#!/usr/bin/env python '''unit testing code for pysam. Execute in the :file:`tests` directory as it requires the Makefile and data files located there. ''' import pysam import unittest import os, re, sys import itertools import collections import subprocess import shutil import logging if sys.version_info[0] < 3: from itertools import izip as zip_longest else: from itertools import zip_longest SAMTOOLS="samtools" WORKDIR="pysam_test_work" def checkBinaryEqual( filename1, filename2 ): '''return true if the two files are binary equal.''' if os.path.getsize( filename1 ) != os.path.getsize( filename2 ): return False infile1 = open(filename1, "rb") infile2 = open(filename2, "rb") def chariter( infile ): while 1: c = infile.read(1) if c == b"": break yield c found = False for c1,c2 in zip_longest( chariter( infile1), chariter( infile2) ): if c1 != c2: break else: found = True infile1.close() infile2.close() return found def runSamtools( cmd ): '''run a samtools command''' try: retcode = subprocess.call(cmd, shell=True) if retcode < 0: print >>sys.stderr, "Child was terminated by signal", -retcode except OSError as e: print >>sys.stderr, "Execution failed:", e def getSamtoolsVersion(): '''return samtools version''' pipe = subprocess.Popen(SAMTOOLS, shell=True, stderr=subprocess.PIPE).stderr lines = b"".join(pipe.readlines()) if sys.version_info[0] >= 3: lines = lines.decode('ascii') return re.search( "Version:\s+(\S+)", lines).groups()[0] class BinaryTest(unittest.TestCase): '''test samtools command line commands and compare against pysam commands. Tests fail, if the output is not binary identical. ''' first_time = True # a list of commands to test commands = \ { "view" : ( ("ex1.view", "view ex1.bam > ex1.view"), ("pysam_ex1.view", (pysam.view, "ex1.bam" ) ), ), "view2" : ( ("ex1.view", "view -bT ex1.fa -o ex1.view2 ex1.sam"), # note that -o ex1.view2 throws exception. ("pysam_ex1.view", (pysam.view, "-bT ex1.fa -oex1.view2 ex1.sam" ) ), ), "sort" : ( ( "ex1.sort.bam", "sort ex1.bam ex1.sort" ), ( "pysam_ex1.sort.bam", (pysam.sort, "ex1.bam pysam_ex1.sort" ) ), ), "mpileup" : ( ("ex1.pileup", "mpileup ex1.bam > ex1.pileup" ), ("pysam_ex1.mpileup", (pysam.mpileup, "ex1.bam" ) ), ), "depth" : ( ("ex1.depth", "depth ex1.bam > ex1.depth" ), ("pysam_ex1.depth", (pysam.depth, "ex1.bam" ) ), ), "faidx" : ( ("ex1.fa.fai", "faidx ex1.fa"), ("pysam_ex1.fa.fai", (pysam.faidx, "ex1.fa") ), ), "index": ( ("ex1.bam.bai", "index ex1.bam" ), ("pysam_ex1.bam.bai", (pysam.index, "pysam_ex1.bam" ) ), ), "idxstats" : ( ("ex1.idxstats", "idxstats ex1.bam > ex1.idxstats" ), ("pysam_ex1.idxstats", (pysam.idxstats, "pysam_ex1.bam" ) ), ), "fixmate" : ( ("ex1.fixmate", "fixmate ex1.bam ex1.fixmate" ), ("pysam_ex1.fixmate", (pysam.fixmate, "pysam_ex1.bam pysam_ex1.fixmate") ), ), "flagstat" : ( ("ex1.flagstat", "flagstat ex1.bam > ex1.flagstat" ), ("pysam_ex1.flagstat", (pysam.flagstat, "pysam_ex1.bam") ), ), "calmd" : ( ("ex1.calmd", "calmd ex1.bam ex1.fa > ex1.calmd" ), ("pysam_ex1.calmd", (pysam.calmd, "pysam_ex1.bam ex1.fa") ), ), "merge" : ( ("ex1.merge", "merge -f ex1.merge ex1.bam ex1.bam" ), # -f option does not work - following command will cause the subsequent # command to fail ("pysam_ex1.merge", (pysam.merge, "pysam_ex1.merge pysam_ex1.bam pysam_ex1.bam") ), ), "rmdup" : ( ("ex1.rmdup", "rmdup ex1.bam ex1.rmdup" ), ("pysam_ex1.rmdup", (pysam.rmdup, "pysam_ex1.bam pysam_ex1.rmdup" )), ), "reheader" : ( ( "ex1.reheader", "reheader ex1.bam ex1.bam > ex1.reheader"), ( "pysam_ex1.reheader", (pysam.reheader, "ex1.bam ex1.bam" ) ), ), "cat": ( ( "ex1.cat", "cat ex1.bam ex1.bam > ex1.cat"), ( "pysam_ex1.cat", (pysam.cat, "ex1.bam ex1.bam" ) ), ), "targetcut": ( ("ex1.targetcut", "targetcut ex1.bam > ex1.targetcut" ), ("pysam_ex1.targetcut", (pysam.targetcut, "pysam_ex1.bam") ), ), "phase": ( ("ex1.phase", "phase ex1.bam > ex1.phase" ), ("pysam_ex1.phase", (pysam.phase, "pysam_ex1.bam") ), ), "import" : ( ("ex1.bam", "import ex1.fa.fai ex1.sam.gz ex1.bam" ), ("pysam_ex1.bam", (pysam.samimport, "ex1.fa.fai ex1.sam.gz pysam_ex1.bam") ), ), "bam2fq": ( ("ex1.bam2fq", "bam2fq ex1.bam > ex1.bam2fq" ), ("pysam_ex1.bam2fq", (pysam.bam2fq, "pysam_ex1.bam") ), ), } # some tests depend on others. The order specifies in which order # the samtools commands are executed. # The first three (faidx, import, index) need to be in that order, # the rest is arbitrary. order = ('faidx', 'import', 'index', # 'pileup1', 'pileup2', deprecated # 'glfview', deprecated 'view', 'view2', 'sort', 'mpileup', 'depth', 'idxstats', 'fixmate', 'flagstat', # 'calmd', 'merge', 'rmdup', 'reheader', 'cat', 'targetcut', 'phase', 'bam2fq', ) def setUp( self ): '''setup tests. For setup, all commands will be run before the first test is executed. Individual tests will then just compare the output files. ''' if BinaryTest.first_time: # remove previous files if os.path.exists( WORKDIR ): shutil.rmtree( WORKDIR ) # copy the source files to WORKDIR os.makedirs( WORKDIR ) shutil.copy( "ex1.fa", os.path.join( WORKDIR, "pysam_ex1.fa" ) ) shutil.copy( "ex1.fa", os.path.join( WORKDIR, "ex1.fa" ) ) shutil.copy( "ex1.sam.gz", os.path.join( WORKDIR, "ex1.sam.gz" ) ) shutil.copy( "ex1.sam", os.path.join( WORKDIR, "ex1.sam" ) ) # cd to workdir savedir = os.getcwd() os.chdir( WORKDIR ) for label in self.order: command = self.commands[label] samtools_target, samtools_command = command[0] try: pysam_target, pysam_command = command[1] except ValueError as msg: raise ValueError( "error while setting up %s=%s: %s" %\ (label, command, msg) ) runSamtools( " ".join( (SAMTOOLS, samtools_command ))) pysam_method, pysam_options = pysam_command try: output = pysam_method( *pysam_options.split(" "), raw=True) except pysam.SamtoolsError as msg: raise pysam.SamtoolsError( "error while executing %s: options=%s: msg=%s" %\ (label, pysam_options, msg) ) if ">" in samtools_command: outfile = open( pysam_target, "wb" ) if sys.version_info[0] < 3: for line in output: outfile.write( line ) else: for line in output: outfile.write(line.encode('ascii')) outfile.close() os.chdir( savedir ) BinaryTest.first_time = False samtools_version = getSamtoolsVersion() def _r( s ): # patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a -> 0.1.12 if s.count('-') > 0: s = s[0:s.find('-')] return re.sub( "[^0-9.]", "", s ) if _r(samtools_version) != _r( pysam.