def parse_and_link(file, symlink_dir, metadata_dict):
"""
Parse metadata out of input filename and construct symlink.
Takes a fastq filename, destination directory, and a metadata dict, which should be of type defaultdict(dict).
Parse the filename to get information on the sample name, run, read #, etc.
Medadata is added to the provided metadata_dict.
Some metadata is used to build symlinks, to guarantee filename uniqueness and a regular naming structure.\
Currently parsing by assuming AGRF naming structure and paired-end reads
Currently will ONLY handle gzipped files, to avoid multiple links to the same data.
"""
match_old = re.match(
r".*?/([^_/]+)_([a-zA-Z0-9-.]+)_s_([0-9]+)_(1|2)_sequence.txt.gz",
file)
match_new = re.match(
r".*?/([a-zA-Z0-9-.]+)_([^_/]+)_[CAGTN]+_L([0-9]+)_R(1|2).fastq.gz",
file)
if match_old:
run_id = match_old.group(1)
sample = match_old.group(2)
lane = int(match_old.group(3))
pair = match_old.group(4)
encoding = 'I'
elif match_new:
run_id = match_new.group(2)
sample = match_new.group(1)
lane = int(match_new.group(3))
pair = match_new.group(4)
encoding = 'S'
else:
print "Unable to parse name of fastq file %s ." % file
sys.exit(1)
newfile = os.path.join(
symlink_dir, "%s_%s_L%d_%s.fastq.gz" % (sample, run_id, lane, pair))
metadata_dict[os.path.basename(newfile)]['sample'] = sample
metadata_dict[os.path.basename(newfile)]['run_id'] = run_id
metadata_dict[os.path.basename(newfile)]['lane'] = lane
metadata_dict[os.path.basename(newfile)]['pair'] = pair
metadata_dict[os.path.basename(newfile)]['encoding'] = encoding
relative_sourcefile = os.path.relpath(file, symlink_dir)
mkLink(relative_sourcefile, newfile)
return newfile
def parse_and_link(file, symlink_dir, metadata_dict):
"""
Parse metadata out of input filename and construct symlink.
Takes a fastq filename, destination directory, and a metadata dict, which should be of type defaultdict(dict).
Parse the filename to get information on the sample name, run, read #, etc.
Medadata is added to the provided metadata_dict.
Some metadata is used to build symlinks, to guarantee filename uniqueness and a regular naming structure.\
Currently parsing by assuming AGRF naming structure and paired-end reads
Currently will ONLY handle gzipped files, to avoid multiple links to the same data.
"""
match_old = re.match(r".*?/([^_/]+)_([a-zA-Z0-9-.]+)_s_([0-9]+)_(1|2)_sequence.txt.gz",file)
match_new = re.match(r".*?/([a-zA-Z0-9-.]+)_([^_/]+)_[CAGTN]+_L([0-9]+)_R(1|2).fastq.gz",file)
if match_old:
run_id = match_old.group(1)
sample = match_old.group(2)
lane = int(match_old.group(3))
pair = match_old.group(4)
encoding = 'I'
elif match_new:
run_id = match_new.group(2)
sample = match_new.group(1)
lane = int(match_new.group(3))
pair = match_new.group(4)
encoding = 'S'
else:
print "Unable to parse name of fastq file %s ." % file
sys.exit(1)
newfile = os.path.join(symlink_dir, "%s_%s_L%d_%s.fastq.gz" %
(sample, run_id, lane, pair))
metadata_dict[os.path.basename(newfile)]['sample'] = sample
metadata_dict[os.path.basename(newfile)]['run_id'] = run_id
metadata_dict[os.path.basename(newfile)]['lane'] = lane
metadata_dict[os.path.basename(newfile)]['pair'] = pair
metadata_dict[os.path.basename(newfile)]['encoding'] = encoding
relative_sourcefile = os.path.relpath(file, symlink_dir)
mkLink(relative_sourcefile, newfile)
return newfile
snpeff_dir = os.path.join(output_dir, "snpeff")
mkDir(snpeff_dir)
# directory for final summary tables
results_dir = os.path.join(output_dir, "results")
mkDir(results_dir)
# Pipeline declarations
# Making references
#Reference file setup
RefName=ref_files['fasta_reference'].split("/")[-1]
print RefName
fasta_reference=os.path.join(ref_dir, RefName)
mkLink(ref_files['fasta_reference'], fasta_reference)
RefDict=ref_files['fasta_dict'].split("/")[-1]
print RefDict
# print ref_files['fasta_dict']
fasta_dict=os.path.join(ref_dir, RefDict)
# print fasta_dict
mkLink(ref_files['fasta_dict'], fasta_dict)
# sys.exit(0)
# RefDict_temp=ref_files['fasta_reference'].split("/")[-1]
# RefDict=RefDict_temp.split(".")[0]+".dict"
# ref_dir=ref_dir+"/"
# print RefDict
# print ref_dir
