def index(self):
""" Sort out indexing """
# Symlink reference:
new_ref = os.path.join(self.rts.base, os.path.basename(self.ref))
os.symlink(self.ref, new_ref)
# Register reference:
self.rts.register(new_ref)
old_ref = self.ref
self.ref = new_ref
ind_suf = [
".1.bt2", ".2.bt2", ".3.bt2", ".4.bt2", ".rev.1.bt2", ".rev.2.bt2"
]
if self.has_index:
# Symlink index:
for sx in ind_suf:
os.symlink(old_ref + sx, new_ref + sx)
else:
# Run indexing:
cmd = u.Cmd(self.log,
prog="bowtie2-build",
opts=self.index_opts,
post_args=[self.ref, self.ref],
sink_err=self.sink_err)
cmd.comm()
# Register index files:
for suf in ind_suf:
self.rts.register(self.ref + suf)
pass
def sort(self, inp=None, outp=None, opts={}):
""" Sort BAM file """
out_name = str()
if type(outp) == file:
self.log.fatal("Sort does not work on pipe output")
elif type(outp) == str:
out_name = self.rts.tempfile(outp)
elif outp == None and type(inp) == str:
base = os.path.basename(inp).split(".bam")[0] + "_sort"
out_name = base
else:
self.log.fatal("No output available!")
cmd = u.Cmd(log=self.log,
prog=self.prog,
pre_args=["sort"],
opts=opts,
post_args=["-", out_name],
inp=inp,
outp=None,
path=self.path,
sink_err=self.sink_err,
cwd=self.rts.base)
cmd.comm()
out_name += ".bam"
self.rts.register(out_name)
return os.path.join(self.rts.base, out_name)
def mk_index(cls, ref, log, index_opts={}):
""" Make a standalone index """
cmd = u.Cmd(log,
prog="bowtie2-build",
opts=index_opts,
post_args=[ref, ref],
sink_err=True)
cmd.comm()
def flagstat(self, bam):
""" Get BAM statistics """
if not os.path.exists(bam):
self.log.fatal("BAM file does not exists.")
cmd = u.Cmd(log=self.log,
prog=self.prog,
pre_args=["flagstat"],
opts={},
post_args=[bam],
path=self.path,
sink_err=self.sink_err)
data = cmd.comm()
stats = {}
feat_map = {
re.compile("(\d+)\s\+\s\d+\sin total \(QC-passed reads \+ QC-failed reads\)"):
tuple(["qc_fail"]),
re.compile("(\d+)\s\+\s\d+\sduplicates"):
tuple(["duplicates"]),
re.compile("(\d+)\s\+\s\d+\smapped\s\((\S+)%\s\+\s\S+%\)"):
tuple(["nr_mapped", "percent_mapped"]),
re.compile("(\d+)\s\+\s\d+\spaired in sequencing"):
tuple(["seq_paired"]),
re.compile("(\d+)\s\+\s\d+\sproperly paired \((\S+)%\s\+\s\S+%\)"):
tuple(["nr_proper_pairs", "percent_proper_pairs"]),
re.compile("(\d+)\s\+\s\d+\swith itself and mate mapped"):
tuple(["nr_proper_with_mate"]),
re.compile("(\d+)\s\+\s\d+\ssingletons\s\((\S+)%\s\+\s\S+%\)"):
tuple(["singletons", "percent_singletons"]),
re.compile("(\d+)\s\+\s\d+\sread1"):
tuple(["nr_read1"]),
re.compile("(\d+)\s\+\s\d+\sread2"):
tuple(["nr_read2"]),
re.compile("(\d+)\s\+\s\d+\swith mate mapped to a different chr \(mapQ.+\)\Z"):
tuple(["chr_mismatch_q5"]),
re.compile("(\d+)\s\+\s\d+\swith mate mapped to a different chr\Z"):
tuple(["chr_mismatch"])
}
for line in data.split("\n"):
for (pattern, names) in feat_map.iteritems():
m = pattern.match(line)
if m != None:
groups = m.groups()
if len(groups) != len(names):
self.log.fatal("Name/group mismatch: %s %s" %
(groups, names))
for i in xrange(len(groups)):
stats[names[i]] = float(groups[i])
return stats
def index(self, bam):
""" Index BAM file """
cmd = u.Cmd(log=self.log,
prog=self.prog,
pre_args=["index"],
opts={},
post_args=[bam],
inp=None,
outp=None,
path=self.path,
sink_err=self.sink_err,
cwd=self.rts.base)
cmd.comm()
self.rts.register(bam + ".sai")
def flagstat_text(self, bam):
""" Get BAM statistics """
if not os.path.exists(bam):
self.log.fatal("BAM file does not exists.")
cmd = u.Cmd(log=self.log,
prog=self.prog,
pre_args=["flagstat"],
opts={},
post_args=[bam],
path=self.path,
sink_err=self.sink_err)
data = cmd.comm()
return data
def view(self, inp=None, outp=None, opts={"-S": None, "-b": None}):
""" View SAM/BAM files """
if outp != None:
outp = os.path.join(self.rts.base, outp)
cmd = u.Cmd(log=self.log,
prog=self.prog,
pre_args=["view"],
opts=opts,
post_args=["-"],
inp=inp,
outp=outp,
path=self.path,
sink_err=self.sink_err)
cmd.comm()
# Register output file.
if type(outp) == str:
self.rts.register(outp)
return cmd.output_fh
def sam(self):
""" Generate sam file """
# Check input:
if len(self.reads) == 0:
self.log.fatal("No fastq files specified")
(path, base) = os.path.split(self.reads[0])
pattern = re.compile(".fq\d")
base = pattern.split(base)[0]
# Generate SAM file:
sam = os.path.join(self.rts.base, base + ".sam")
# Register sam file:
self.rts.register(sam)
# Construct post args:
inp_flags = ["-1", "-2"]
inf = []
for i in xrange(len(self.reads)):
inf.append(inp_flags[i])
inf.append(self.reads[i])
# Add bwt base:
tmp = [self.ref]
tmp.extend(inf)
inf = tmp
# Construct command object:
cmd = u.Cmd(self.log,
prog="bowtie2",
opts=self.aln_opts,
post_args=inf,
outp=sam,
cwd=self.rts.base,
sink_err=self.sink_err)
cmd.comm()
return sam