__samtools_version__): raise ValueError("versions of pysam/samtools and samtools differ: %s != %s" % \ (pysam.__samtools_version__, samtools_version )) def checkCommand( self, command ): if command: samtools_target, pysam_target = self.commands[command][0][0], self.commands[command][1][0] samtools_target = os.path.join( WORKDIR, samtools_target ) pysam_target = os.path.join( WORKDIR, pysam_target ) self.assertTrue( checkBinaryEqual( samtools_target, pysam_target ), "%s failed: files %s and %s are not the same" % (command, samtools_target, pysam_target) ) def testImport( self ): self.checkCommand( "import" ) def testIndex( self ): self.checkCommand( "index" ) def testSort( self ): self.checkCommand( "sort" ) def testMpileup( self ): self.checkCommand( "mpileup" ) def testDepth( self ): self.checkCommand( "depth" ) def testIdxstats( self ): self.checkCommand( "idxstats" ) def testFixmate( self ): self.checkCommand( "fixmate" ) def testFlagstat( self ): self.checkCommand( "flagstat" ) def testMerge( self ): self.checkCommand( "merge" ) def testRmdup( self ): self.checkCommand( "rmdup" ) def testReheader( self ): self.checkCommand( "reheader" ) def testCat( self ): self.checkCommand( "cat" ) def testTargetcut( self ): self.checkCommand( "targetcut" ) def testPhase( self ): self.checkCommand( "phase" ) def testBam2fq( self ): self.checkCommand( "bam2fq" ) # def testPileup1( self ): # self.checkCommand( "pileup1" ) # def testPileup2( self ): # self.checkCommand( "pileup2" ) # deprecated # def testGLFView( self ): # self.checkCommand( "glfview" ) def testView( self ): self.checkCommand( "view" ) def testEmptyIndex( self ): self.assertRaises( IOError, pysam.index, "exdoesntexist.bam" ) def __del__(self): if os.path.exists( WORKDIR ): shutil.rmtree( WORKDIR ) class IOTest(unittest.TestCase): '''check if reading samfile and writing a samfile are consistent.''' def checkEcho( self, input_filename, reference_filename, output_filename, input_mode, output_mode, use_template = True ): '''iterate through *input_filename* writing to *output_filename* and comparing the output to *reference_filename*. The files are opened according to the *input_mode* and *output_mode*. If *use_template* is set, the header is copied from infile using the template mechanism, otherwise target names and lengths are passed explicitly. ''' infile = pysam.Samfile( input_filename, input_mode ) if use_template: outfile = pysam.Samfile( output_filename, output_mode, template = infile ) else: outfile = pysam.Samfile( output_filename, output_mode, referencenames = infile.references, referencelengths = infile.lengths, add_sq_text = False ) iter = infile.fetch() for x in iter: outfile.write( x ) infile.close() outfile.close() self.assertTrue( checkBinaryEqual( reference_filename, output_filename), "files %s and %s are not the same" % (reference_filename, output_filename) ) def testReadWriteBam( self ): input_filename = "ex1.bam" output_filename = "pysam_ex1.bam" reference_filename = "ex1.bam" self.checkEcho( input_filename, reference_filename, output_filename, "rb", "wb" ) def testReadWriteBamWithTargetNames( self ): input_filename = "ex1.bam" output_filename = "pysam_ex1.bam" reference_filename = "ex1.bam" self.checkEcho( input_filename, reference_filename, output_filename, "rb", "wb", use_template = False ) def testReadWriteSamWithHeader( self ): input_filename = "ex2.sam" output_filename = "pysam_ex2.sam" reference_filename = "ex2.sam" self.checkEcho( input_filename, reference_filename, output_filename, "r", "wh" ) def testReadWriteSamWithoutHeader( self ): input_filename = "ex2.sam" output_filename = "pysam_ex2.sam" reference_filename = "ex1.sam" self.checkEcho( input_filename, reference_filename, output_filename, "r", "w" ) def testReadSamWithoutHeaderWriteSamWithoutHeader( self ): input_filename = "ex1.sam" output_filename = "pysam_ex1.sam" reference_filename = "ex1.sam" # disabled - reading from a samfile without header # is not implemented. # self.checkEcho( input_filename, reference_filename, output_filename, # "r", "w" ) def testFetchFromClosedFile( self ): samfile = pysam.Samfile( "ex1.bam", "rb" ) samfile.close() self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120) def testClosedFile( self ): '''test that access to a closed samfile raises ValueError.''' samfile = pysam.Samfile( "ex1.bam", "rb" ) samfile.close() self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120) self.assertRaises( ValueError, samfile.pileup, 'chr1', 100, 120) self.assertRaises( ValueError, samfile.getrname, 0 ) self.assertRaises( ValueError, samfile.tell ) self.assertRaises( ValueError, samfile.seek, 0 ) self.assertRaises( ValueError, getattr, samfile, "nreferences" ) self.assertRaises( ValueError, getattr, samfile, "references" ) self.assertRaises( ValueError, getattr, samfile, "lengths" ) self.assertRaises( ValueError, getattr, samfile, "text" ) self.assertRaises( ValueError, getattr, samfile, "header" ) # write on closed file self.assertEqual( 0, samfile.write(None) ) def testAutoDetection( self ): '''test if autodetection works.''' samfile = pysam.Samfile( "ex3.sam" ) self.assertRaises( ValueError, samfile.fetch, 'chr1' ) samfile.close() samfile = pysam.Samfile( "ex3.bam" ) samfile.fetch('chr1') samfile.close() def testReadingFromSamFileWithoutHeader( self ): '''read from samfile without header. ''' samfile = pysam.Samfile( "ex7.sam" ) self.assertRaises( NotImplementedError, samfile.__iter__ ) def testReadingFromFileWithoutIndex( self ): '''read from bam file without index.''' assert not os.path.exists( "ex2.bam.bai" ) samfile = pysam.Samfile( "ex2.bam", "rb" ) self.assertRaises( ValueError, samfile.fetch ) self.assertEqual( len(list( samfile.fetch(until_eof = True) )), 3270 ) def testReadingUniversalFileMode( self ): '''read from samfile without header. ''' input_filename = "ex2.sam" output_filename = "pysam_ex2.sam" reference_filename = "ex1.sam" self.checkEcho( input_filename, reference_filename, output_filename, "rU", "w" ) class TestFloatTagBug( unittest.TestCase ): '''see issue 71''' def testFloatTagBug( self ): '''a float tag before another exposed a parsing bug in bam_aux_get - expected to fail This test is expected to fail until samtools is fixed. ''' samfile = pysam.Samfile("tag_bug.bam") read = samfile.fetch(until_eof=True).next() self.assertTrue( ('XC',1) in read.tags ) self.assertEqual(read.opt('XC'), 1) class TestTagParsing( unittest.TestCase ): '''tests checking the accuracy of tag setting and retrieval.''' def makeRead( self ): a = pysam.AlignedRead() a.qname = "read_12345" a.tid = 0 a.seq="ACGT" * 3 a.flag = 0 a.rname = 0 a.pos = 1 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,25) ) a.mrnm = 0 a.mpos=200 a.isize = 0 a.qual ="1234" * 3 # todo: create tags return a def testNegativeIntegers( self ): x = -2 aligned_read = self.makeRead() aligned_read.tags = [("XD", int(x) ) ] # print (aligned_read.tags) def testNegativeIntegers2( self ): x = -2 r = self.makeRead() r.tags = [("XD", int(x) ) ] outfile = pysam.Samfile( "test.bam", "wb", referencenames = ("chr1",), referencelengths = (1000,) ) outfile.write (r ) outfile.close() class TestIteratorRow(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def checkRange( self, rnge ): '''compare results from iterator with those from samtools.''' ps = list(self.samfile.fetch(region=rnge)) sa = list(pysam.view( "ex1.bam", rnge, raw = True) ) self.assertEqual( len(ps), len(sa), "unequal number of results for range %s: %i != %i" % (rnge, len(ps), len(sa) )) # check if the same reads are returned and in the same order for line, (a, b) in enumerate( zip( ps, sa ) ): d = b.split("\t") self.assertEqual( a.qname, d[0], "line %i: read id mismatch: %s != %s" % (line, a.rname, d[0]) ) self.assertEqual( a.pos, int(d[3])-1, "line %i: read position mismatch: %s != %s, \n%s\n%s\n" % \ (line, a.pos, int(d[3])-1, str(a), str(d) ) ) if sys.version_info[0] < 3: qual = d[10] else: qual = d[10].encode('ascii') self.assertEqual( a.qual, qual, "line %i: quality mismatch: %s != %s, \n%s\n%s\n" % \ (line, a.qual, qual, str(a), str(d) ) ) def testIteratePerContig(self): '''check random access per contig''' for contig in self.samfile.references: self.checkRange( contig ) def testIterateRanges(self): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range( 1, length, 90): self.checkRange( "%s:%i-%i" % (contig, start, start + 90) ) # this includes empty ranges def tearDown(self): self.samfile.close() class TestIteratorRowAll(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testIterate(self): '''compare results from iterator with those from samtools.''' ps = list(self.samfile.fetch()) sa = list(pysam.view( "ex1.bam", raw = True) ) self.assertEqual( len(ps), len(sa), "unequal number of results: %i != %i" % (len(ps), len(sa) )) # check if the same reads are returned for line, pair in enumerate( zip( ps, sa ) ): data = pair[1].split("\t") self.assertEqual( pair[0].qname, data[0], "read id mismatch in line %i: %s != %s" % (line, pair[0].rname, data[0]) ) def tearDown(self): self.samfile.close() class TestIteratorColumn(unittest.TestCase): '''test iterator column against contents of ex3.bam.''' # note that samfile contains 1-based coordinates # 1D means deletion with respect to reference sequence # mCoverages = { 'chr1' : [ 0 ] * 20 + [1] * 36 + [0] * (100 - 20 -35 ), 'chr2' : [ 0 ] * 20 + [1] * 35 + [0] * (100 - 20 -35 ), } def setUp(self): self.samfile=pysam.Samfile( "ex4.bam","rb" ) def checkRange( self, rnge ): '''compare results from iterator with those from samtools.''' # check if the same reads are returned and in the same order for column in self.samfile.pileup(region=rnge): thiscov = len(column.pileups) refcov = self.mCoverages[self.samfile.getrname(column.tid)][column.pos] self.assertEqual( thiscov, refcov, "wrong coverage at pos %s:%i %i should be %i" % (self.samfile.getrname(column.tid), column.pos, thiscov, refcov)) def testIterateAll(self): '''check random access per contig''' self.checkRange( None ) def testIteratePerContig(self): '''check random access per contig''' for contig in self.samfile.references: self.checkRange( contig ) def testIterateRanges(self): '''check random access per range''' for contig, length in zip(self.samfile.references, self.samfile.lengths): for start in range( 1, length, 90): self.checkRange( "%s:%i-%i" % (contig, start, start + 90) ) # this includes empty ranges def testInverse( self ): '''test the inverse, is point-wise pileup accurate.''' for contig, refseq in self.mCoverages.items(): refcolumns = sum(refseq) for pos, refcov in enumerate( refseq ): columns = list(self.samfile.pileup( contig, pos, pos+1) ) if refcov == 0: # if no read, no coverage self.assertEqual( len(columns), refcov, "wrong number of pileup columns returned for position %s:%i, %i should be %i" %(contig,pos,len(columns), refcov) ) elif refcov == 1: # one read, all columns of the read are returned self.assertEqual( len(columns), refcolumns, "pileup incomplete at position %i: got %i, expected %i " %\ (pos, len(columns), refcolumns)) def tearDown(self): self.samfile.close() class TestAlignedReadFromBam(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex3.bam","rb" ) self.reads=list(self.samfile.fetch()) def testARqname(self): self.assertEqual( self.reads[0].qname, "read_28833_29006_6945", "read name mismatch in read 1: %s != %s" % (self.reads[0].qname, "read_28833_29006_6945") ) self.assertEqual( self.reads[1].qname, "read_28701_28881_323b", "read name mismatch in read 2: %s != %s" % (self.reads[1].qname, "read_28701_28881_323b") ) def testARflag(self): self.assertEqual( self.reads[0].flag, 99, "flag mismatch in read 1: %s != %s" % (self.reads[0].flag, 99) ) self.assertEqual( self.reads[1].flag, 147, "flag mismatch in read 2: %s != %s" % (self.reads[1].flag, 147) ) def testARrname(self): self.assertEqual( self.reads[0].rname, 0, "chromosome/target id mismatch in read 1: %s != %s" % (self.reads[0].rname, 0) ) self.assertEqual( self.reads[1].rname, 1, "chromosome/target id mismatch in read 2: %s != %s" % (self.reads[1].rname, 1) ) def testARpos(self): self.assertEqual( self.reads[0].pos, 33-1, "mapping position mismatch in read 1: %s != %s" % (self.reads[0].pos, 33-1) ) self.assertEqual( self.reads[1].pos, 88-1, "mapping position mismatch in read 2: %s != %s" % (self.reads[1].pos, 88-1) ) def testARmapq(self): self.assertEqual( self.reads[0].mapq, 20, "mapping quality mismatch in read 1: %s != %s" % (self.reads[0].mapq, 20) ) self.assertEqual( self.reads[1].mapq, 30, "mapping quality mismatch in read 2: %s != %s" % (self.reads[1].mapq, 30) ) def testARcigar(self): self.assertEqual( self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)], "read name length mismatch in read 1: %s != %s" % (self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)]) ) self.assertEqual( self.reads[1].cigar, [(0, 35)], "read name length mismatch in read 2: %s != %s" % (self.reads[1].cigar, [(0, 35)]) ) def testARmrnm(self): self.assertEqual( self.reads[0].mrnm, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].mrnm, 0) ) self.assertEqual( self.reads[1].mrnm, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].mrnm, 1) ) self.assertEqual( self.reads[0].rnext, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].rnext, 0) ) self.assertEqual( self.reads[1].rnext, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].rnext, 1) ) def testARmpos(self): self.assertEqual( self.reads[0].mpos, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].mpos, 200-1) ) self.assertEqual( self.reads[1].mpos, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].mpos, 500-1) ) self.assertEqual( self.reads[0].pnext, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].pnext, 200-1) ) self.assertEqual( self.reads[1].pnext, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].pnext, 500-1) ) def testARisize(self): self.assertEqual( self.reads[0].isize, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].isize, 167) ) self.assertEqual( self.reads[1].isize, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].isize, 412) ) self.assertEqual( self.reads[0].tlen, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].tlen, 167) ) self.assertEqual( self.reads[1].tlen, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].tlen, 412) ) def testARseq(self): self.assertEqual( self.reads[0].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 1: %s != %s" % (self.reads[0].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") ) self.assertEqual( self.reads[1].seq, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "sequence size mismatch in read 2: %s != %s" % (self.reads[1].seq, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") ) self.assertEqual( self.reads[3].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 4: %s != %s" % (self.reads[3].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") ) def testARqual(self): self.assertEqual( self.reads[0].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "quality string mismatch in read 1: %s != %s" % (self.reads[0].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") ) self.assertEqual( self.reads[1].qual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "quality string mismatch in read 2: %s != %s" % (self.reads[1].qual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") ) self.assertEqual( self.reads[3].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "quality string mismatch in read 3: %s != %s" % (self.reads[3].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") ) def testARquery(self): self.assertEqual( self.reads[0].query, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "query mismatch in read 1: %s != %s" % (self.reads[0].query, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") ) self.assertEqual( self.reads[1].query, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "query size mismatch in read 2: %s != %s" % (self.reads[1].query, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") ) self.assertEqual( self.reads[3].query, b"TAGCTAGCTACCTATATCTTGGTCTT", "query mismatch in read 4: %s != %s" % (self.reads[3].query, b"TAGCTAGCTACCTATATCTTGGTCTT") ) def testARqqual(self): self.assertEqual( self.reads[0].qqual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "qquality string mismatch in read 1: %s != %s" % (self.reads[0].qqual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") ) self.assertEqual( self.reads[1].qqual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "qquality string mismatch in read 2: %s != %s" % (self.reads[1].qqual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") ) self.assertEqual( self.reads[3].qqual, b"<<<<<<<<<<<<<<<<<:<9/,&,22", "qquality string mismatch in read 3: %s != %s" % (self.reads[3].qqual, b"<<<<<<<<<<<<<<<<<:<9/,&,22") ) def testPresentOptionalFields(self): self.assertEqual( self.reads[0].opt('NM'), 1, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 1) ) self.assertEqual( self.reads[0].opt('RG'), 'L1', "optional field mismatch in read 1, RG: %s != %s" % (self.reads[0].opt('RG'), 'L1') ) self.assertEqual( self.reads[1].opt('RG'), 'L2', "optional field mismatch in read 2, RG: %s != %s" % (self.reads[1].opt('RG'), 'L2') ) self.assertEqual( self.reads[1].opt('MF'), 18, "optional field mismatch in read 2, MF: %s != %s" % (self.reads[1].opt('MF'), 18) ) def testPairedBools(self): self.assertEqual( self.reads[0].is_paired, True, "is paired mismatch in read 1: %s != %s" % (self.reads[0].is_paired, True) ) self.assertEqual( self.reads[1].is_paired, True, "is paired mismatch in read 2: %s != %s" % (self.reads[1].is_paired, True) ) self.assertEqual( self.reads[0].is_proper_pair, True, "is proper pair mismatch in read 1: %s != %s" % (self.reads[0].is_proper_pair, True) ) self.assertEqual( self.reads[1].is_proper_pair, True, "is proper pair mismatch in read 2: %s != %s" % (self.reads[1].is_proper_pair, True) ) def testTags( self ): self.assertEqual( self.reads[0].tags, [('NM', 1), ('RG', 'L1'), ('PG', 'P1'), ('XT', 'U')] ) self.assertEqual( self.reads[1].tags, [('MF', 18), ('RG', 'L2'), ('PG', 'P2'),('XT', 'R') ] ) def testOpt( self ): self.assertEqual( self.reads[0].opt("XT"), "U" ) self.assertEqual( self.reads[1].opt("XT"), "R" ) def testMissingOpt( self ): self.assertRaises( KeyError, self.reads[0].opt, "XP" ) def testEmptyOpt( self ): self.assertRaises( KeyError, self.reads[2].opt, "XT" ) def tearDown(self): self.samfile.close() class TestAlignedReadFromSam(TestAlignedReadFromBam): def setUp(self): self.samfile=pysam.Samfile( "ex3.sam","r" ) self.reads=list(self.samfile.fetch()) # needs to be implemented # class TestAlignedReadFromSamWithoutHeader(TestAlignedReadFromBam): # # def setUp(self): # self.samfile=pysam.Samfile( "ex7.sam","r" ) # self.reads=list(self.samfile.fetch()) class TestHeaderSam(unittest.TestCase): header = {'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], 'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891', 'PU': 'SC_1_10', "CN":"name:with:colon"}, {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891', 'PU': 'SC_2_12', "CN":"name:with:colon"}], 'PG': [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}], 'HD': {'VN': '1.0'}, 'CO' : [ 'this is a comment', 'this is another comment'], } def