#!/usr/bin/env python

"""
test_uclust.py : provides unit tests for the uclust.py module

Modified from Daniel McDonald's test_cd_hit.py code on Feb-4-2010 """

from os import getcwd, rmdir, remove
from subprocess import Popen, PIPE, STDOUT
from os.path import isfile
from cogent.util.misc import remove_files
from cogent.core.moltype import DNA
from cogent.util.unit_test import TestCase, main
from cogent.app.util import get_tmp_filename, ApplicationError
from cogent.app.uclust import (Uclust, 
 uclust_fasta_sort_from_filepath,
 uclust_cluster_from_sorted_fasta_filepath,
 uclust_convert_uc_to_cdhit_from_filepath,
 parse_uclust_clstr_file, get_output_filepaths,
 get_clusters_from_fasta_filepath,
 uclust_search_and_align_from_fasta_filepath,
 process_uclust_pw_alignment_results)

__author__ = "William Walters"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Daniel McDonald","William Walters","Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
__status__ = "Development"

class UclustTests(TestCase):

    def setUp(self):
        
        self.tmp_unsorted_fasta_filepath = \
         get_tmp_filename(prefix="uclust_test", suffix=".fasta")
        tmp_unsorted_fasta = open(self.tmp_unsorted_fasta_filepath,"w")
        tmp_unsorted_fasta.write('\n'.join(raw_dna_seqs))
        tmp_unsorted_fasta.close()
        
        self.tmp_sorted_fasta_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".fasta")
        tmp_sorted_fasta = open(self.tmp_sorted_fasta_filepath,"w")
        tmp_sorted_fasta.write('\n'.join(sorted_dna_seqs))
        tmp_sorted_fasta.close()
        
        self.tmp_uc_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".uc")
        tmp_uc = open(self.tmp_uc_filepath,"w")
        tmp_uc.write('\n'.join(uc_dna_clusters))
        tmp_uc.close()
         
        self.tmp_clstr_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".clstr")
         
        self.WorkingDir = '/tmp/uclust_test'
        self.tmpdir = '/tmp/'
        
        self.files_to_remove = [self.tmp_unsorted_fasta_filepath,
                                self.tmp_sorted_fasta_filepath,
                                self.tmp_uc_filepath,
                                self.tmp_clstr_filepath]
    
    def tearDown(self):
        remove_files(self.files_to_remove,error_on_missing=False)
        
    def test_fasta_sorting(self):
        """ Should sort fasta seqs from largest to smallest in outfile 
        
        Since a fasta file has to be passed to the app controller for uclust,
        a temporary fasta file is created, and the raw fasta seqs supplied
        in this module are written to it.  This file is sent to the app 
        controller, and the resulting sorted file is compared to the expected
        results to ensure proper function of uclust as called by this app
        controller."""

        test_app = Uclust({'--tmpdir':self.tmpdir})

        
        test_app_res = test_app(data = \
         {'--mergesort':self.tmp_unsorted_fasta_filepath,\
         '--output':self.tmp_sorted_fasta_filepath})

        sorted_fasta_actual = [l.strip() 
            for l in open(test_app_res['Output'].name,"U")]
        sorted_fasta_expected = [l.strip() for l in sorted_dna_seqs if l]
            
        self.assertEqual(sorted_fasta_actual,sorted_fasta_expected)
        
        test_app_res.cleanUp()

    def test_clustering_fasta_filepath(self):
        """ Should create clusters in uclust format from sorted fasta file 
        
        Since a fasta file has to be passed to the app controller for uclust,
        a temporary fasta file is created, and the sorted seqs supplied
        in this module are written to it.  This file is sent to the app 
        controller, and the resulting uclust file is compared to the expected
        results to ensure proper function of uclust as called by this app
        controller."""
        
