original_fastq_files = []
for fastq_dir in working_files['fastq_dirs']:
#original_fastq_files += glob(os.path.join(fastq_dir, '*.fastq.gz'))
#original_fastq_files += glob(os.path.join(fastq_dir, '*_sequence.txt.gz'))
original_fastq_files += glob(os.path.join(fastq_dir, '*.fastq.gz'))
if len(original_fastq_files)==0:
print "No input files found. Do the filenames follow the naming convention?"
print "Directories searched:"
print "\n".join(working_files['fastq_dirs'])
sys.exit(1)
# Parse metadata out of input file names and construct symlinks
# Metadata is put into a dict (for the rest of ruffus) and some of it also into symlinks (for filename uniqueness)
# currently parsing by assuming AGRF naming structure and paired-end reads
mkDir(working_files['fastq_symlink_dir'])
all_fastq_files = []
for file in original_fastq_files:
name = os.path.basename(file)
#print name
#pu,remaining = name.split("_")
#barcode = pu.split(".")[0]
#lane = pu.split(".")[1]
#id = pu[:5] + "." + lane
#sm = os.path.basename(os.path.dirname(file))
#sm = string.replace(sm,"_","-")
#print "sm = " + sm + "\npu = " + pu + "\nlane = " + lane + "\nid = " + id + "\nbarcode = " + barcode
##file = sm + "_" + name
#file2 = sm + "_" + barcode + ".L" + lane + "_" + remaining
sys.exit(1)
trimmed_fastq_files = []
for fastq_dirs in working_files['fastq_dirs']:
trimmed_fastq_files += glob(os.path.join(fastq_dir, '*trimmed-paired.fastq.gz'))
if len(trimmed_fastq_files)==0:
print "No trimmed fastq files found. Do the filenames follow the naming convention?"
print "Directories searched:"
print "\n".join(working_files['fastq_dirs'])
sys.exit(1)
# Parse metadata out of input file names and construct symlinks
# Metadata is put into a dict (for the rest of ruffus) and some of it also into symlinks (for filename uniqueness)
# currently parsing by assuming AGRF naming structure and paired-end reads
mkDir(working_files['fastq_symlink_dir'])
all_fastq_files = []
for file in original_fastq_files:
symlink = parse_and_link(file, working_files['fastq_symlink_dir'], fastq_metadata)
all_fastq_files.append(symlink)
all_trimmed_fastq_files = []
for file in trimmed_fastq_files:
symlink = parse_and_link(file, working_files['fastq_symlink_dir'], fastq_metadata)
all_trimmed_fastq_files.append(symlink)
# Make a list of files we will actually use
if pipeline_options.pipeline['restrict_samples']:
# if pipeline_options.pipeline['allowed_samples']:
# allowed_samples = set(pipeline_options.pipeline['allowed_samples'])
fastq_metadata = defaultdict(dict)
original_fastq_files = []
for fastq_dir in working_files['fastq_dirs']:
original_fastq_files += glob(os.path.join(fastq_dir, '*.fastq.gz'))
if len(original_fastq_files) == 0:
print "No input files found. Do the filenames follow the naming convention?"
print "Directories searched:"
print "\n".join(working_files['fastq_dirs'])
sys.exit(1)
# Parse metadata out of input file names and construct symlinks
# Metadata is put into a dict (for the rest of ruffus) and some of it also into symlinks (for filename uniqueness)
# currently parsing by assuming AGRF naming structure and paired-end reads
mkDir(working_files['fastq_symlink_dir'])
all_fastq_files = []
for file in original_fastq_files:
symlink = parse_and_link(file, working_files['fastq_symlink_dir'],
fastq_metadata)
all_fastq_files.append(symlink)
# Make a list of files we will actually use
if pipeline_options.pipeline['restrict_samples']:
allowed_samples = set(pipeline_options.pipeline['allowed_samples'])
fastq_files = [
file for file in sorted(all_fastq_files)
if (fastq_metadata[os.path.basename(file)]['sample'] in allowed_samples
)
]
else:
