertAlmostEqual(relative_entropy[135], 2.0)
        self.assertAlmostEqual(relative_entropy[136], 1.4083272214176723)
        self.assertAlmostEqual(relative_entropy[137], 2.0)
        self.assertAlmostEqual(relative_entropy[138], 2.0)
        self.assertAlmostEqual(relative_entropy[139], 2.0)
        self.assertAlmostEqual(relative_entropy[140], 2.0)
        self.assertAlmostEqual(relative_entropy[141], 2.0)
        self.assertAlmostEqual(relative_entropy[142], 2.0)
        self.assertAlmostEqual(relative_entropy[143], 2.0)
        self.assertAlmostEqual(relative_entropy[144], 2.0)
        self.assertAlmostEqual(relative_entropy[145], 2.0)
        self.assertAlmostEqual(relative_entropy[146], 2.0)
        self.assertAlmostEqual(relative_entropy[147], 2.0)
        self.assertAlmostEqual(relative_entropy[148], 1.4083272214176723)
        self.assertAlmostEqual(relative_entropy[149], 2.0)
        self.assertAlmostEqual(relative_entropy[150], 2.0)
        self.assertAlmostEqual(relative_entropy[151], 2.0)
        self.assertAlmostEqual(relative_entropy[152], 2.0)
        self.assertAlmostEqual(relative_entropy[153], 2.0)
        self.assertAlmostEqual(relative_entropy[154], 2.0)
        self.assertAlmostEqual(relative_entropy[155], 2.0)
        # create a new-style Alignment object
        del seq_record
        del align_info
        del dictionary
        del value
        alignment = msa.alignment
        self.assertEqual(len(alignment), 7)
        seq_record = alignment.sequences[0]
        self.assertEqual(seq_record.description, "gi|6273285|gb|AF191659.1|AF191")
        self.assertEqual(
            alignment[0],
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            Seq(
                "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGTACCAGA"
            ),
        )
        seq_record = alignment.sequences[1]
        self.assertEqual(seq_record.description, "gi|6273284|gb|AF191658.1|AF191")
        self.assertEqual(
            alignment[1],
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATAATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = alignment.sequences[2]
        self.assertEqual(seq_record.description, "gi|6273287|gb|AF191661.1|AF191")
        self.assertEqual(
            alignment[2],
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = alignment.sequences[3]
        self.assertEqual(seq_record.description, "gi|6273286|gb|AF191660.1|AF191")
        self.assertEqual(
            alignment[3],
            "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            "TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATAATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = alignment.sequences[4]
        self.assertEqual(seq_record.description, "gi|6273290|gb|AF191664.1|AF191")
        self.assertEqual(
            alignment[4],
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        seq_record = alignment.sequences[5]
        self.assertEqual(seq_record.description, "gi|6273289|gb|AF191663.1|AF191")
        self.assertEqual(
            alignment[5],
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTATACCAGA",
        )
        seq_record = alignment.sequences[6]
        self.assertEqual(seq_record.description, "gi|6273291|gb|AF191665.1|AF191")
        self.assertEqual(
            alignment[6],
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            seq_record.seq,
            "TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(alignment.shape, (7, 156))
        substitutions = alignment.substitutions
        self.assertEqual(len(substitutions), 4)
        self.assertEqual(substitutions.shape, (4, 4))
        self.assertAlmostEqual(substitutions[("A", "A")], 1395)
        self.assertAlmostEqual(substitutions[("A", "C")], 3)
        self.assertAlmostEqual(substitutions[("A", "G")], 13)
        self.assertAlmostEqual(substitutions[("A", "T")], 6)
        self.assertAlmostEqual(substitutions[("C", "A")], 3)
        self.assertAlmostEqual(substitutions[("C", "C")], 271)
        self.assertAlmostEqual(substitutions[("C", "G")], 0)
        self.assertAlmostEqual(substitutions[("C", "T")], 16)
        self.assertAlmostEqual(substitutions[("G", "A")], 5)
        self.assertAlmostEqual(substitutions[("G", "C")], 0)
        self.assertAlmostEqual(substitutions[("G", "G")], 480)
        self.assertAlmostEqual(substitutions[("G", "T")], 0)
        self.assertAlmostEqual(substitutions[("T", "A")], 6)
        self.assertAlmostEqual(substitutions[("T", "C")], 12)
        self.assertAlmostEqual(substitutions[("T", "G")], 0)
        self.assertAlmostEqual(substitutions[("T", "T")], 874)
        motif = motifs.Motif(alphabet="ACGT", alignment=alignment)
        self.assertEqual(
            motif.consensus,
            "TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        self.assertEqual(
            motif.degenerate_consensus,
            "TATACATTAAAGRAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATATATATAATATATTTCAAATTYCCTTATATATCCAAATATAAAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGTACCAGA",
        )
        matrix = motif.counts
        self.assertEqual(
            str(matrix),
            """\
        0      1      2      3      4      5      6      7      8      9     10     11     12     13     14     15     16     17     18     19     20     21     22     23     24     25     26     27     28     29     30     31     32     33     34     35     36     37     38     39     40     41     42     43     44     45     46     47     48     49     50     51     52     53     54     55     56     57     58     59     60     61     62     63     64     65     66     67     68     69     70     71     72     73     74     75     76     77     78     79     80     81     82     83     84     85     86     87     88     89     90     91     92     93     94     95     96     97     98     99    100    101    102    103    104    105    106    107    108    109    110    111    112    113    114    115    116    117    118    119    120    121    122    123    124    125    126    127    128    129    130    131    132    133    134    135    136    137    138    139    140    141    142    143    144    145    146    147    148    149    150    151    152    153    154    155
A:   0.00   7.00   0.00   7.00   0.00   7.00   0.00   1.00   7.00   7.00   7.00   0.00   4.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   1.00   6.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   1.00   0.00   7.00   0.00   0.00   7.00   0.00   7.00
C:   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   3.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   2.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00
G:   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   3.00   0.00   7.00   7.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00