        

        test_app = Uclust({'--id':0.9},HALT_EXEC=False)
        test_app_res = test_app(data = \
         {'--input':self.tmp_sorted_fasta_filepath,\
         '--uc':self.tmp_uc_filepath})
        
        uc_file = open(test_app_res['ClusterFile'].name,"U")
        # compare the actual and expect uc files, ignoring comment lines
        uc_file_actual = [l.strip() for l in uc_file 
         if not l.startswith('#')]
        uc_file_expected = [l.strip() for l in uc_dna_clusters 
         if not l.startswith('#')]
        
        self.assertEqual(uc_file_actual, uc_file_expected)
    
        test_app_res.cleanUp()

    def test_convert_to_cdhit_from_uc_filepath(self):
        """ Should convert given uclust (.uc) file to cdhit (.clstr) format 
        
        Since a .uc file has to be passed to the app controller for uclust,
        a temporary .uc file is created, and the clusters supplied
        in this module are written to it.  This file is sent to the app 
        controller, and the resulting .clstr file is compared to the expected
        results to ensure proper function of uclust as called by this app
        controller."""
        test_app = Uclust()
        
        test_app_res = test_app(data = \
           {'--uc2clstr':self.tmp_uc_filepath,'--output':self.tmp_clstr_filepath})

        clstr_file = open(test_app_res['Output'].name,"U")
        clstr_res = []
        for line in clstr_file:
            clstr_res.append(line.replace('\t',''))
            
        self.assertEqual(clstr_res, clstr_clusters)
   
        test_app_res.cleanUp()
    
class UclustConvenienceWrappers(TestCase):
    """ Unit tests for uclust convenience wrappers """

    def setUp(self):
        
        self.tmp_unsorted_fasta_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".fasta")
        tmp_unsorted_fasta = open(self.tmp_unsorted_fasta_filepath,"w")
        tmp_unsorted_fasta.write('\n'.join(raw_dna_seqs))
        tmp_unsorted_fasta.close()
         
         
        self.tmp_sorted_fasta_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".fasta")
        tmp_sorted_fasta = open(self.tmp_sorted_fasta_filepath,"w")
        tmp_sorted_fasta.write('\n'.join(sorted_dna_seqs))
        tmp_sorted_fasta.close()
        
        self.tmp_uc_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".uc")
        tmp_uc = open(self.tmp_uc_filepath,"w")
        tmp_uc.write('\n'.join(uc_dna_clusters))
        tmp_uc.close()
        
        self.tmp_clstr_filepath = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".clstr")
        
        self.search_align_out1_expected = search_align_out1_expected
        self.search_align_out_fasta_pairs1 = search_align_out_fasta_pairs1
        self.search_align_out_uc1 = search_align_out_uc1
        self.search_align_query1_fp = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".clstr")
        open(self.search_align_query1_fp,'w').write(search_align_query1)
        self.search_align_template1_fp = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".clstr")
        open(self.search_align_template1_fp,'w').write(search_align_template1)
        
        
        self.search_align_out2_expected = search_align_out2_expected
        self.search_align_query2_fp = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".clstr")
        open(self.search_align_query2_fp,'w').write(search_align_query2)
        self.search_align_template2_fp = \
         get_tmp_filename(prefix = "uclust_test", suffix = ".clstr")
        open(self.search_align_template2_fp,'w').write(search_align_template2)
        
        self.files_to_remove = [self.tmp_unsorted_fasta_filepath,
                                self.tmp_sorted_fasta_filepath,
                                self.tmp_uc_filepath,
                                self.tmp_clstr_filepath,
                                self.search_align_query1_fp,
                                self.search_align_template1_fp,
                                self.search_align_query2_fp,
                                self.search_align_template2_fp]
        
    def tearDown(self):
        remove_files(self.files_to_remove,error_on_missing=False)


    def test_uclust_fasta_sort_from_filepath(self):
        """ Given an unsorted fasta filepath, will return sorted file """
        
        app_res = \
         uclust_fasta_sort_from_filepath(self.tmp_unsorted_fasta_filepath)
        
        sorted_fasta_actual = [l.strip() 
            for l in open(app_res['Output'].name,"U")]
        sorted_fasta_expected = [l.strip() for l in sorted_dna_seqs if l]
        
        self.assertEqual(sorted_fasta_actual,sorted_fasta_expected)
        
        app_res.cleanUp()
        
        
    def test_uclust_cluster_from_sorted_fasta_filepath(self):
        """ Given a sorted fasta filepath, will return uclust (.uc) file """
        

        app_res = \
         uclust_cluster_from_sorted_fasta_filepath(self.tmp_sorted_fasta_filepath, \
         percent_ID = 0.90,HALT_EXEC=False)

