#!/usr/bin/env python # Author: Greg Caporaso (gregcaporaso@gmail.com) # test_formatdb.py """ Description File created on 16 Sep 2009. """ from __future__ import division from os.path import split, exists from cogent import LoadSeqs from cogent.util.unit_test import TestCase, main from cogent.app.util import get_tmp_filename from cogent.util.misc import remove_files from cogent.app.blast import blastn from cogent.app.formatdb import FormatDb, build_blast_db_from_seqs,\ build_blast_db_from_fasta_path, build_blast_db_from_fasta_file __author__ = "Greg Caporaso" __copyright__ = "Copyright 2007-2009, The Cogent Project" __credits__ = ["Greg Caporaso"] __license__ = "GPL" __version__ = "1.4.1" __maintainer__ = "Greg Caporaso" __email__ = "gregcaporaso@gmail.com" __status__ = "Production" class FormatDbTests(TestCase): def setUp(self): self.in_seqs1_fp =\ get_tmp_filename(prefix='FormatDbTests',suffix='.fasta') self.in_seqs1_file = open(self.in_seqs1_fp,'w') self.in_seqs1_file.write(in_seqs1) self.in_seqs1_file.close() self.in_seqs1 = LoadSeqs(self.in_seqs1_fp,aligned=False) self.test_seq = test_seq self.in_aln1_fp =\ get_tmp_filename(prefix='FormatDbTests',suffix='.fasta') self.in_aln1_file = open(self.in_aln1_fp,'w') self.in_aln1_file.write(in_aln1) self.in_aln1_file.close() self.in_aln1 = LoadSeqs(self.in_aln1_fp) self.files_to_remove = [self.in_seqs1_fp,self.in_aln1_fp] def tearDown(self): remove_files(self.files_to_remove) def test_call(self): """FormatDb: Calling on a nucleotide data functions as expected """ fdb = FormatDb(WorkingDir='/tmp') result = fdb(self.in_seqs1_fp) # test sucessful run self.assertEqual(result['ExitStatus'],0) expected_result_keys = set(\ ['log','nhr','nin','nsd','nsi','nsq','ExitStatus','StdOut','StdErr']) self.assertEqual(set(result.keys()),expected_result_keys) inputfile_basename = split(self.in_seqs1_fp)[1] # got all the expected out files, and filepaths are as expected outpaths = [] for ext in ['log','nhr','nin','nsd','nsi','nsq']: outpath = '/tmp/%s.%s' % (inputfile_basename,ext) outpaths.append(outpath) self.assertEqual(result[ext].name,outpath) result.cleanUp() # all created files are cleaned up for outpath in outpaths: self.assertFalse(exists(outpath),\ "%s was not cleaned up." % outpath) def test_blast_against_new_db(self): """Formatdb: blastall against a newly created DB functions as expected """ fdb = FormatDb(WorkingDir='/tmp') result = fdb(self.in_seqs1_fp) blast_res = blastn(self.test_seq,blast_db=self.in_seqs1_fp) result.cleanUp() # Test that a blast result was returned self.assertTrue('s1' in blast_res,\ "Not getting any blast results.") # Test that the sequence we expect was a good blast hit subject_ids = [r['SUBJECT ID'] for r in blast_res['s1'][0]] self.assertTrue('11472384' in subject_ids,\ "Not getting expected blast results.") def test_build_blast_db_from_seqs(self): """build_blast_db_from_seqs convenience function works as expected """ blast_db, db_files = build_blast_db_from_seqs(self.in_seqs1,output_dir='/tmp') self.assertTrue(blast_db.startswith('/tmp/Blast_tmp_db')) self.assertTrue(blast_db.endswith('.fasta')) expected_db_files = set([blast_db + ext\ for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']]) self.assertEqual(set(db_files),expected_db_files) # result returned when blasting against new db self.assertEqual(\ len(blastn(self.test_seq,blast_db=blast_db)),1) # Make sure all db_files exist for fp in db_files: self.assertTrue(exists(fp)) # Remove all db_files exist remove_files(db_files) # Make sure nothing weird happened in the remove for fp in db_files: self.assertFalse(exists(fp)) def test_build_blast_db_from_fasta_path(self): """build_blast_db_from_fasta_path convenience function works as expected """ blast_db, db_files = \ build_blast_db_from_fasta_path(self.in_seqs1_fp) self.assertEqual(blast_db,self.in_seqs1_fp) expected_db_files = set([self.in_seqs1_fp + ext\ for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']]) self.assertEqual(set(db_files),expected_db_files) # result returned when blasting against new db self.assertEqual(\ len(blastn(self.test_seq,blast_db=blast_db)),1) # Make sure all db_files exist for fp in db_files: self.assertTrue(exists(fp)) # Remove all db_files exist remove_files(db_files) # Make sure nothing weird happened in the remove for fp in db_files: self.assertFalse(exists(fp)) def test_build_blast_db_from_fasta_path_aln(self): """build_blast_db_from_fasta_path works with alignment as input """ blast_db, db_files = build_blast_db_from_fasta_path(self.in_aln1_fp) self.assertEqual(blast_db,self.in_aln1_fp) expected_db_files = set([blast_db + ext\ for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']]) self.assertEqual(set(db_files),expected_db_files) # result returned when blasting against new db self.assertEqual(\ len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1) # Make sure all db_files exist for fp in db_files: self.assertTrue(exists(fp)) # Remove all db_files exist remove_files(db_files) # Make sure nothing weird happened in the remove for fp in db_files: self.assertFalse(exists(fp)) def test_build_blast_db_from_fasta_file(self): """build_blast_db_from_fasta_file works with open files as input """ blast_db, db_files = \ build_blast_db_from_fasta_file(open(self.in_aln1_fp),output_dir='/tmp/') self.assertTrue(blast_db.startswith('/tmp/BLAST_temp_db')) self.assertTrue(blast_db.endswith('.fasta')) expected_db_files = set([blast_db] + [blast_db + ext\ for ext in ['.nhr','.nin','.nsq','.nsd','.nsi','.log']]) self.assertEqual(set(db_files),expected_db_files) # result returned when blasting against new db self.assertEqual(\ len(blastn(self.test_seq,blast_db=blast_db,e_value=0.0)),1) # Make sure all db_files exist for fp in db_files: self.assertTrue(exists(fp)) # Remove all db_files exist remove_files(db_files) # Make sure nothing weird happened in the remove for fp in db_files: self.assertFalse(exists(fp)) in_seqs1 = """>11472286 GATGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGAACACTTTGTGTTTTGAGTTAATAGTTCGATAGTAGATAGTAAATAGTGAACACTATGAACTAGTAAACTATTTAACTAGAAACTCTTAAACGCAGAGCGTTTAGTGGCGAACGGGTGAGTAATACATTGGTATCTACCTCGGAGAAGGACATAGCCTGCCGAAAGGTGGGGTAATTTCCTATAGTCCCCGCACATATTTGTTCTTAAATCTGTTAAAATGATTATATGTTTTATGTTTATTTGATAAAAAGCAGCAAGACAAATGAGTTTTATATTGGTTATACAGCAGATTTAAAAAATAGAATTAGGTCTCATAATCAGGGAGAAAACAAATCAACTAAATCTAAAATACCTTGGGAATTGGTTTACTATGAAGCCTACAAAAACCAAACATCAGCAAGGGTTAGAGAATCAAAGTTGAAACATTATGGGCAATCATTAACTAGACTTAAGAGAAGAATTGGTTTTTGAGAACAAATATGTGCGGGGTAAAGCAGCAATGCGCTCCGAGAGGAACCTCTGTCCTATCAGCTTGTTGGTAAGGTAATGGCTTACCAAGGCGACGACGGGTAGCTGGTGTGAGAGCACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCACAATGGGCGCAAGCCTGATGGAGCAATGCCGCGTGAAGGATGAAGATTTTCGGATTGTAAACTTCTTTTAAGTAGGAAGATTATGACGGTACTACTTGAATAAGCATCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGATGCAAGCGTTATCCGGAATTACTGGGCGTAAAGCGTGTGTAGGTGGTTTATTAAGTTAAATGTTAAATTTTCAGGCTTAACTTGGAAACCGCATTTAATACTGGTAGACTTTGAGGACAAGAGAGGCAGGCGGAATTAGCGGAGTAGCGGTGAAATGCGTAGATATCGCTAAGAACACCAATGGCGAAGGCAGCCTGCTGGTTTGCACCTGACACTGAGATACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACGATGGTCACTAGCTGTTAGGGGCTCGACCCCTTTAGTAGCGAAGCTAACGCGTTAAGTGACCCGCCTGGGGAGTACGATCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAACGTGAGGTTTAATTCGTCTCTAAGCGAAAAACCTTACCGAGGCTTGACATCTCCGGAAGACCTTAGAAATAAGGTTGTGCCCGAAAGGGAGCCGGATGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTCGGTTAAGTCCGTTAACGAGCGCAACCCTTGCTGTGTGTTGTATTTTTCACACAGGACTATCCTGGTCAACAGGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCTCTTACGCCTCGGGCTACACTCGCGTTACAATGGCCGGTACAATGGGCTGCCAACTCGTAAGGGGGAGCTAATCCCATCAAAACCGGTCCCAGTTCGGATTGAGGGCTGCAATTCGCCCTCATGAAGTCGGAATCGCTAGTAACCGCGAATCAGCACGTCGCGGTGAATGCGTTCTCGGGTCTTGTACACACTGCCCGTCACACCACGAAAGTTAGTAACGCCCGAAGTGCCCTGTATGGGGTCCTAAGGTGGGGCTAGCGATTGGGGTG >11472384 AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAAACGCCGTGGTTAATACCCGTGGCGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTCCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTCGGGTCTTCATTGACTTGGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTATGGAATCCTGCTGAGAGGTGGGAGTGCCCGAAAGGGAGCCATAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCCTAGTTGCTACGCAAGAGCACTCTAGGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTCGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCACTCTGCAACTCGAGTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTCGAGCGAACGTGTCGAACGTTGAGCGCTCACGCTTATCGGCTGTGAAATTAGGACAGTAAGTCAGACAGACTGAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGATGGTTCGAATCCATCCAGACCCACCATTGTCT >11468680 TAAACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGTGCTTGCACCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACATGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGATCTACGGATGAAAGCGGGGGACCTTCGGGCCTCGCGCTATAGGGTTGGCCGATGGCTGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCCTTGGCTCTAATACAGTCGGGGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGCTAAGACCGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTGGTGACTGGCAGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTTGGGGATTCATTTCCTTAGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGGTCGGAATCCCGCTGAGAGGTGGGAGTGCTCGAAAGAGAACCGGCGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCTTAGTTGCTACGCAAGAGCACTCTAAGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTTGCCAACCCGCGAGGGGGAGCTAATCCCAGAAAACCGATCGTAGTCCGGATTGCACTCTGCAACTCGAGTGCATGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCCAGAGCTATCTCGCAAAGTTGAGCGCTCACGCTTATCGGCTGTAAATTTAAAGACAGACTCAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGTTGGTTCGAATCCAACCAGACCCACCATTGTCTG >11458037 GACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGTTTCGAAGATCGGACTTCGAATTTCGAATTTCGATCATCGAGATAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTACCCATAAAGCCGGGACAACCCTTGGAAACGAGGGCTAATACCGGATAAGCTTGAGAAGTGGCATCACTTTTTAAGGAAAGGTGGCCGATGAGAATGCTGCCGATTATGGATGGACCCGCGTCTGATTAGCTGGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCCGGCCTGAGAGGGTGAACGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGTATGATGAAGGTTTTCGGATTGTAAAGTACTGTCTATGGGGAAGAATGGTGTGCTTGAGAATATTAAGTACAAATGACGGTACCCAAGGAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGATAGTTAAGTCCGGTGTGAAAGATCAGGGCTCAACCCTGAGAGTGCATCGGAAACTGGGTATCTTGAGGACAGGAGAGGAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTGCTAGGTGTAGAGGGTATCGACCCCTTCTGTGCCGCAGTTAACACAATAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCAGGGCTTGACATCCTCTGAACTTGCTGGAAACAGGAAGGTGCCCTTCGGGGAGCAGAGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAATCCCGCAACGAGCGCAACCCCTGTATTTAGTTGCTAACGCGTAGAGGCGAGCACTCTGGATAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGTTCTGGGCTACACACGTGCTACAATGGCCGGTACAGACGGAAGCGAAGCCGCGAGGCGGAGCAAATCCGAGAAAGCCGGTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGTCGGAATCGCTAGTAATCGCAGGTCAGCATACTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTCTGCAACACCCGAAGCCGGTGAGGTAACCGACTCGAGATTCGAGGCTCGAAGTTCGAGGATCGAAGTGTAAGCGAAATTAATAAGTCTTAGTAAAGCTAAAAAGCATTAAGACCGATAAGATGATCTTGCAATCGAACATCGAACATCGAATTTCGAACCTCGAGTTGGAGCTAGCCGTCGAAGGTGGGGCCGATAATTGGGGTG >11469739 AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAGCTAACTTCTGATTCCTTCGGGATGATGAGGTTAGCAGAAAGTGGCGAACGGGTGAGTAACGCGTGGGTAATCTACCCTGTAAGTGGGGGATAACCCTCCGAAAGGAGGGCTAATACCGCATAATATCTTTATCCCAAAAGAGGTAAAGATTAAAGATGGCCTCTATACTATGCTATCGCTTCAGGATGAGTCCGCGTCCTATTAGTTAGTTGGTGGGGTAATGGCCTACCAAGACGACAATGGGTAGCCGGTCTGAGAGGATGTACGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGACAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCCTTGGGTTGTAAAATCCTGTTCTGGGGGAAGAAAGCTTAAAGGTCCAATAAACCCTTAAGCCTGACGGTACCCCAAGAGAAAGCTCCGGCTAATTATGTGCCAGCAGCCGCGGTAATACATAAGGAGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCTCGTAGGCGGTCTTAAAAGTCAGTTGTGAAATTATCAGGCTCAACCTGATAAGGTCATCTGAAACTCTAAGACTTGAGGTTAGAAGAGGAAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTATCTCTGACGCTGAGGAGCGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGTAGCTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGACTTGACATTATCTTGCCCGTCTAAGAAATTAGATCTTCTTCCTTTGGAAGACAGGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTGTGCTTAGTTGCTAACTTGTTTTACAAGTGCACTCTAGGCAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTTAAGCCAATCCCAAAAAGCAGGCCCCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTAGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAAAGTTGGCGATACCTGAAGTTACTAGGCTAACCTGGCACTCAACTAAGTTCACTAACTTATTTGCTTAAAATAAGGCTTAATGTGCTTAGTTGAGTGCCGGGAGGCAGGTACCGAAGGTATGGCTGGCGATTGGGGTGAAGTCGTAACAAGGTGGAAA >11469752 AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGGCAGCGAGTTCCTCACCGAGGTTCGGAACAGTTGACAGTAAACAGTTGACAGTAAACAGTAACTTCAGAAATGAAGCGGACTGTGAACTGTTTACTGTAACCTGTTAGCTATTATTTCGAGCTTTAGTGAGGAATGTCGGCGAGCGGCGGACGGCTGAGTAACGCGTAGGAACGTACCCCAAACTGAGGGATAAGCACCAGAAATGGTGTCTAATACCGCATATGGCCCAGCACCTTTTTTAATCAACCACGACCCTAAAATCGTGAATAATTGGTAGGAAAAGGTGTTGGGTTAAAGCTTCGGCGGTTTGGGAACGGCCTGCGTATGATTAGCTTGTTGGTGAGGTAAAAGCTCACCAAGGCGACGATCATTAGCTGGTCTGAGAGGATGATCAGCCAGACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCACAATGGGCGAAAGCCTGATGGAGCAACGCCGTGTGCAGGATGAAAGCCTTCGGGTCGTAAACTGCTTTTATATGTGAAGACTTCGACGGTAGCATATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTCATACGGAGGATCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGTTGGTAGTGAAATTGTGTGGCTCAACCATACACCCATTACTAAAACTGCTAAGCTAGAGTATATGAGAGGTAGCTGGAATTCCTAGTGTAGGAGTGAAATCCGTANATATTAGGAGGAACACCGATGGCGTAGGCAGGCTACTGGCATATTACTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCTGTAAACGATGGATGCTAGCTGTTATGAGTATCGACCCTTGTAGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACGAGCGCAAGCTTAAAACATAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGATGATAAGCGAAGAACCTTACCAAGGCTTGACATCCCTGGAATTTCTCCGAAAGGAGAGAGTGCCTTCGGGAATCAGGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATTAACGAGCGCAACCCTTGTAAATAGTTGGATTTTTCTATTTAGACTGCCTCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCAGTATTTCTCTTACGCCTTGGGCTACAAACACGCTACAATGGCCGGTACAAAGGGCAGCCAACCCGCGAGGGGGAGCAAATCCCATCAAAGCCGGTCTCAGTTCGGATAGCAGGCTGAAATTCGCCTGCTTGAAGTCGGAATCGCTAGTAACGGTGAGTCAGCTATATTACCGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCAAGGCATGAAAGTCATCAATACCTGACGTCTGGATTTATTCTGGCCTAAGGTAGGGGCGATGATTGGGCCTAAGTCGTAACAAGGTAA >11460523 AGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCGAAATCGGGCACTCAATTTTGCTTTTCAAACATTAACTGATGAAACGACCAGAGAGATTGTTCCAGTTTAAAGAGTGAAAAGCAGGCTTGAGTGCCTGAGAGTAGAGTGGCGCACGGGTGAGTAACGCGTAAATAATCTACCCCTGCATCTGGGATAACCCACCGAAAGGTGAGCTAATACCGGATACGTTCTTTTAACCGCGAGGTTTTAAGAAGAAAGGTGGCCTCTGATATAAGCTACTGTGCGGGGAGGAGTTTGCGTACCATTAGCTAGTTGGTAGGGTAATGGCCTACCAAGGCATCGATGGTTAGCGGGTCTGAGAGGATGATCCGCCACACTGGAACTGGAACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTCGTAAAATCCTGTCAGATGGAAAGAAGTGTTATATGGATAATACCTGTATAGCTTGACGGTACCATCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTCTGTTATGTCAGATGTGAAAGTCCACGGCTCAACCGTGGAAGTGCATTTGAAACTGACAGACTTGAGTACTGGAGGGGGTGGTGGAATTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAATACCGGTGGCGAAGGCGACCACCTGGCCAGATACTGACGCTGAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCAACTAGGTGTTGGGATGGTTAATCGTCTCATTGCCGGAGCTAACGCATTAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCTGGTCTTGACATCCCGAGAATCTCAAGGAAACTTGAGAGTGCCTCTTGAGGAACTCGGTGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTTTAGTTGCCATCATTAAGTTGGGCACTCTAAAGAGACTGCCGGTGTCAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGACCAGGGCTACACACGTACTACAATGGCATAGACAAAGGGCAGCGACATCGCGAGGTGAAGCGAATCCCATAAACCATGTCTCAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTTGGAATCGCTAGTAATCGTAGATCAGCATGCTACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGGGAGTTGGTTGTACCAGAAGCAGTTGAGCGAACTATTCGTAGACGCAGGCTGCCAAGGTATGATTGGTAACTGGGGTGAAGTCGTAACAAGGTAACC >11460543 