T:   7.00   0.00   7.00   0.00   0.00   0.00   7.00   6.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   4.00   0.00   3.00   0.00   1.00   0.00   1.00   0.00   1.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   7.00   7.00   0.00   1.00   0.00   0.00   7.00   7.00   4.00   0.00   0.00   7.00   7.00   0.00   7.00   0.00   7.00   0.00   5.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   7.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   7.00   0.00   0.00   0.00   7.00   0.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   7.00   0.00   6.00   0.00   7.00   7.00   0.00   0.00   7.00   7.00   7.00   0.00   0.00   7.00   0.00   7.00   0.00   0.00   0.00   0.00   0.00   0.00
""",
        )
        self.assertEqual(
            format(motif, "transfac"),
            """\
P0      A      C      G      T
01      0      0      0      7      T
02      7      0      0      0      A
03      0      0      0      7      T
04      7      0      0      0      A
05      0      7      0      0      C
06      7      0      0      0      A
07      0      0      0      7      T
08      1      0      0      6      T
09      7      0      0      0      A
10      7      0      0      0      A
11      7      0      0      0      A
12      0      0      7      0      G
13      4      0      3      0      R
14      7      0      0      0      A
15      0      0      7      0      G
16      0      0      7      0      G
17      0      0      7      0      G
18      0      0      7      0      G
19      0      0      7      0      G
20      7      0      0      0      A
21      0      0      0      7      T
22      0      0      7      0      G
23      0      7      0      0      C
24      0      0      7      0      G
25      0      0      7      0      G
26      7      0      0      0      A
27      0      0      0      7      T
28      7      0      0      0      A
29      7      0      0      0      A
30      7      0      0      0      A
31      0      0      0      7      T
32      0      0      7      0      G
33      0      0      7      0      G
34      7      0      0      0      A
35      7      0      0      0      A
36      7      0      0      0      A
37      0      0      7      0      G
38      0      0      7      0      G
39      0      7      0      0      C
40      0      0      7      0      G
41      7      0      0      0      A
42      7      0      0      0      A
43      7      0      0      0      A
44      0      0      7      0      G
45      7      0      0      0      A
46      7      0      0      0      A
47      7      0      0      0      A
48      0      0      7      0      G
49      7      0      0      0      A
50      7      0      0      0      A
51      0      0      0      7      T
52      7      0      0      0      A
53      0      0      0      7      T
54      7      0      0      0      A
55      0      0      0      7      T
56      7      0      0      0      A
57      0      0      0      4      T
58      4      0      0      0      A
59      0      0      0      3      T
60      3      0      0      0      A
61      0      0      0      1      T
62      1      0      0      0      A
63      0      0      0      1      T
64      1      0      0      0      A
65      0      0      0      1      T
66      1      0      0      0      A
67      7      0      0      0      A
68      0      0      0      7      T
69      7      0      0      0      A
70      0      0      0      7      T
71      7      0      0      0      A
72      0      0      0      7      T
73      0      0      0      7      T
74      0      0      0      7      T
75      1      6      0      0      C
76      6      0      0      1      A
77      7      0      0      0      A
78      7      0      0      0      A
79      0      0      0      7      T
80      0      0      0      7      T
81      0      3      0      4      Y
82      0      7      0      0      C
83      0      7      0      0      C
84      0      0      0      7      T
85      0      0      0      7      T
86      7      0      0      0      A
87      0      0      0      7      T
88      7      0      0      0      A
89      0      0      0      7      T
90      7      0      0      0      A
91      0      2      0      5      T
92      0      7      0      0      C
93      0      7      0      0      C
94      7      0      0      0      A
95      7      0      0      0      A
96      7      0      0      0      A
97      0      0      0      7      T
98      7      0      0      0      A
99      0      0      0      7      T
100      7      0      0      0      A
101      7      0      0      0      A
102      7      0      0      0      A
103      7      0      0      0      A
104      7      0      0      0      A
105      0      0      0      7      T
106      7      0      0      0      A
107      0      0      0      7      T
108      0      7      0      0      C
109      0      0      0      7      T
110      7      0      0      0      A
111      7      0      0      0      A
112      0      0      0      7      T
113      7      0      0      0      A
114      7      0      0      0      A
115      7      0      0      0      A
116      0      0      0      7      T
117      0      0      0      7      T
118      7      0      0      0      A
119      0      0      7      0      G
120      7      0      0      0      A
121      0      0      0      7      T
122      0      0      7      0      G
123      7      0      0      0      A
124      7      0      0      0      A
125      0      0      0      7      T
126      7      0      0      0      A
127      0      0      0      7      T
128      0      7      0      0      C
129      7      0      0      0      A
130      7      0      0      0      A
131      7      0      0      0      A
132      0      0      7      0      G
133      7      0      0      0      A
134      7      0      0      0      A
135      0      0      0      7      T
136      0      7      0      0      C
137      0      1      0      6      T
138      7      0      0      0      A
139      0      0      0      7      T
140      0      0      0      7      T
141      0      0      7      0      G
142      7      0      0      0      A
143      0      0      0      7      T
144      0      0      0      7      T
145      0      0      0      7      T
146      7      0      0      0      A
147      0      0      7      0      G
148      0      0      0      7      T
149      1      0      6      0      G
150      0      0      0      7      T
151      7      0      0      0      A
152      0      7      0      0      C
153      0      7      0      0      C
154      7      0      0      0      A
155      0      0      7      0      G
156      7      0      0      0      A
XX
//
""",
        )
        self.assertAlmostEqual(sum(motif[5:50].relative_entropy), 88.42309908538343)
        relative_entropy = motif.relative_entropy
        self.assertAlmostEqual(sum(relative_entropy[5:50]), 88.42309908538343)
        self.assertAlmostEqual(sum(relative_entropy), 306.20805926645323)
        self.assertEqual(alignment[:, 1], "AAAAAAA")
        self.assertAlmostEqual(motif.relative_entropy[1], 2.0)
        self.assertEqual(alignment[:, 7], "TTTATTT")
        self.assertAlmostEqual(relative_entropy[7], 1.4083272214176723)

