def _rnaseq_metrics(self, align_bam, gtf_file, rrna_file):
metrics = self._check_metrics_file(align_bam, "rnaseq_metrics")
if not file_exists(metrics):
with file_transaction(metrics) as tx_metrics:
picard_rnaseq_metrics(self._picard, align_bam, gtf_file, rrna_file, tx_metrics)
return metrics
def _rnaseq_metrics(self, align_bam, gtf_file, rrna_file):
metrics = self._check_metrics_file(align_bam, "rnaseq_metrics")
if not file_exists(metrics):
with file_transaction(metrics) as tx_metrics:
picard_rnaseq_metrics(self._picard, align_bam, gtf_file,
rrna_file, tx_metrics)
return metrics
def __call__(self, in_file):
out_file = self.out_file(in_file)
if file_exists(out_file):
return out_file
out_file = picardrun.picard_rnaseq_metrics(self.picard, in_file,
self.ref, self.ribo,
out_file)
return out_file
def main(config_file):
if config_file:
with open(config_file) as in_handle:
config = yaml.load(in_handle)
dirs = config["in_dir"]
conditions = config["conditions"]
glob_string = config["glob_string"]
files = list(flatten([glob.glob(os.path.join(x, glob_string)) for x in dirs]))
out_dir = config["dir"]["results"]
safe_makedir(out_dir)
curr_files = []
for condition in conditions:
condition_files = [x for x in files if condition in x]
out_file = os.path.join(out_dir, condition + "_v2_v3.bam")
print "Combining %s into %s." % (condition_files, out_file)
sh.samtools.merge(list(flatten([out_file, condition_files])))
# bsub_call = list(flatten(["-q", "hsph", "-o", "out" + condition, "-e", "err" + condition, "samtools", "merge", out_file, condition_files]))
#sh.bsub(bsub_call)
sorted_prefix = remove_suffix(out_file) + ".sorted"
sorted_file = sorted_prefix + ".bam"
sh.samtools.sort(out_file, sorted_prefix)
sh.samtools.index(sorted_file)
mapped_file = append_stem(sorted_file, "mapped")
sh.samtools.view(sorted_file, F=4, b=True, o=mapped_file)
sh.samtools.index(mapped_file)
# find the reads that don't intersect with the rrna
in_file = mapped_file
out_file = os.path.join(out_dir, condition + "_noribo" + "_v2_v3.bam")
ribo = config["ribo"]
print "Filtering %s for rRNA in %s into %s." % (in_file, ribo, out_file)
sh.bedtools.intersect("-abam", in_file, "-v", "-b", ribo, _out=out_file)
filtered_file = out_file
print "Calculating RNASeq metrics on %s." % (out_file)
in_file = out_file
ref = blastn.prepare_ref_file(config["stage"]["new_coverage"]["ref"],
config)
ribo = config["stage"]["new_coverage"]["ribo"]
picard = BroadRunner(config["program"]["picard"])
out_dir = os.path.join(config["dir"]["results"], "new_coverage")
safe_makedir(out_dir)
out_file = replace_suffix(os.path.basename(in_file), "metrics")
out_file = os.path.join(out_dir, out_file)
metrics_file = picardrun.picard_rnaseq_metrics(picard, in_file, ref,
ribo, out_file)
jelly_dir = os.path.join(config["dir"]["results"], "jellyfish")
safe_makedir(jelly_dir)
# convert the filtered file to fastq for jellyfish counting
fastq_file = os.path.join(jelly_dir,
os.path.basename(replace_suffix(filtered_file,
"fastq")))
sh.bam2fastx(filtered_file, fastq=True, _out=fastq_file)
for mer in config["stage"]["jellyfish"]["mer_lengths"]:
base, _ = os.path.splitext(os.path.basename(fastq_file))
out_prefix = base + "_%dmer" % (mer)
out_file = os.path.join(jelly_dir, out_prefix)
if not file_exists(out_file):
sh.jellyfish.count(fastq_file,
config["stage"]["jellyfish"]["options"],
m=mer, o=out_file)