compareHeaders( self, a, b ): '''compare two headers a and b.''' for ak,av in a.iteritems(): self.assertTrue( ak in b, "key '%s' not in '%s' " % (ak,b) ) self.assertEqual( av, b[ak] ) def setUp(self): self.samfile=pysam.Samfile( "ex3.sam","r" ) def testHeaders(self): self.compareHeaders( self.header, self.samfile.header ) self.compareHeaders( self.samfile.header, self.header ) def testNameMapping( self ): for x, y in enumerate( ("chr1", "chr2")): tid = self.samfile.gettid( y ) ref = self.samfile.getrname( x ) self.assertEqual( tid, x ) self.assertEqual( ref, y ) self.assertEqual( self.samfile.gettid("chr?"), -1 ) self.assertRaises( ValueError, self.samfile.getrname, 2 ) def tearDown(self): self.samfile.close() class TestHeaderBam(TestHeaderSam): def setUp(self): self.samfile=pysam.Samfile( "ex3.bam","rb" ) class TestUnmappedReads(unittest.TestCase): def testSAM(self): samfile=pysam.Samfile( "ex5.sam","r" ) self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 ) samfile.close() def testBAM(self): samfile=pysam.Samfile( "ex5.bam","rb" ) self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 ) samfile.close() class TestPileupObjects(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testPileupColumn(self): for pcolumn1 in self.samfile.pileup( region="chr1:105" ): if pcolumn1.pos == 104: self.assertEqual( pcolumn1.tid, 0, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn1.tid, 0) ) self.assertEqual( pcolumn1.pos, 105-1, "position mismatch in position 1: %s != %s" % (pcolumn1.pos, 105-1) ) self.assertEqual( pcolumn1.n, 2, "# reads mismatch in position 1: %s != %s" % (pcolumn1.n, 2) ) for pcolumn2 in self.samfile.pileup( region="chr2:1480" ): if pcolumn2.pos == 1479: self.assertEqual( pcolumn2.tid, 1, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn2.tid, 1) ) self.assertEqual( pcolumn2.pos, 1480-1, "position mismatch in position 1: %s != %s" % (pcolumn2.pos, 1480-1) ) self.assertEqual( pcolumn2.n, 12, "# reads mismatch in position 1: %s != %s" % (pcolumn2.n, 12) ) def testPileupRead(self): for pcolumn1 in self.samfile.pileup( region="chr1:105" ): if pcolumn1.pos == 104: self.assertEqual( len(pcolumn1.pileups), 2, "# reads aligned to column mismatch in position 1: %s != %s" % (len(pcolumn1.pileups), 2) ) # self.assertEqual( pcolumn1.pileups[0] # need to test additional properties here def tearDown(self): self.samfile.close() class TestContextManager(unittest.TestCase): def testManager( self ): with pysam.Samfile('ex1.bam', 'rb') as samfile: samfile.fetch() self.assertEqual( samfile._isOpen(), False ) class TestExceptions(unittest.TestCase): def setUp(self): self.samfile=pysam.Samfile( "ex1.bam","rb" ) def testMissingFile(self): self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.bam", "rb" ) self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.sam", "r" ) self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.bam", "r" ) self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.sam", "rb" ) def testBadContig(self): self.assertRaises( ValueError, self.samfile.fetch, "chr88" ) def testMeaninglessCrap(self): self.assertRaises( ValueError, self.samfile.fetch, "skljf" ) def testBackwardsOrderNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, 'chr1', 100, 10 ) def testBackwardsOrderOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, region="chr1:100-10") def testOutOfRangeNegativeNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, -10 ) self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, 0 ) self.assertRaises( ValueError, self.samfile.fetch, "chr1", -5, -10 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 5, -10 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 5, 0 ) self.assertRaises( ValueError, self.samfile.count, "chr1", -5, -10 ) def testOutOfRangeNegativeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5-10" ) self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5-0" ) self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5--10" ) self.assertRaises( ValueError, self.samfile.count, region="chr1:-5-10" ) self.assertRaises( ValueError, self.samfile.count, region="chr1:-5-0" ) self.assertRaises( ValueError, self.samfile.count, region="chr1:-5--10" ) def testOutOfRangNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999, 99999999999 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999, 99999999999 ) def testOutOfRangeLargeNewFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 ) self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 ) def testOutOfRangeLargeOldFormat(self): self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999" ) self.assertRaises( ValueError, self.samfile.count, "chr1:99999999999999999-999999999999999999" ) def testZeroToZero(self): '''see issue 44''' self.assertEqual( len(list(self.samfile.fetch('chr1', 0, 0))), 0) def tearDown(self): self.samfile.close() class TestWrongFormat(unittest.TestCase): '''test cases for opening files not in bam/sam format.''' def testOpenSamAsBam( self ): self.assertRaises( ValueError, pysam.Samfile, 'ex1.sam', 'rb' ) def testOpenBamAsSam( self ): # test fails, needs to be implemented. # sam.fetch() fails on reading, not on opening # self.assertRaises( ValueError, pysam.Samfile, 'ex1.bam', 'r' ) pass def testOpenFastaAsSam( self ): # test fails, needs to be implemented. # sam.fetch() fails on reading, not on opening # self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'r' ) pass def testOpenFastaAsBam( self ): self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'rb' ) class TestFastaFile(unittest.TestCase): mSequences = { 'chr1' : b"CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAGCTCCCTGTCACCCAATGGACCTGTGATATCTGGATTCTGGGAAATTCTTCATCCTGGACCCTGAGAGATTCTGCAGCCCAGCTCCAGATTGCTTGTGGTCTGACAGGCTGCAACTGTGAGCCATCACAATGAACAACAGGAAGAAAAGGTCTTTCAAAAGGTGATGTGTGTTCTCATCAACCTCATACACACACATGGTTTAGGGGTATAATACCTCTACATGGCTGATTATGAAAACAATGTTCCCCAGATACCATCCCTGTCTTACTTCCAGCTCCCCAGAGGGAAAGCTTTCAACGCTTCTAGCCATTTCTTTTGGCATTTGCCTTCAGACCCTACACGAATGCGTCTCTACCACAGGGGGCTGCGCGGTTTCCCATCATGAAGCACTGAACTTCCACGTCTCATCTAGGGGAACAGGGAGGTGCACTAATGCGCTCCACGCCCAAGCCCTTCTCACAGTTTCTGCCCCCAGCATGGTTGTACTGGGCAATACATGAGATTATTAGGAAATGCTTTACTGTCATAACTATGAAGAGACTATTGCCAGATGAACCACACATTAATACTATGTTTCTTATCTGCACATTACTACCCTGCAATTAATATAATTGTGTCCATGTACACACGCTGTCCTATGTACTTATCATGACTCTATCCCAAATTCCCAATTACGTCCTATCTTCTTCTTAGGGAAGAACAGCTTAGGTATCAATTTGGTGTTCTGTGTAAAGTCTCAGGGAGCCGTCCGTGTCCTCCCATCTGGCCTCGTCCACACTGGTTCTCTTGAAAGCTTGGGCTGTAATGATGCCCCTTGGCCATCACCCAGTCCCTGCCCCATCTCTTGTAATCTCTCTCCTTTTTGCTGCATCCCTGTCTTCCTCTGTCTTGATTTACTTGTTGTTGGTTTTCTGTTTCTTTGTTTGATTTGGTGGAAGACATAATCCCACGCTTCCTATGGAAAGGTTGTTGGGAGATTTTTAATGATTCCTCAATGTTAAAATGTCTATTTTTGTCTTGACACCCAACTAATATTTGTCTGAGCAAAACAGTCTAGATGAGAGAGAACTTCCCTGGAGGTCTGATGGCGTTTCTCCCTCGTCTTCTTA", 