    def test_read_fasta(self):
        path = os.path.join(os.curdir, "Quality", "example.fasta")
        msa = AlignIO.read(path, "fasta")
        self.assertEqual(len(msa), 3)
        seq_record = msa[0]
        self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_413_324")
        self.assertEqual(seq_record.seq, "CCCTTCTTGTCTTCAGCGTTTCTCC")
        seq_record = msa[1]
        self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_540_792")
        self.assertEqual(seq_record.seq, "TTGGCAGGCCAAGGCCGATGGATCA")
        seq_record = msa[2]
        self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_443_348")
        self.assertEqual(seq_record.seq, "GTTGCTTCTGGCGTGGGTGGGGGGG")
        self.assertEqual(msa.get_alignment_length(), 25)
        self.assertEqual(
            str(msa),
            """\
Alignment with 3 rows and 25 columns
CCCTTCTTGTCTTCAGCGTTTCTCC EAS54_6_R1_2_1_413_324
TTGGCAGGCCAAGGCCGATGGATCA EAS54_6_R1_2_1_540_792
GTTGCTTCTGGCGTGGGTGGGGGGG EAS54_6_R1_2_1_443_348""",
        )
        alignment = msa.alignment
        self.assertEqual(len(alignment), 3)
        seq_record = alignment.sequences[0]
        self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_413_324")
        self.assertEqual(seq_record.seq, "CCCTTCTTGTCTTCAGCGTTTCTCC")
        seq_record = alignment.sequences[1]
        self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_540_792")
        self.assertEqual(seq_record.seq, "TTGGCAGGCCAAGGCCGATGGATCA")
        seq_record = alignment.sequences[2]
        self.assertEqual(seq_record.description, "EAS54_6_R1_2_1_443_348")
        self.assertEqual(seq_record.seq, "GTTGCTTCTGGCGTGGGTGGGGGGG")
        self.assertEqual(alignment.length, 25)
        motif = motifs.Motif(alphabet="ACGT", alignment=alignment)
        self.assertEqual(motif.consensus, "CTCGCATCCCAAGCAGGATGGATCA")
        self.assertEqual(motif.degenerate_consensus, "BYBKYHKBBBVHKBVSSDKKKVKSV")
        self.assertEqual(
            str(alignment),
            """\
EAS54_6_R         0 CCCTTCTTGTCTTCAGCGTTTCTCC 25
EAS54_6_R         0 TTGGCAGGCCAAGGCCGATGGATCA 25
EAS54_6_R         0 GTTGCTTCTGGCGTGGGTGGGGGGG 25
""",
        )
        self.assertEqual(
            motif.counts.calculate_consensus(identity=0.6), "NTNGCNTNNNNNGNNGGNTGGNTCN"
        )