TGGTTTGATCCTGGCTCAGGACAAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAGAAGCCAGCTTTTGATTCCTTCGGGATGAGAAAGCAGGTAGAAAGTGGCGAACGGGTGAGTAACGCGTGGGTAATCTACCCTGTAAGTAGGGGATAACCCTCTGAAAAGAGGGCTAATACCGCATAATATCTTTACCCCATAAGAAGTAAAGATTAAAGATGGCCTCTGTATATGCTATCGCTTCAGGATGAGCCCGCGTCCTATTAGTTAGTTGGTAAGGTAATGGCTTACCAAGACCACGATGGGTAGCCGGTCTGAGAGGATGTACGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCGCAATGGGGGAAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTTGTAAAATCCTGTTTTGGGGGACGAAACCTTAAGGGTCCAATAAACCCTTAAATTGACGGTACCCCAAGAGAAAGCTCCGGCTAATTATGTGCCAGCAGCCGCGGTAATACATAAGGAGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGTTCGTAGGCGGTCTTAAAAGTCAGGTGTGAAATTATCAGGCTTAACCTGATACGGTCATCTGAAACTTTAAGACTTGAGGTTAGGAGAGGAAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGCCTAACTCTGACGCTGAGGAACGAAAGCTAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTAGCTGTAAACGATGGATACTAGGTGTGGGAGGTATCGACCCCTTCTGTGCCGWCACTAACGCATTAAGTATCCCGCCTGGGGAGTACGGTCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCGGGGCTTGACATTGTCTTGCCCGTTTAAGAAATTAAATTTTCTTCCCTTTTAGGGAAGACAAGATAACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCACAACGAGCGCAACCCTTATTCTTAGTTGCTAGTTTGTTTACAAACGCACTCTAAAGAGACTGCCGCAGATAATGCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTACGTCCCGGGCTACACACGTGCTACAATGGCCTGTACAGAGGGTAGCGAAAGAGCGATCTCAAGCTAATCCCTTAAAACAGGTCTCAGTTCGGATTGGAGGCTGCAACTCGCCTCCATGAAGTCGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGAAAGTTGGCGATACCTGAAGTTACTGTGCTAACCCGGCACTCAACTAAGTACATTAAGTCTTATTTTAAGCTATTGTATTTAGTTGAGTGCCGGGAGGCAGGTACCTAAGGTATGGCTAGCGATTGGGGTGAAGTCGTAACAAGGTAGCCG >11480235 TGGTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGCGCCTTATACATGCAAGTCGAACGAGCCTTGTGCTTCGCACAAGGAAATTCCAAGCACCAAGCACCAAATCTCAAACAAATCCCAATGACCAAAATTCCAAAAACCTAAACATTTTAAATGTTTAGAATTTGGAAAATTGGAATTTGGAATTTATTTGTTATTTGGAATTTATGATTTGGGATTTTCTCGCGCGGAGANCNTNAGTGGCGAACGGGTGAGTAATACGTTGGTATCTACCCCAAAGTAGAGAATAAGCCCGAGAAATCGGGGTTAATACTCTATGTGTTCGAAAGAACAAAGACTTCGGTTGCTTTGGGAAGAACCTGCGGCCTATCAGCTTGTTGGTAAGGTAACGGCTTACCAAGGCTTTGACGGGTAGCTGGTCTGGGAAGACGACCAGCCACAATGGGACTTAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATCTTCGGCAATGCCCGAAAGGTGACCGAGCGACGCCGCGTAGAGGAAGAAGATCTTTGGATTGTAAACTCTTTTTCTCCTAGACAAAGTTCTGATTGTATAGGAGGAATAAGGGGTTTCTAAACTCGTGCCAGCAGAAGCGGTAATACGAGTGCCCCAAGCGTTATCCGGAATCATTGGGCGTAGAGCGTTGTATAGGTGGTTTAAAAAGTCCAAAATTAAATCTTTAGGCTCAACCTAAAATCTGTTTTGGAAACTTTTAGACTTGAATAAAATCGACGSGAGTGGAACTTCCAGAGTAGGGGTTACATCCGTTGATACTGGAAGGAACGCCGAAGGCGAAAGCAACTCGCGAGATTTTATTGACGCCGCGTACACGAAAGCGTGGGGAGCGAAAAGTATTAGATACACTTGTAGTCCACGCCGTAAACTATGGATACTAGCAATTTGAAGCTTCGACCCTTCAAGTTGCGGACTAACGCGTTAAGTATCTCGCCTGGGAAGTACGGCCGCAAGGCTAAAACTCAAAGGAATAGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGATAAGCGTGGAACCTTACCAGGGCTTAGACGTACAGAGAATTCCTTGGAAACAAGGAAGTGCTTCGGGAACTCTGTACTCAGGTACTGCATGGCTGTCGTCAGTATGTACTGTGAAGCACTCCCTTAATTGGGGCAACATACGCAACCCCTATCCTAAGTTAGAAATGTCTTAGGAAACCGCTTCGATTCATCGGAGAGGAAGATGGGGACGACGTCAAGTCAGCATGGTCCTTGATGTCCTGGGCGACACACGTGCTACAATGGCTAGTATAACGGGATGCGTAGGTGCGAACCGAAGCTAATCCTTAAAAAACTAGTCTAAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGCCGGAATCGCTAGTAACCGCAAATCAGCCACGTTGCGGTGAATACGTTCTCGGGCCTTGTACTCACTGCCCGTCACGTCAAAAAAGTCGGTAATACCCGAAGCACCCTTTTAAAGGGTTCTAAGGTAGGACCGATGATTGGGACGAAGTCGTAACAAGGTAGCCG >11480408 