'chr2' : b"TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTATAAAGGAAATCCCATCAGAATAACAATGGGCTTCTCAGCAGAAACCTTACAAGCCAGAAGAGATTGGATCTAATTTTTGGACTTCTTAAAGAAAAAAAAACCTGTCAAACACGAATGTTATGCCCTGCTAAACTAAGCATCATAAATGAAGGGGAAATAAAGTCAAGTCTTTCCTGACAAGCAAATGCTAAGATAATTCATCATCACTAAACCAGTCCTATAAGAAATGCTCAAAAGAATTGTAAAAGTCAAAATTAAAGTTCAATACTCACCATCATAAATACACACAAAAGTACAAAACTCACAGGTTTTATAAAACAATTGAGACTACAGAGCAACTAGGTAAAAAATTAACATTACAACAGGAACAAAACCTCATATATCAATATTAACTTTGAATAAAAAGGGATTAAATTCCCCCACTTAAGAGATATAGATTGGCAGAACAGATTTAAAAACATGAACTAACTATATGCTGTTTACAAGAAACTCATTAATAAAGACATGAGTTCAGGTAAAGGGGTGGAAAAAGATGTTCTACGCAAACAGAAACCAAATGAGAGAAGGAGTAGCTATACTTATATCAGATAAAGCACACTTTAAATCAACAACAGTAAAATAAAACAAAGGAGGTCATCATACAATGATAAAAAGATCAATTCAGCAAGAAGATATAACCATCCTACTAAATACATATGCACCTAACACAAGACTACCCAGATTCATAAAACAAATACTACTAGACCTAAGAGGGATGAGAAATTACCTAATTGGTACAATGTACAATATTCTGATGATGGTTACACTAAAAGCCCATACTTTACTGCTACTCAATATATCCATGTAACAAATCTGCGCTTGTACTTCTAAATCTATAAAAAAATTAAAATTTAACAAAAGTAAATAAAACACATAGCTAAAACTAAAAAAGCAAAAACAAAAACTATGCTAAGTATTGGTAAAGATGTGGGGAAAAAAGTAAACTCTCAAATATTGCTAGTGGGAGTATAAATTGTTTTCCACTTTGGAAAACAATTTGGTAATTTCGTTTTTTTTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTTTGCATGCCAGAAAAAAATATTTACAGTAACT", } def setUp(self): self.file=pysam.Fastafile( "ex1.fa" ) def testFetch(self): for id, seq in self.mSequences.items(): self.assertEqual( seq, self.file.fetch( id ) ) for x in range( 0, len(seq), 10): self.assertEqual( seq[x:x+10], self.file.fetch( id, x, x+10) ) # test x:end self.assertEqual( seq[x:], self.file.fetch( id, x) ) # test 0:x self.assertEqual( seq[:x], self.file.fetch( id, None, x) ) # unknown sequence returns "" self.assertEqual( b"", self.file.fetch("chr12") ) def testOutOfRangeAccess( self ): '''test out of range access.''' # out of range access returns an empty string for contig, s in self.mSequences.iteritems(): self.assertEqual( self.file.fetch( contig, len(s), len(s)+1), b"" ) self.assertEqual( self.file.fetch( "chr3", 0 , 100), b"" ) def testFetchErrors( self ): self.assertRaises( ValueError, self.file.fetch ) self.assertRaises( ValueError, self.file.fetch, "chr1", -1, 10 ) self.assertRaises( ValueError, self.file.fetch, "chr1", 20, 10 ) def testLength( self ): self.assertEqual( len(self.file), 2 ) def tearDown(self): self.file.close() class TestAlignedRead(unittest.TestCase): '''tests to check if aligned read can be constructed and manipulated. ''' def checkFieldEqual( self, read1, read2, exclude = []): '''check if two reads are equal by comparing each field.''' for x in ("qname", "seq", "flag", "rname", "pos", "mapq", "cigar", "mrnm", "mpos", "isize", "qual", "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate", "bin"): if x in exclude: continue self.assertEqual( getattr(read1, x), getattr(read2,x), "attribute mismatch for %s: %s != %s" % (x, getattr(read1, x), getattr(read2,x))) def testEmpty( self ): a = pysam.AlignedRead() self.assertEqual( a.qname, None ) self.assertEqual( a.seq, None ) self.assertEqual( a.qual, None ) self.assertEqual( a.flag, 0 ) self.assertEqual( a.rname, 0 ) self.assertEqual( a.mapq, 0 ) self.assertEqual( a.cigar, None ) self.assertEqual( a.tags, [] ) self.assertEqual( a.mrnm, 0 ) self.assertEqual( a.mpos, 0 ) self.assertEqual( a.isize, 0 ) def buildRead( self ): '''build an example read.''' a = pysam.AlignedRead() a.qname = "read_12345" a.seq="ACGT" * 10 a.flag = 0 a.rname = 0 a.pos = 20 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,9), (1,1), (0,20) ) a.mrnm = 0 a.mpos=200 a.isize=167 a.qual="1234" * 10 # todo: create tags return a def testUpdate( self ): '''check if updating fields affects other variable length data ''' a = self.buildRead() b = self.buildRead() # check qname b.qname = "read_123" self.checkFieldEqual( a, b, "qname" ) b.qname = "read_12345678" self.checkFieldEqual( a, b, "qname" ) b.qname = "read_12345" self.checkFieldEqual( a, b) # check cigar b.cigar = ( (0,10), ) self.checkFieldEqual( a, b, "cigar" ) b.cigar = ( (0,10), (2,1), (0,10) ) self.checkFieldEqual( a, b, "cigar" ) b.cigar = ( (0,10), (2,1), (0,9), (1,1), (0,20) ) self.checkFieldEqual( a, b) # check seq b.seq = "ACGT" self.checkFieldEqual( a, b, ("seq", "qual") ) b.seq = "ACGT" * 3 self.checkFieldEqual( a, b, ("seq", "qual") ) b.seq = "ACGT" * 10 self.checkFieldEqual( a, b, ("qual",)) # reset qual b = self.buildRead() # check flags: for x in ( "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate"): setattr( b, x, True ) self.assertEqual( getattr(b, x), True ) self.checkFieldEqual( a, b, ("flag", x,) ) setattr( b, x, False ) self.assertEqual( getattr(b, x), False ) self.checkFieldEqual( a, b ) def testLargeRead( self ): '''build an example read.''' a = pysam.AlignedRead() a.qname = "read_12345" a.seq="ACGT" * 200 a.flag = 0 a.rname = 0 a.pos = 20 a.mapq = 20 a.cigar = ( (0, 4 * 200), ) a.mrnm = 0 a.mpos=200 a.isize=167 a.qual="1234" * 200 return a def testTagParsing( self ): '''test for tag parsing see http://groups.google.com/group/pysam-user-group/browse_thread/thread/67ca204059ea465a ''' samfile=pysam.Samfile( "ex8.bam","rb" ) for entry in samfile: before = entry.tags entry.tags = entry.tags after = entry.tags self.assertEqual( after, before ) def testUpdateTlen( self ): '''check if updating tlen works''' a = self.buildRead() oldlen = a.tlen oldlen *= 2 a.tlen = oldlen self.assertEqual( a.tlen, oldlen ) def testPositions( self ): a = self.buildRead() self.assertEqual( a.positions, [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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] ) self.assertEqual( a.aligned_pairs, [(0, 20), (1, 21), (2, 22), (3, 23), (4, 24), (5, 25), (6, 26), (7, 27), (8, 28), (9, 29), (None, 30), (10, 31), (11, 32), (12, 33), (13, 34), (14, 35), (15, 36), (16, 37), (17, 38), (18, 39), (19, None), (20, 40), (21, 41), (22, 42), (23, 43), (24, 44), (25, 45), (26, 46), (27, 47), (28, 48), (29, 49), (30, 50), (31, 51), (32, 52), (33, 53), (34, 54), (35, 55), (36, 56), (37, 57), (38, 58), (39, 59)] ) self.assertEqual( a.positions, [x[1] for x in a.aligned_pairs if x[0] != None and