class TestFromAlignmentsWithSameReference(unittest.TestCase):

    def test_pwas_built_with_strings(self):
        """Test that from_alignments_with_same_reference creates the correct Alignment when PWA inputs were built with strings"""
        aligner = PairwiseAligner()

        # Input sequences
        reference_str = "ACGT"
        seq1_str = "ACGGT"
        seq2_str = "AT"

        # Generate pairwise alignments
        pwa1 = next(aligner.align(reference_str, seq1_str))
        pwa2 = next(aligner.align(reference_str, seq2_str))

        # Use the method being tested
        msa = Alignment.from_alignments_with_same_reference([pwa1, pwa2])

        # Check that the output is of correct type
        self.assertIsInstance(msa, Alignment)

        # Check the number of sequences in the MSA
        self.assertEqual(len(msa), 3)

        # Validate that from_alignments_with_same_reference gives the right msa
        self.assertEqual(str(msa[0]), "ACG-T")
        self.assertEqual(str(msa[1]), "ACGGT")
        self.assertEqual(str(msa[2]), "A---T")

    def test_pwas_built_with_seqs(self):
        """Test that from_alignments_with_same_reference works with PWAs built with Seq objects."""
        aligner = PairwiseAligner()

        # Input sequences
        reference_seq = Seq("ACGT")
        seq1_seq = Seq("ACGGT")
        seq2_seq = Seq("AT")

        # Generate pairwise alignments
        pwa1 = next(aligner.align(reference_seq, seq1_seq))
        pwa2 = next(aligner.align(reference_seq, seq2_seq))

        # Use the method being tested
        msa = Alignment.from_alignments_with_same_reference([pwa1, pwa2])

        # Check that the output is of correct type
        self.assertIsInstance(msa, Alignment)

        # Validate that from_alignments_with_same_reference gives the right msa
        self.assertEqual(str(msa[0]), "ACG-T")
        self.assertEqual(str(msa[1]), "ACGGT")
        self.assertEqual(str(msa[2]), "A---T")

        # Works with undefined sequences
        pwa1_undefined = Alignment([Seq(None, 4), Seq(None, 5)], pwa1.coordinates)
        pwa2_undefined = Alignment([Seq(None, 4), Seq(None, 2)], pwa2.coordinates)
        msa_undefined = Alignment.from_alignments_with_same_reference(
            [pwa1_undefined, pwa2_undefined]
        )
        self.assertTrue((msa_undefined.coordinates == msa.coordinates).all())

    def test_metadata_preservation(self):
        """Test that sequence metadata (IDs and descriptions) are preserved in the Alignment.

        Sequence metadata may exist if pairwise alignments are built with SeqRecords.
        This also tests that from_alignments_with_same_reference works with pairwise alignments built with SeqRecord objects.
        """
        aligner = PairwiseAligner()

        # Input sequences
        reference_seqr = SeqRecord(Seq("ACGT"), id="reference", description="desc 1")
        seq1_seqr = SeqRecord(Seq("ACGGT"), id="seq1", description="desc 2")
        seq2_seqr = SeqRecord(Seq("AT"), id="seq2", description="desc 3")

        # Generate pairwise alignments
        pwa1 = next(aligner.align(reference_seqr, seq1_seqr))
        pwa2 = next(aligner.align(reference_seqr, seq2_seqr))

        # Use the method being tested
        msa = Alignment.from_alignments_with_same_reference([pwa1, pwa2])

        # Validate that from_alignments_with_same_reference gives the right msa
        self.assertEqual(str(msa[0]), "ACG-T")
        self.assertEqual(str(msa[1]), "ACGGT")
        self.assertEqual(str(msa[2]), "A---T")

