def gmap_setup(gsnap_dir, out_dir, ref_fasta):
ref_base = op.splitext(ref_fasta)[0]
ref_dir = op.dirname(ref_fasta)
ref_name = op.basename(ref_base)
make_path = "%(out_dir)s/Makefile.%(ref_name)s" % locals()
gsnap_setup = op.join(gsnap_dir, "util", "gmap_setup")
# have to cd to the out_dir because gsnap writes to cwd.
cmd = "\n cd %(ref_dir)s && \n"
cmd += gsnap_setup
cmd += " -D %(ref_dir)s -o %(make_path)s -d %(ref_base)s %(ref_fasta)s > %(out_dir)s/gmap_setup.log && "
cmd += "\n make -f %(make_path)s coords > gmap_coords.log && "
cmd += "\n make -f %(make_path)s gmapdb > gmap_gmapdb.log &&"
cmd += "\n %(gsnap_dir)s/src/cmetindex -d %(ref_name)s -D %(ref_dir)s > gmap_cmetindex.log 2> gmap_cmetindex.error.log"
cmd %= locals()
print >>sys.stderr, "[ command ] $", cmd
cmd_last = op.join(out_dir, "ran_gsnap_setup.sh")
if not op.exists(cmd_last) or not is_up_to_date_b(ref_fasta, cmd_last) or not is_same_cmd(cmd, cmd_last):
fh = open(cmd_last, "w")
print >>fh, cmd
fh.close()
elif is_up_to_date_b(ref_fasta, cmd_last) and not is_same_cmd(cmd, cmd_last):
fh = open(cmd_last, "w")
print >>fh, cmd
fh.close()
if not op.exists(op.join(out_dir, make_path)) or not (is_up_to_date_b(op.join(out_dir, make_path), cmd_last)):
# TODO ^ add check for cmetindex files as well.
p = Popen(cmd.replace('\n', ' '), shell=True)
print >>sys.stderr, "^ executing gmap/gsnap setup^"
if p.wait() != 0:
pclean = Popen("cd %(out_dir)s; make -f %(make_path)s clean" % locals())
pclean.wait()
pass
else:
print >>sys.stderr, "^ NOT executing gmap/gsnap setup. everything is up to date.^"
return ref_base
def run_gsnap(gsnap_dir, gsnap_args, out_dir, ref_fasta, reads_paths, cpu_count):
#/opt/src/gmap/gmap-2010-03-09/src/gsnap --npaths 1 --quiet-if-excessive -A sam --nofails --nthreads 4 -D ./ -d hg19e_gmap --cmet bs_reads.fasta > bs.align.sam
ref_base = op.splitext(ref_fasta)[0]
ref_name = op.basename(ref_base)
ref_dir = op.dirname(ref_fasta)
reads_paths = [op.abspath(r) for r in reads_paths]
log = op.join(out_dir, "gsnap_run.log")
reads_paths_str = " ".join(reads_paths)
out_sam = op.abspath(op.join(out_dir, "methylcoded.gsnap.sam"))
cmd = "%(gsnap_dir)s/src/gsnap --quiet-if-excessive -A sam"
cmd += " --nofails --nthreads %(cpu_count)i -D %(ref_dir)s %(gsnap_args)s"
cmd += " -d %(ref_name)s --cmet %(reads_paths_str)s > %(out_sam)s 2> %(log)s"
cmd %= locals()
cmd_path = op.join(out_dir, "ran_gsnap.sh")
new_cmd = False
if not is_same_cmd(cmd, cmd_path):
fh = open(cmd_path, "w")
print >>fh, cmd
fh.close()
new_cmd = True
print >>sys.stderr, "\n" + cmd
if not new_cmd and all(is_up_to_date_b(r, out_sam) for r in reads_paths) \
and all(is_up_to_date_b(r, cmd_path) for r in reads_paths):
print >>sys.stderr, "^ NOT executing gsnap. everything is up to date.^"
else:
fh = open(cmd_path, "w")
print >>fh, cmd
fh.close()
print >>sys.stderr, "^ executing gsnap. ^"
p = Popen(cmd.replace('\n', ' '), shell=True)
if p.wait() != 0:
os.unlink(out_sam)
print >>sys.stderr, "ERROR:\n", open(log).read()
sys.exit(1)
return out_sam
def main(out_dir, ref_fasta, reads, gsnap_path, gsnap_args):
fa_reads = out_dir + "/" + op.basename(reads[0]).rstrip("_1") + ".fasta"
if all(is_fastq(r) for r in reads):
print >>sys.stderr, "using existing reads files"
gsnap_reads = reads
elif all(is_up_to_date_b(r, fa_reads) for r in reads):
# fasta reads. up to date.
gsnap_reads = reads
else:
# its a pair of fasta files. put into gsnap format.
if len(reads) > 1:
out_fa = open(fa_reads, "w")
fastx_to_gsnap_fasta(reads, out_fa)
out_fa.close()
gsnap_reads = (fa_reads,)
else:
# if it's a single fasta, don't need to write any new files.
gsnap_reads = (reads[0],)
gmap_setup(gsnap_path, out_dir, ref_fasta)
gsnap_sam = run_gsnap(gsnap_path, gsnap_args, out_dir, ref_fasta, gsnap_reads, cpu_count=CPU_COUNT)
paired_end = len(reads) > 1
parse_gsnap_sam(gsnap_sam, ref_fasta, out_dir, paired_end)