x[1] != None] ) # alen is the length of the aligned read in genome self.assertEqual( a.alen, a.aligned_pairs[-1][0] + 1 ) # aend points to one beyond last aligned base in ref self.assertEqual( a.positions[-1], a.aend - 1 ) class TestDeNovoConstruction(unittest.TestCase): '''check BAM/SAM file construction using ex3.sam (note these are +1 coordinates): read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1 read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2 ''' header = { 'HD': {'VN': '1.0'}, 'SQ': [{'LN': 1575, 'SN': 'chr1'}, {'LN': 1584, 'SN': 'chr2'}], } bamfile = "ex6.bam" samfile = "ex6.sam" def checkFieldEqual( self, read1, read2, exclude = []): '''check if two reads are equal by comparing each field.''' for x in ("qname", "seq", "flag", "rname", "pos", "mapq", "cigar", "mrnm", "mpos", "isize", "qual", "bin", "is_paired", "is_proper_pair", "is_unmapped", "mate_is_unmapped", "is_reverse", "mate_is_reverse", "is_read1", "is_read2", "is_secondary", "is_qcfail", "is_duplicate"): if x in exclude: continue self.assertEqual( getattr(read1, x), getattr(read2,x), "attribute mismatch for %s: %s != %s" % (x, getattr(read1, x), getattr(read2,x))) def setUp( self ): a = pysam.AlignedRead() a.qname = "read_28833_29006_6945" a.seq="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG" a.flag = 99 a.rname = 0 a.pos = 32 a.mapq = 20 a.cigar = ( (0,10), (2,1), (0,25) ) a.mrnm = 0 a.mpos=199 a.isize=167 a.qual="<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<" a.tags = ( ("NM", 1), ("RG", "L1") ) b = pysam.AlignedRead() b.qname = "read_28701_28881_323b" b.seq="ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA" b.flag = 147 b.rname = 1 b.pos = 87 b.mapq = 30 b.cigar = ( (0,35), ) b.mrnm = 1 b.mpos=499 b.isize=412 b.qual="<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<" b.tags = ( ("MF", 18), ("RG", "L2") ) self.reads = (a,b) def testSAMWholeFile( self ): tmpfilename = "tmp_%i.sam" % id(self) outfile = pysam.Samfile( tmpfilename, "wh", header = self.header ) for x in self.reads: outfile.write( x ) outfile.close() self.assertTrue( checkBinaryEqual( tmpfilename, self.samfile ), "mismatch when construction SAM file, see %s %s" % (tmpfilename, self.samfile)) os.unlink( tmpfilename ) def testBAMPerRead( self ): '''check if individual reads are binary equal.''' infile = pysam.Samfile( self.bamfile, "rb") others = list(infile) for denovo, other in zip( others, self.reads): self.checkFieldEqual( other, denovo ) self.assertEqual( other.compare( denovo ), 0 ) def testSAMPerRead( self ): '''check if individual reads are binary equal.''' infile = pysam.Samfile( self.samfile, "r") others = list(infile) for denovo, other in zip( others, self.reads): self.checkFieldEqual( other, denovo ) self.assertEqual( other.compare( denovo), 0 ) def testBAMWholeFile( self ): tmpfilename = "tmp_%i.bam" % id(self) outfile = pysam.Samfile( tmpfilename, "wb", header = self.header ) for x in self.reads: outfile.write( x ) outfile.close() self.assertTrue( checkBinaryEqual( tmpfilename, self.bamfile ), "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile)) os.unlink( tmpfilename ) class TestDoubleFetch(unittest.TestCase): '''check if two iterators on the same bamfile are independent.''' def testDoubleFetch( self ): samfile1 = pysam.Samfile('ex1.bam', 'rb') for a,b in zip(samfile1.fetch(), samfile1.fetch()): self.assertEqual( a.compare( b ), 0 ) def testDoubleFetchWithRegion( self ): samfile1 = pysam.Samfile('ex1.bam', 'rb') chr, start, stop = 'chr1', 200, 3000000 self.assertTrue(len(list(samfile1.fetch ( chr, start, stop))) > 0) #just making sure the test has something to catch for a,b in zip(samfile1.fetch( chr, start, stop), samfile1.fetch( chr, start, stop)): self.assertEqual( a.compare( b ), 0 ) def testDoubleFetchUntilEOF( self ): samfile1 = pysam.Samfile('ex1.bam', 'rb') for a,b in zip(samfile1.fetch( until_eof = True), samfile1.fetch( until_eof = True )): self.assertEqual( a.compare( b), 0 ) class TestRemoteFileFTP(unittest.TestCase): '''test remote access. ''' # Need to find an ftp server without password on standard # port. url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam" region = "1:1-1000" def testFTPView( self ): return result = pysam.view( self.url, self.region ) self.assertEqual( len(result), 36 ) def testFTPFetch( self ): return samfile = pysam.Samfile(self.url, "rb") result = list(samfile.fetch( region = self.region )) self.assertEqual( len(result), 36 ) class TestRemoteFileHTTP( unittest.TestCase): url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/ex1.bam" region = "chr1:1-1000" local = "ex1.bam" def testView( self ): samfile_local = pysam.Samfile(self.local, "rb") ref = list(samfile_local.fetch( region = self.region )) result = pysam.view( self.url, self.region ) self.assertEqual( len(result), len(ref) ) def testFetch( self ): samfile = pysam.Samfile(self.url, "rb") result = list(samfile.fetch( region = self.region )) samfile_local = pysam.Samfile(self.local, "rb") ref = list(samfile_local.fetch( region = self.region )) self.assertEqual( len(ref), len(result) ) for x, y in zip(result, ref): self.assertEqual( x.compare( y ), 0 ) def testFetchAll( self ): samfile = pysam.Samfile(self.url, "rb") result = list(samfile.fetch()) samfile_local = pysam.Samfile(self.local, "rb") ref = list(samfile_local.fetch() ) self.assertEqual( len(ref), len(result) ) for x, y in zip(result, ref): self.assertEqual( x.compare( y ), 0 ) class TestLargeOptValues( unittest.TestCase ): ints = ( 65536, 214748, 2147484, 2147483647 ) floats = ( 65536.0, 214748.0, 2147484.0 ) def check( self, samfile ): i = samfile.fetch() for exp in self.ints: rr = i.next() obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in [ -x for x in self.ints ]: rr = i.next() obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in self.floats: rr = i.next() obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) for exp in [ -x for x in self.floats ]: rr = i.next() obs = rr.opt("ZP") self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr))) def testSAM( self ): samfile = pysam.Samfile("ex10.sam", "r") self.check( samfile ) def testBAM( self ): samfile = pysam.Samfile("ex10.bam", "rb") self.check( samfile ) # class TestSNPCalls( unittest.TestCase ): # '''test pysam SNP calling ability.''' # def checkEqual( self, a, b ): # for x in ("reference_base", # "pos", # "genotype", # "consensus_quality", # "snp_quality", # "mapping_quality", # "coverage" ): # self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" % # (x, getattr(a, x), getattr(b,x), str(a), str(b))) # def testAllPositionsViaIterator( self ): # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # try: # refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base != "*"] # except pysam.SamtoolsError: # pass # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # calls = list(pysam.IteratorSNPCalls(i)) # for x,y in zip( refs, calls ): # self.checkEqual( x, y ) # def testPerPositionViaIterator( self ): # # test pileup for each position. This is a slow operation # # so this test is disabled # return # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ): # if x.reference_base == "*": continue # i = samfile.pileup( x.chromosome, x.pos, x.pos+1, # fastafile = fastafile, # stepper = "samtools" ) # z = [ zz for zz in pysam.IteratorSamtools(i) if zz.pos == x.pos ] # self.assertEqual( len(z), 1 ) # self.checkEqual( x, z[0] ) # def testPerPositionViaCaller( self ): # # test pileup for each position. This is a fast operation # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # caller = pysam.SNPCaller( i ) # for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ): # if x.reference_base == "*": continue # call = caller.call( x.chromosome, x.pos ) # self.checkEqual( x, call ) # class TestIndelCalls( unittest.TestCase ): # '''test pysam indel calling.''' # def checkEqual( self, a, b ): # for x in ("pos", # "genotype", # "consensus_quality", # "snp_quality", # "mapping_quality", # "coverage", # "first_allele", # "second_allele", # "reads_first", # "reads_second", # "reads_diff"): # if b.genotype == "*/*" and x == "second_allele": # # ignore test for second allele (positions chr2:439 and chr2:1512) # continue # self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" % # (x, getattr(a, x), getattr(b,x), str(a), str(b))) # def testAllPositionsViaIterator( self ): # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # try: # refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base == "*"] # except pysam.SamtoolsError: # pass # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # calls = [ x for x in list(pysam.IteratorIndelCalls(i)) if x != None ] # for x,y in zip( refs, calls ): # self.checkEqual( x, y ) # def testPerPositionViaCaller( self ): # # test pileup for each position. This is a fast operation # samfile = pysam.Samfile( "ex1.bam", "rb") # fastafile = pysam.Fastafile( "ex1.fa" ) # i = samfile.pileup( stepper = "samtools", fastafile = fastafile ) # caller = pysam.IndelCaller( i ) # for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ): # if x.reference_base != "*": continue # call = caller.call( x.chromosome, x.pos ) # self.checkEqual( x, call ) class TestLogging( unittest.TestCase ): '''test around bug issue 42, failed in versions < 0.4 ''' def check( self, bamfile, log ): if log: logger = logging.getLogger('franklin') logger.setLevel(logging.INFO) formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s') log_hand = logging.FileHandler('log.txt') log_hand.setFormatter(formatter) logger.addHandler(log_hand) bam = pysam.Samfile(bamfile, 'rb') cols = bam.pileup() self.assert_( True ) def testFail1( self ): self.check( "ex9_fail.bam", False ) self.check( "ex9_fail.bam", True ) def testNoFail1( self ): self.check( "ex9_nofail.bam", False ) self.check( "ex9_nofail.bam", True ) def testNoFail2( self ): self.check( "ex9_nofail.bam", True ) self.check( "ex9_nofail.bam", True ) # TODOS # 1. finish testing all properties within pileup objects # 2. check exceptions and bad input problems (missing files, optional fields that aren't present, etc...) # 3. check: presence of sequence class TestSamfileUtilityFunctions( unittest.TestCase ): def testCount( self ): samfile = pysam.Samfile( "ex1.bam", "rb" ) for contig in ("chr1", "chr2" ): for start in xrange( 0, 2000, 100 ): end = start + 1 self.assertEqual( len( list( samfile.fetch( contig, start, end ) ) ), samfile.count( contig, start, end ) ) # test empty intervals self.assertEqual( len( list( samfile.fetch( contig, start, start ) ) ), samfile.count( contig, start, start ) ) # test half empty intervals self.assertEqual( len( list( samfile.fetch( contig, start ) ) ), samfile.count( contig, start ) ) def testMate( self ): '''test mate access.''' readnames = [ x.split(b"\t")[0] for x in open( "ex1.sam", "rb" ).readlines() ] if sys.version_info[0] >= 3: readnames = [ name.decode('ascii') for name in readnames ] counts = collections.defaultdict( int ) for x in readnames: counts[x] += 1 samfile = pysam.Samfile( "ex1.bam", "rb" ) for read in samfile.fetch(): if not read.is_paired: self.assertRaises( ValueError, samfile.mate, read ) elif read.mate_is_unmapped: self.assertRaises( ValueError, samfile.mate, read ) else: if counts[read.qname] == 1: self.assertRaises( ValueError, samfile.mate, read ) else: mate = samfile.mate( read ) self.assertEqual( read.qname, mate.qname ) self.assertEqual( read.is_read1, mate.is_read2 ) self.assertEqual( read.is_read2, mate.is_read1 ) self.assertEqual( read.pos, mate.mpos ) self.assertEqual( read.mpos, mate.pos ) def testIndexStats( self ): '''test if total number of mapped/unmapped reads is correct.''' samfile = pysam.Samfile( "ex1.bam", "rb" ) self.assertEqual( samfile.mapped, 3235 ) self.assertEqual( samfile.unmapped, 35 ) class TestSamtoolsProxy( unittest.TestCase ): '''tests for sanity checking access to samtools functions.''' def testIndex( self ): self.assertRaises( IOError, pysam.index, "missing_file" ) def testView( self ): # note that view still echos "open: No such file or directory" self.assertRaises( pysam.SamtoolsError, pysam.view, "missing_file" ) def testSort( self ): self.assertRaises( pysam.SamtoolsError, pysam.sort, "missing_file" ) class TestSamfileIndex( unittest.TestCase): def testIndex( self ): samfile = pysam.Samfile( "ex1.bam", "rb" ) index = pysam.IndexedReads( samfile ) index.build() reads = collections.defaultdict( int ) for read in samfile: reads[read.qname] += 1 for qname, counts in reads.iteritems(): found = list(index.find( qname )) self.assertEqual( len(found), counts ) for x in found: self.assertEqual( x.qname, qname ) if __name__ == "__main__": # build data files print ("building data files") subprocess.call( "make", shell=True) print ("starting tests") unittest.main() print ("completed tests")