        
        uc_file = open(app_res['ClusterFile'].name,"U")
        # compare the actual and expect uc files, ignoring comment lines
        uc_file_actual = [l.strip() for l in uc_file 
         if not l.startswith('#')]
        uc_file_expected = [l.strip() for l in uc_dna_clusters 
         if not l.startswith('#')]
        
        self.assertEqual(uc_file_actual, uc_file_expected)
        app_res.cleanUp()
        
    def test_uclust_convert_uc_to_cdhit_from_filepath(self):
        """ Given a uclust (.uc) file will return converted clstr file """

        app_res = uclust_convert_uc_to_cdhit_from_filepath(self.tmp_uc_filepath)

        
        clstr_file = open(app_res['Output'].name,"U")
        clstr_res = []
        for line in clstr_file:
            clstr_res.append(line.replace('\t',''))
            
        self.assertEqual(clstr_res, clstr_clusters)
        app_res.cleanUp()
        
    def test_parse_uclust_clstr_file(self):
        """ Ensures that list of lists of OTUs will be returned """
        
        clusters_res = parse_uclust_clstr_file(clstr_clusters)
        
        self.assertEqual(clusters_res, expected_cluster_list)
    
    def test_get_output_filepaths(self):
        """ Properly generates output filepath names """
        
        fasta_res, uc_res, cd_hit_res, output_dir_res = \
         get_output_filepaths("/tmp/","test_seqs.fasta")
        
        self.assertEqual(fasta_res, "/tmp/test_seqs_sorted.fasta")
        self.assertEqual(uc_res, "/tmp/test_seqs_sorted.uc")
        self.assertEqual(cd_hit_res, "/tmp/test_seqs_cdhit.clstr")
        self.assertEqual(output_dir_res, "/tmp")
        
        fasta_res, uc_res, cd_hit_res, output_dir_res = \
         get_output_filepaths(".","test_seqs.fasta")
        self.assertEqual(fasta_res, ".//test_seqs_sorted.fasta")
        self.assertEqual(uc_res, ".//test_seqs_sorted.uc")
        self.assertEqual(cd_hit_res, ".//test_seqs_cdhit.clstr")
        self.assertEqual(output_dir_res, "./")
        
    def test_get_clusters_from_fasta_filepath(self):
        """ Tests for return of lists of OTUs from given fasta filepath """
        
        clusters_res = \
         get_clusters_from_fasta_filepath(self.tmp_unsorted_fasta_filepath, \
          percent_ID = 0.90)

        self.assertEqual(clusters_res, expected_cluster_list)
        
    def test_process_uclust_pw_alignment_results(self):
        """parsing of pairwise alignment fasta pairs file functions as expected
        """
        actual = list(process_uclust_pw_alignment_results(\
         self.search_align_out_fasta_pairs1,self.search_align_out_uc1))
        expected = self.search_align_out1_expected
        
        # iterate over results so error output will highlight the bad match
        for a,e in zip(actual,expected):
            self.assertEqual(a,e)
        
        # make sure the full result objects are the same
        self.assertEqual(actual,expected)
        
    def test_uclust_search_and_align_from_fasta_filepath(self):
        """ uclust_search_and_align_from_fasta_filepath functions as expected """
        # rev comp matches allowed (default)
        actual = list(uclust_search_and_align_from_fasta_filepath(
         self.search_align_query1_fp,self.search_align_template1_fp))
        self.assertEqual(actual,self.search_align_out1_expected)
        
        # rev comp matches not allowed
        actual = list(uclust_search_and_align_from_fasta_filepath(
         self.search_align_query1_fp,self.search_align_template1_fp,
         enable_rev_strand_matching=False))
        self.assertEqual(actual,self.search_align_out1_expected[:2])
        
    def test_uclust_search_and_align_from_fasta_filepath_protein(self):
        """ uclust_search_and_align_from_fasta_filepath functions with protein """
        # rev comp matches allowed (default)
        actual = list(uclust_search_and_align_from_fasta_filepath(
         self.search_align_query2_fp,self.search_align_template2_fp))
        self.assertEqual(actual,self.search_align_out2_expected)
        
