69 lines
2.9 KiB
Python
69 lines
2.9 KiB
Python
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from SAM import *
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def read2align( refSeq, readSeq, chr, pos, cigar ):
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"""Converts the read bases, a reference sequence, and a cigar string into a pair of
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alignments strings for refSeq and readSeq. The alignment string has base equivalents
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between the reference and the read bases"""
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#
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# only works for non-indel containing reads right now!
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#
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contig = refSeq[chr]
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refAlign = contig[pos:pos+len(readSeq)]
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readAlign = readSeq
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return refAlign, readAlign
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def MappedReadFromSamRecord(ref, r):
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"""Converts SameRead into a SimpleSamRecord object"""
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#
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# This is a temp. function while we wait for Ted's C++ SAM/BAM io system to come online
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#
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refAlign, readAlign = read2align(ref, r.getSeq(), r.getRname(), r.getPos(), r.getCigar)
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return MappedRead( r.getQName(), r.getFlags(), r.getRname(), r.getPos(), r.getMapq(),
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r.getCigar(), r.getSeq(), refAlign, readAlign, r.getQuals() )
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class MappedRead(object):
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"""Higher level object representing a mapped read.
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Attempts to be more accessible than a raw SAM record, doing a lot of processing on the record w.r.t.
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the reference to make analysis of the reads easier. This is the fundamental data structure
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used to represent reads through the walker engine"""
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def __init__( self, qname, flags, chr, pos, mapq, cigar, readBases, refAlign, readAlign, qualsByBase ):
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# basic information about the read
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self.qname = qname
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self.mapq = mapq
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self.cigar = cigar
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self.bases = readBases # actual bases of reads, unaligned, may be fw or reverse
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self.quals = qualsByBase # as a vector of floats, by base position
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# dealing with position information, more than a standard record Hasbro
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self.chr = chr
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self.start = pos
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self.readlen = len(readBases)
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self.end = pos + len(refAlign) - 1
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# print 'refAlign', refAlign, len(refAlign)
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# dealing with stand
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self.flags = flags
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self.isForwardStrand = SAMFlagIsSet(flags, SAM_QUERYSTRAND)
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self.isReverseStrand = not SAMFlagIsSet(flags, SAM_QUERYSTRAND)
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self.isPrimary = SAMFlagIsSet(flags, SAM_NOTPRIMARY)
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self.isUnmapped = SAMFlagIsSet(flags, SAM_UNMAPPED)
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self.isPaired = SAMFlagIsSet(flags, SAM_SEQPAIRED)
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self.isMapPaired = SAMFlagIsSet(flags, SAM_MAPPAIRED)
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self.isFirstReadInPair = SAMFlagIsSet(flags, SAM_ISFIRSTREAD)
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self.isSecondReadInPair = SAMFlagIsSet(flags, SAM_ISSECONDREAD)
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#self.isMapPaired = SAMFlagIsSet(flags, SAM_MATEUNMAPPED)
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#self.isMapPaired = SAMFlagIsSet(flags, SAM_MATESTRAND)
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# everything will be reverse complemented already
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self.refAlign = refAlign #
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self.readAlign = readAlign # all should be forward strand
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def __str__(self):
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return '<MappedRead %s:%d-%d>' % (self.chr, self.start, self.end)
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__repr__ = __str__
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