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Description: work around blasr 5's strict fasta/fastq header requirement
blasr 5 can only produce sam/bam output if the fasta/fastq header is
"PacBio compatible", or in the format <string>/<number>/<number>_<number>. See
https://github.com/PacificBiosciences/blasr/issues/312#issuecomment-269055488
If blasr's input requirements for fasta and fastq files can be relaxed,
this patch can be dropped. Alternatively, pbsuite could be revised to
not store results in the fastq headers, but that is a more intrusive change.
Author: Afif Elghraoui <afif@debian.org>
Bug: https://sourceforge.net/p/pb-jelly/tickets/5/
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844034
Last-Update: 2016-12-28
--- pbsuite.orig/pbsuite/honey/bampie.py
+++ pbsuite/pbsuite/honey/bampie.py
@@ -125,8 +125,8 @@
maq = int(read.mapq)
loc = mateplace + ":" + str(pos)
- fout.write("@%s_%d%s%d%s\n%s\n+\n%s\n" % (read.qname, \
- maq, tai, strand, loc, seq, qal))
+ fout.write("@%d%s%d%s__%s\n%s\n+\n%s\n" % \
+ (maq, tai, strand, loc, read.qname, seq, qal))
code, length = read.cigar[-1]
if code == 4 and length >= minLength:
@@ -143,8 +143,8 @@
qal = read.qual[-length:][::-1]
maq = int(read.mapq)
loc = mateplace + ":" + str(pos)
- fout.write("@%s_%d%s%d%s\n%s\n+\n%s\n" % (read.qname, \
- maq, tai, strand, loc, seq, qal))
+ fout.write("@%d%s%d%s__%s\n%s\n+\n%s\n" % \
+ (maq, tai, strand, loc, read.qname, seq, qal))
fout.close()
return nreads, ntails, nmultitails
@@ -163,7 +163,7 @@
prolog and eplog will only point to the primary and the primary will point to both
"""
- datGrab = re.compile("^(?P<rn>.*)_(?P<maq>\d+)(?P<log>[pe])(?P<strand>[01])(?P<ref>.*):(?P<pos>\d+)$")
+ datGrab = re.compile("^(?P<maq>\d+)(?P<log>[pe])(?P<strand>[01])(?P<ref>.*):(?P<pos>\d+)__(?P<rn>.*)$")
bout = None
for ibam, tbam in mappedFiles:
sam = pysam.Samfile(tbam, 'r')
--- pbsuite.orig/pbsuite/jelly/m4pie.py
+++ pbsuite/pbsuite/jelly/m4pie.py
@@ -52,8 +52,8 @@
ntails += 1
seq = reads[read.qname][:pTail]
shift = 0
- fout.write(">%s_%d%s%d\n%s\n" % (read.qname, \
- shift, 'p', len, seq))
+ fout.write(">%d%s%d__%s\n%s\n" % \
+ (shift, 'p', len, read.qname, seq))
if eTail >= minLength:
if hasTail:
@@ -61,8 +61,8 @@
ntails += 1
seq = reads[read.qname][-eTail:]
shift = read.qend
- fout.write(">%s_%d%s%d\n%s\n" % (read.qname, \
- shift, 'e', len, seq))
+ fout.write(">%d%s%d__%s\n%s\n" % \
+ (shift, 'e', len, read.qname, seq))
fout.close()
return nreads, ntails, nmultitails
@@ -105,7 +105,7 @@
prolog and eplog will only point to the primary and the primary will point to both
"""
- datGrab = re.compile("^(?P<rn>.*)_(?P<shift>\d+)(?P<log>[pe])(?P<length>\d+)$")
+ datGrab = re.compile("^(?P<shift>\d+)(?P<log>[pe])(?P<length>\d+)__(?P<rn>.*)$")
aligns = M4File(tailMapFn)
mode = 'a' if inplace else 'w'
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