    def test_uclust_supported_version(self):
        """uclust version is supported """
        command = 'uclust --version'
        proc = Popen(command,shell=True,universal_newlines=True,\
                         stdout=PIPE,stderr=STDOUT)
        stdout = proc.stdout.read()
        version_string = stdout.strip().split('v')[-1]
        version = tuple(map(int,version_string.split('.')))
        self.assertTrue(version >= (1,1,577),\
         "Unsupported uclust version. 1.1.577 or later "+\
         "is required, but running %s." % version_string)

raw_dna_seqs = """>uclust_test_seqs_0
ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT
>uclust_test_seqs_1
GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT
>uclust_test_seqs_2
CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT
>uclust_test_seqs_3
CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT
>uclust_test_seqs_4
ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT
>uclust_test_seqs_5
CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA
>uclust_test_seqs_6
CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT
>uclust_test_seqs_7
AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
>uclust_test_seqs_8
CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT
>uclust_test_seqs_9
GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA
""".split('\n')

sorted_dna_seqs=""">uclust_test_seqs_7
AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT
>uclust_test_seqs_4
ACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT
>uclust_test_seqs_2
CCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT
>uclust_test_seqs_3
CCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT
>uclust_test_seqs_1
GCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT
>uclust_test_seqs_5
CCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA
>uclust_test_seqs_6
CGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT
>uclust_test_seqs_0
ACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT
>uclust_test_seqs_8
CGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT
>uclust_test_seqs_9
GGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA
""".split('\n')

# Clusters are created at a 0.90% identity
uc_dna_clusters= """# uclust --input /tmp/uclust_testBGwZvcikrbNefYGRTk0u.fasta --id 0.9 --uc /tmp/uclust_testrbcO0CyBVpV9AwH3OIK1.uc
# version=1.1.577
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
S	0	80	*	*	*	*	*	uclust_test_seqs_7	*
S	1	79	*	*	*	*	*	uclust_test_seqs_4	*
S	2	78	*	*	*	*	*	uclust_test_seqs_2	*
S	3	77	*	*	*	*	*	uclust_test_seqs_3	*
S	4	76	*	*	*	*	*	uclust_test_seqs_1	*
S	5	75	*	*	*	*	*	uclust_test_seqs_5	*
S	6	74	*	*	*	*	*	uclust_test_seqs_6	*
S	7	73	*	*	*	*	*	uclust_test_seqs_0	*
H	6	72	91.7	+	0	0	2I72M	uclust_test_seqs_8	uclust_test_seqs_6
S	8	71	*	*	*	*	*	uclust_test_seqs_9	*
C	0	1	*	*	*	*	*	uclust_test_seqs_7	*
C	1	1	*	*	*	*	*	uclust_test_seqs_4	*
C	2	1	*	*	*	*	*	uclust_test_seqs_2	*
C	3	1	*	*	*	*	*	uclust_test_seqs_3	*
C	4	1	*	*	*	*	*	uclust_test_seqs_1	*
C	5	1	*	*	*	*	*	uclust_test_seqs_5	*
C	6	2	91.7	*	*	*	*	uclust_test_seqs_6	*
C	7	1	*	*	*	*	*	uclust_test_seqs_0	*
C	8	1	*	*	*	*	*	uclust_test_seqs_9	*""".split('\n')


clstr_clusters=['>Cluster 0\n',
'0       80nt, >uclust_test_seqs_7... *\n',
'>Cluster 1\n',
'0       79nt, >uclust_test_seqs_4... *\n',
'>Cluster 2\n',
'0       78nt, >uclust_test_seqs_2... *\n',
'>Cluster 3\n',
'0       77nt, >uclust_test_seqs_3... *\n',
'>Cluster 4\n',
'0       76nt, >uclust_test_seqs_1... *\n',
'>Cluster 5\n',
'0       75nt, >uclust_test_seqs_5... *\n',
'>Cluster 6\n',
'0       74nt, >uclust_test_seqs_6... *\n',
'1       72nt, >uclust_test_seqs_8... at +/92%\n',
'>Cluster 7\n',
'0       73nt, >uclust_test_seqs_0... *\n',
'>Cluster 8\n',
'0       71nt, >uclust_test_seqs_9... *\n']

expected_cluster_list=[['uclust_test_seqs_7'], ['uclust_test_seqs_4'], ['uclust_test_seqs_2'], ['uclust_test_seqs_3'], ['uclust_test_seqs_1'], ['uclust_test_seqs_5'], ['uclust_test_seqs_6', 'uclust_test_seqs_8'], ['uclust_test_seqs_0'], ['uclust_test_seqs_9']]