AATTTAGCGGCCGCGAATTCGCCCTTGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGGGATATCCGAGCGGAAGGTTTCGGCCGGAAGGTTGGGTATTCGAGTGGCGGACGGGTGAGTAACGCGTGAGCAATCTGTCCCGGACAGGGGGATAACACTTGGAAACAGGTGCTAATACCGCATAAGACCACAGCATCGCATGGTGCAGGGGTAAAAGGAGCGATCCGGTCTGGGGTGAGCTCGCGTCCGATTAGATAGTTGGTGAGGTAACGGCCCACCAAGTCAACGATCGGTAGCCGACCTGAGAGGGTGATCGGCCACATTGGAACTGAGAGACGGTCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCAACGCCGCGTGAGTGAAGAAGGCCTTCGGGTTGTAAAGCTCTGTTATGCGAGACGAAGGAAGTGACGGTATCGCATAAGGAAGCCCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGGGCGAGCGTTGTCCGGAATGACTGGGCGTAAAGGGCGTGTAGGCGGCCGTTTAAGTATGGAGTGAAAGTCCATTTTTCAAGGATGGAATTGCTTTGTAGACTGGATGGCTTGAGTGCGGAAGAGGTAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGAGATTGGGAGGAACACCAGTGGCGAAGGCGACTTACTGGGCCGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCGGTAAACGATGAATGCTAGGTGTTGCGGGTATCGACCCCTGCAGTGCCGGAGTAAACACAATAAGCATTCCGCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAGGGAATTGACGGGGGCCCGCACAAGCAGCGGAGCATGTTGTTTAATTCGAAGCAACGCGAAGAACCTTACCAGGTCTTGACATCCAGTTAAGCTCATAGAGATATGAGGTCCCTTCGGGGGAACTGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATGGTCAGTTACTAACGCGTGAAGGCGAGGACTCTGACGAGACTGCCGGGGACAACTCGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACAAACGTGCTACAATGGTGACTACAAAGAGGAGCGAGACTGTAAAGTGGAGCGGATCTCAAAAAAGTCATCCCAGTTCGGATTGTGGGCTGCAACCCGCCCACATGAAGTTGGAGTTGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGGAGCACCCGAAGTCAGTGAGGTAACCGGAAGGAGCCAGCTGCCGAAGGTGAGACCGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTAAGGGCGAATTCGTTTAAACCTGCAGGACTAG """ test_seq = """>s1 (11472384) AGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAAACGCCGTGGTTAATACCCGTGGCGGATGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTCCGCTAAGACAGATGTGAAATCCCCGGGCTTAACCTGGGAACTGCATTTGTGACTGGCGGGCTAGAGTATGGCAGAGGGGGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGCCAATACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTCGGGTCTTCATTGACTTGGTAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTATGGAATCCTGCTGAGAGGTGGGAGTGCCCGAAAGGGAGCCATAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCCCTAGTTGCTACGCAAGAGCACTCTAGGGAGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTCGGAACAGAGGGTCGCCAACCCGCGAGGGGGAGCCAATCCCAGAAAACCGATCGTAGTCCGGATCGCACTCTGCAACTCGAGTGCGTGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTTTACCAGAAGTGGCTAGTCTAACCGCAAGGAGGACGGTCACCACGGTAGGATTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTCGAGCGAACGTGTCGAACGTTGAGCGCTCACGCTTATCGGCTGTGAAATTAGGACAGTAAGTCAGACAGACTGAGGGGTCTGTAGCTCAGTCGGTTAGAGCACCGTCTTGATAAGGCGGGGGTCGATGGTTCGAATCCATCCAGACCCACCATTGTCT """ in_aln1 = """>a1 AAACCTTT----TTTTAAATTCCGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTC >a2 AAACCTTT----TTTTAAATTCCGCAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTC >a3 AAACCTTT----TTTTAAATTCCGGAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTC >a4 AAACCTTT----TTTTAAATTCCGTAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGCACGGGGGCAACCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGTCCTGTAGTGGGGGATAGCCCGGCGAAAGCCGGATTAATACCGCATACGCTCTACGGAGGAAAGGGGGGGATCTTAGGACCTCCCGCTACAGGGGCGGCCGATGGCAGATTAGCTAGTTGGTGGGGTAAAGGCCTACCAAGGCGACGATCTGTAGCTGGTCTGAGAGGACGACCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTC """ if __name__ == "__main__": main()