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|
# Copyright 2008-2014 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.
"""Tests for Bio.AlignIO.EmbossIO"""
import unittest
from Bio._py3k import StringIO
from Bio.AlignIO.EmbossIO import EmbossWriter, EmbossIterator
# http://emboss.sourceforge.net/docs/themes/alnformats/align.simple
simple_example = \
"""########################################
# Program: alignret
# Rundate: Wed Jan 16 17:16:13 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 4
# 1: IXI_234
# 2: IXI_235
# 3: IXI_236
# 4: IXI_237
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 95/131 (72.5%)
# Similarity: 127/131 (96.9%)
# Gaps: 25/131 (19.1%)
# Score: 100.0
#
#
#=======================================
IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50
IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41
IXI_236 1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT 48
IXI_237 1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT 45
|||||:|||||||||::::::: |||||:||||:::::|||||:|||||
IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100
IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81
IXI_236 49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G 96
IXI_237 46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G 93
||:||||||||||||||||||||:::::::::::||||||||||||| |
IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131
IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112
IXI_236 97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE 127
IXI_237 94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE 124
|||:||||:|||||:|||||||::|||||||
#---------------------------------------
#---------------------------------------
"""
# http://emboss.sourceforge.net/docs/themes/alnformats/align.pair
pair_example = \
"""########################################
# Program: water
# Rundate: Wed Jan 16 17:23:19 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 112/131 (85.5%)
# Similarity: 112/131 (85.5%)
# Gaps: 19/131 (14.5%)
# Score: 591.5
#
#
#=======================================
IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50
||||||||||||||| ||||||||||||||||||||||||||
IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41
IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100
|||||||||||||||||||||||| ||||||||||||||||
IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81
IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131
|||||||||||||||||||||||||||||||
IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112
#---------------------------------------
#---------------------------------------
""" # noqa for pep8 W291 trailing whitespace
pair_example2 = \
"""########################################
# Program: needle
# Rundate: Sun 27 Apr 2007 17:20:35
# Commandline: needle
# [-asequence] Spo0F.faa
# [-bsequence] paired_r.faa
# -sformat2 pearson
# Align_format: srspair
# Report_file: ref_rec .needle
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94968718|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 124
# Identity: 32/124 (25.8%)
# Similarity: 64/124 (51.6%)
# Gaps: 17/124 (13.7%)
# Score: 112.0
#
#
#=======================================
ref_rec 1 KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDL 46
:|:.|| :.|.|::|.: :.|.....:|.:|.||:.:..:..|.:
gi|94968718|r 1 -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRV 47
ref_rec 47 VLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALT 96
|::|..:|||.|::..|:::....:|.|:::|.:.|...::.:.|.||..
gi|94968718|r 48 VVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANG 97
ref_rec 97 HFAK-PFDIDEIRDAV-------- 111
:..| ..|:|.|: ||
gi|94968718|r 98 YILKSAIDLDLIQ-AVRRVANGET 120
#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94968761|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 119
# Identity: 34/119 (28.6%)
# Similarity: 58/119 (48.7%)
# Gaps: 9/119 ( 7.6%)
# Score: 154.0
#
#
#=======================================
ref_rec 1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLD 50
||||||:......|:..|...|::.....|.::||:|...:..||:|.|
gi|94968761|r 1 -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSD 49
ref_rec 51 MKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK 100
:.:||.||:.:|:.:|.......|::|:....::|..::..||||....|
gi|94968761|r 50 VVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEK 99
ref_rec 101 PFDIDEIRDAV-------- 111
|...|::...|
gi|94968761|r 100 PLSTDKLLLTVENALKLKR 118
#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94967506|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 120
# Identity: 29/120 (24.2%)
# Similarity: 53/120 (44.2%)
# Gaps: 9/120 ( 7.5%)
# Score: 121.0
#
#
#=======================================
ref_rec 1 -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLL 49
.|::|||..|..:.:..||.:.|:..........|.:.:.....||.::
gi|94967506|r 1 LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIV 50
ref_rec 50 DMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA 99
|:.:....|:|:|:|.:|....:..:|:|....|:|...|...||:.:..
gi|94967506|r 51 DVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQ 100
ref_rec 100 KPFDIDEIRDAV-------- 111
||.|||.:.:..
