def process_labels(contigs_fpaths, labels, all_labels_from_dirs):
# 1. labels if the provided by -l options
if labels:
# process duplicates, empties
for i, label in enumerate(labels):
if not label:
labels[i] = get_label_from_par_dir_and_fname(contigs_fpaths[i])
# 2. labels from parent directories if -L flag was privided
elif all_labels_from_dirs:
labels = get_labels_from_par_dirs(contigs_fpaths)
# 3. otherwise, labels from fnames
else:
# labels from fname
labels = [qutils.rm_extentions_for_fasta_file(os.path.basename(fpath)) for fpath in contigs_fpaths]
for duplicated_label in get_duplicated(labels):
for i, (label, fpath) in enumerate(zip(labels, contigs_fpaths)):
if label == duplicated_label:
labels[i] = get_label_from_par_dir_and_fname(contigs_fpaths[i])
# fixing remaining duplicates by adding index
for duplicated_label in get_duplicated(labels):
j = 0
for i, (label, fpath) in enumerate(zip(labels, contigs_fpaths)):
if label == duplicated_label:
if j == 0:
labels[i] = label
else:
labels[i] = label + ' ' + str(j)
j += 1
return labels
def process_labels(contigs_fpaths, labels, all_labels_from_dirs):
# 1. labels if the provided by -l options
if labels:
# process duplicates, empties
for i, label in enumerate(labels):
if not label:
labels[i] = get_label_from_par_dir_and_fname(contigs_fpaths[i])
# 2. labels from parent directories if -L flag was privided
elif all_labels_from_dirs:
labels = get_labels_from_par_dirs(contigs_fpaths)
# 3. otherwise, labels from fnames
else:
# labels from fname
labels = [qutils.rm_extentions_for_fasta_file(os.path.basename(fpath)) for fpath in contigs_fpaths]
for duplicated_label in get_duplicated(labels):
for i, (label, fpath) in enumerate(zip(labels, contigs_fpaths)):
if label == duplicated_label:
labels[i] = get_label_from_par_dir_and_fname(contigs_fpaths[i])
# fixing remaining duplicates by adding index
for duplicated_label in get_duplicated(labels):
j = 0
for i, (label, fpath) in enumerate(zip(labels, contigs_fpaths)):
if label == duplicated_label:
if j == 0:
labels[i] = label
else:
labels[i] = label + ' ' + str(j)
j += 1
return labels
def get_label_from_par_dir_and_fname(contigs_fpath):
abspath = os.path.abspath(contigs_fpath)
name = qutils.rm_extentions_for_fasta_file(os.path.basename(contigs_fpath))
label = os.path.basename(os.path.dirname(abspath)) + '_' + name
return label
def get_label_from_par_dir_and_fname(contigs_fpath):
abspath = os.path.abspath(contigs_fpath)
name = qutils.rm_extentions_for_fasta_file(os.path.basename(contigs_fpath))
label = os.path.basename(os.path.dirname(abspath)) + '_' + name
return label