        # Check that id and description are retained
        self.assertEqual(msa.sequences[0].id, "reference")
        self.assertEqual(msa.sequences[1].id, "seq1")
        self.assertEqual(msa.sequences[2].id, "seq2")
        self.assertEqual(msa.sequences[0].description, "desc 1")
        self.assertEqual(msa.sequences[1].description, "desc 2")

    def test_mismatched_references(self):
        """Test that mismatched reference sequences raise a ValueError."""
        aligner = PairwiseAligner()
        pwa1 = next(aligner.align("ACGAAAT", "ACGGT"))
        pwa2 = next(aligner.align("ACCT", "AT"))

        with self.assertRaises(ValueError) as context:
            Alignment.from_alignments_with_same_reference([pwa1, pwa2])
        self.assertIn("All reference sequences must", str(context.exception))

        # Works with undefined sequences
        pwa1_undefined = Alignment([Seq(None, 7), Seq(None, 5)], pwa1.coordinates)
        pwa2_undefined = Alignment([Seq(None, 4), Seq(None, 2)], pwa2.coordinates)
        with self.assertRaises(ValueError) as context:
            Alignment.from_alignments_with_same_reference(
                [pwa1_undefined, pwa2_undefined]
            )
        self.assertIn("All reference sequences must", str(context.exception))

        # Works with mix
        pwa1_undefined = Alignment([Seq(None, 7), Seq(None, 5)], pwa1.coordinates)
        with self.assertRaises(ValueError) as context:
            Alignment.from_alignments_with_same_reference([pwa1_undefined, pwa2])
        self.assertIn("All reference sequences must", str(context.exception))

    def test_empty_input(self):
        """Test that empty input raises a ValueError."""
        with self.assertRaises(ValueError):
            Alignment.from_alignments_with_same_reference([])

    def test_input_with_three_sequences(self):
        """Test that the method works with input Alignments of three sequences"""
        # Input sequences
        reference_str = "ACGT"
        seq1_str = "ACGGT"
        seq2_str = "AT"
        seq3_str = "AGT"
        seq4_str = "ACT"

        # Coordinates for each alignment
        coords1 = np.array([[0, 1, 2, 3, 3, 4], [0, 1, 2, 3, 4, 5], [0, 1, 1, 1, 1, 2]])

        coords2 = np.array([[0, 1, 2, 3, 4], [0, 1, 1, 2, 3], [0, 1, 2, 2, 3]])

        # Generate input alignments
        alignment1 = Alignment([reference_str, seq1_str, seq2_str], coords1)
        alignment2 = Alignment([reference_str, seq3_str, seq4_str], coords2)

        # Use the method being tested
        msa = Alignment.from_alignments_with_same_reference([alignment1, alignment2])

        # Check that the output is of correct type
        self.assertIsInstance(msa, Alignment)

        # Check the number of sequences in the MSA
        self.assertEqual(len(msa), 5)

        # Validate that from_alignments_with_same_reference gives the right msa
        self.assertEqual(str(msa[0]), "ACG-T")
        self.assertEqual(str(msa[1]), "ACGGT")
        self.assertEqual(str(msa[2]), "A---T")
        self.assertEqual(str(msa[3]), "A-G-T")
        self.assertEqual(str(msa[4]), "AC--T")

    def test_mixed_input(self):
        """Test that the method works with input Alignments of mixed number of sequences"""
        aligner = PairwiseAligner()

        # Input sequences
        reference_str = "ACGT"
        seq1_str = "ACT"
        seq2_str = "ACGGT"
        seq3_str = "AT"

        # Coordinates for an alignment of three sequences
        coords = np.array([[0, 1, 2, 3, 3, 4], [0, 1, 2, 3, 4, 5], [0, 1, 1, 1, 1, 2]])

        # Generate input alignments
        pwa = next(aligner.align(reference_str, seq1_str))
        not_pwa = Alignment([reference_str, seq2_str, seq3_str], coords)

        # Use the method being tested
        msa = Alignment.from_alignments_with_same_reference([pwa, not_pwa])

        # Check that the output is of correct type
        self.assertIsInstance(msa, Alignment)

        # Check the number of sequences in the MSA
        self.assertEqual(len(msa), 4)

        # Validate that from_alignments_with_same_reference gives the right msa
        self.assertEqual(str(msa[0]), "ACG-T")
        self.assertEqual(str(msa[1]), "AC--T")
        self.assertEqual(str(msa[2]), "ACGGT")
        self.assertEqual(str(msa[3]), "A---T")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)