search_align_query1 = """>1_like
TACGGCTACCTTGTTACGACTTCATCCCAATCATTTGTTCCACCTTCGACGGCTA
>2_like
ATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAG
>2_like_rc
CTTAGTTGCCATCCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCAT
>rand
TTGCGACGAGCGGACGGCCGGGTGTATGTCGTCATATATATGTGTCTGCCTATCGTTACGTACACTCGTCGTCT
"""

search_align_template1 = """>1
AGAAAGGAGGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATTTGTTCCACCTTCGACGGCTAGCTCCAAATGGTTACTCCACCGGCTTCGGGTGTTACAAACTC
>2
AGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAGCTTAAGGGTTGCGCT
"""

search_align_query2 = """>1_like
PRTEINACYYPL
>2_like
AGGYTPPLVN
>rand
GGTYPARREE
"""

search_align_template2 = """>1
PRTELNACYYPL
>2
AGGYTRPPLVN
"""

search_align_out2_expected = [
 ('1_like','1','PRTEINACYYPL','PRTELNACYYPL',91.70000),
 ('2_like','2','AGGYT-PPLVN','AGGYTRPPLVN',100.0)]

search_align_out_fasta_pairs1 = """>1_like
-------------------------------TACGGCTACCTTGTTACGACTTCATCCCAATCATTTGTTCCACCTTCGACGGCTA------------------------------------------
>1+
AGAAAGGAGGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATTTGTTCCACCTTCGACGGCTAGCTCCAAATGGTTACTCCACCGGCTTCGGGTGTTACAAACTC

>2_like
-------------------ATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAG---------------
>2+
AGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAGCTTAAGGGTTGCGCT

>2_like_rc
---------------CTTAGTTGCCATCCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCAT-------------------
>2-
AGCGCAACCCTTAAGCTTAGTTGCCATCCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGATTTGGGCT
""".split('\n')

search_align_out_uc1 = """# uclust --input sm_query.fasta --lib sm_template.fasta --id 0.75 --libonly --rev --maxaccepts 8 --maxrejects 32 --fastapairs sm_pw.fasta --uc sm_result.uc
# version=1.1.577
# Tab-separated fields:
# 1=Type, 2=ClusterNr, 3=SeqLength or ClusterSize, 4=PctId, 5=Strand, 6=QueryStart, 7=SeedStart, 8=Alignment, 9=QueryLabel, 10=TargetLabel
# Record types (field 1): L=LibSeed, S=NewSeed, H=Hit, R=Reject, D=LibCluster, C=NewCluster, N=NoHit
# For C and D types, PctId is average id with seed.
# QueryStart and SeedStart are zero-based relative to start of sequence.
# If minus strand, SeedStart is relative to reverse-complemented seed.
L	0	128	*	*	*	*	*	1	*
H	0	55	98.2	+	0	0	31I55M42I	1_like	1
L	1	92	*	*	*	*	*	2	*
H	1	58	100.0	+	0	0	19I58M15I	2_like	2
H	1	58	100.0	-	0	0	15I58M19I	2_like_rc	2
N	*	74	*	*	*	*	*	rand	*
D	0	2	*	*	*	*	98.2	1	*
D	1	3	*	*	*	*	100.0	2	*
""".split('\n')

search_align_out1_expected = [
         ('1_like','1','-------------------------------TACGGCTACCTTGTTACGACTTCATCCCAATCATTTGTTCCACCTTCGACGGCTA------------------------------------------','AGAAAGGAGGTGATCCAGCCGCACCTTCCGATACGGCTACCTTGTTACGACTTCACCCCAATCATTTGTTCCACCTTCGACGGCTAGCTCCAAATGGTTACTCCACCGGCTTCGGGTGTTACAAACTC',98.2),
         
         ('2_like','2','-------------------ATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAG---------------','AGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAGCTTAAGGGTTGCGCT',100.0),\
         
         ('2_like_rc RC','2','-------------------ATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAG---------------','AGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGGATGGCAACTAAGCTTAAGGGTTGCGCT',100.0)]

         
if __name__ == '__main__':
    main()