gi|94967506|r 101 KPIDIDALLNIAERALEHKE 120
#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94970045|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 118
# Identity: 30/118 (25.4%)
# Similarity: 64/118 (54.2%)
# Gaps: 9/118 ( 7.6%)
# Score: 126.0
#
#
#=======================================
ref_rec 1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVL 48
:|:|:|:..:|....:.....||:...|.:|.:||.:.:| ||.|:::
gi|94970045|r 1 -VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLI 49
ref_rec 49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF 98
.|:.:||:.|..:.:.:..|....:|:.|:.|.: :.:..:.|:.:.:.|
gi|94970045|r 50 TDLVMPGISGRVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAF 98
ref_rec 99 -AKPFDID----EIRDAV 111
.|||.:| :||:.:
gi|94970045|r 99 LRKPFRMDALSAKIREVL 116
#=======================================
#
# Aligned_sequences: 2
# 1: ref_rec
# 2: gi|94970041|receiver
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 125
# Identity: 35/125 (28.0%)
# Similarity: 70/125 (56.0%)
# Gaps: 18/125 (14.4%)
# Score: 156.5
#
#
#=======================================
ref_rec 1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVL 48
.:|:|:|:.|:|.|:..:.:::||...:|.:|.:||:|| :.::.|::|
gi|94970041|r 1 TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLL 50
ref_rec 49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF 98
.|:.:.||.|.|:.:|:::...:::||.|:.|.:..:::. |.||..
gi|94970041|r 51 SDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTES 96
ref_rec 99 A----KPFDIDEIRDAV-------- 111
| |||..|.:...|
gi|94970041|r 97 AEFLQKPFTSDSLLRKVRAVLQKRQ 121
#---------------------------------------
#---------------------------------------
""" # noqa for pep8 W291 trailing whitespace
pair_example3 = """########################################
# Program: needle
# Rundate: Mon 14 Jul 2008 11:45:42
# Commandline: needle
# [-asequence] asis:TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC
# [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT
# -filter
# Align_format: srspair
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: asis
# 2: asis
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity: 210/667 (31.5%)
# Similarity: 210/667 (31.5%)
# Gaps: 408/667 (61.2%)
# Score: 561.0
#
#
#=======================================
asis 1 TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAAT 50
asis 0 -------------------------------------------------- 0
asis 51 AGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGA 100
asis 0 -------------------------------------------------- 0
asis 101 CTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTG 150
asis 0 -------------------------------------------------- 0
asis 151 GGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGA 200
.||||||
asis 1 ------------TTATTAA------------------------------- 7
asis 201 TACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGG 244
.|||||.|| |||..|..|| ||||.||||.||.| ||.|
asis 8 -TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG 50
asis 245 GAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAG 288
||.|.|||||.|||.||||.|||| | |||||||||
asis 51 ---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAG 90
asis 289 GTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTA 331
||.|.||||||| ||||||||.| ||.| |||.|.|||||
asis 91 GTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTA 134
asis 332 TTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTC 377
||| |||||| .||||...||||..|||||.
asis 135 TTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTT 167
asis 378 GT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA-------- 418
.| ||||||||||| || ||.||.||.||
asis 168 ATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTC 202
asis 419 -------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GT 449
||..||.||.|.|||..||||.|| ||||| |
asis 203 ATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG- 251
asis 450 TTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTT 498
||| |.||| |||||||||.||| .||||||...|||||||||
asis 252 ---AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTT 292
asis 499 TTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTT 548
||||||||..| ||||||||
asis 293 TTTTTATTAAG-AAAGGTTT------------------------------ 311
asis 549 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGT 598
asis 311 -------------------------------------------------- 311
asis 599 GAAAGGGGGTTAATAGC 615
asis 311 ----------------- 311
#---------------------------------------
#---------------------------------------""" # noqa for pep8 W291 trailing whitespace
class TestEmbossIO(unittest.TestCase):
def test_pair_example(self):
alignments = list(EmbossIterator(StringIO(pair_example)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
def test_simple_example(self):
alignments = list(EmbossIterator(StringIO(simple_example)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 4)
self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"])
def test_pair_plus_simple(self):
alignments = list(EmbossIterator(StringIO(pair_example + simple_example)))
self.assertEqual(len(alignments), 2)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(len(alignments[1]), 4)
self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
self.assertEqual([r.id for r in alignments[1]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"])
def test_pair_example2(self):
alignments = list(EmbossIterator(StringIO(pair_example2)))
self.assertEqual(len(alignments), 5)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual([r.id for r in alignments[0]], ["ref_rec", "gi|94968718|receiver"])
self.assertEqual([r.id for r in alignments[4]], ["ref_rec", "gi|94970041|receiver"])
def test_pair_example3(self):
alignments = list(EmbossIterator(StringIO(pair_example3)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual([r.id for r in alignments[0]], ["asis", "asis"])
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
