def main():
parser = argparse.ArgumentParser( description='Updates 9th-column key/value pairs in GFF file using a batch-update file')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='A GFF3 file' )
parser.add_argument('-u', '--update_file', type=str, required=True, help='A two-column file (FeatureID, value)' )
parser.add_argument('-a', '--attribute', type=str, required=True, help='The attribute value to update' )
parser.add_argument('-o', '--output_file', type=str, required=True, help='Path to an output file to be created' )
parser.add_argument('-k', '--key', type=str, required=False, default='ID', help='Which key in the 9th column helps identify the row to be updated?' )
parser.add_argument('-t', '--type', type=str, required=False, help='Filter rows updated based on the 3rd (type) column' )
args = parser.parse_args()
# protect the user
if args.input_file == args.output_file:
raise Exception("ERROR: Don't set --input_file and --output_file to be the same thing. Bad things will happen. Bad Things.")
outfh = open(args.output_file, 'wt')
# first read in the values to be updated
changes = dict()
for line in open(args.update_file):
cols = line.rstrip().split("\t")
if len(cols) != 2:
print("WARNING: Skipping the following update line because two columns were expected:\n{0}".format(line))
continue
changes[cols[0]] = cols[1]
for line in open(args.input_file):
cols = line.rstrip().split("\t")
if len(cols) == 9:
if args.type is None or args.type == cols[2]:
atts = gff.column_9_dict(cols[8])
if args.key in atts and atts[args.key] in changes:
atts[args.attribute] = changes[atts[args.key]]
cols[8] = gff.build_column_9_from_dict(atts)
outfh.write("\t".join(cols) + "\n")
def main():
parser = argparse.ArgumentParser( description='Put a description of your script here')
## output file to be written
parser.add_argument('-i', '--input_file', type=str, required=True, help='Path to an input file to be read' )
parser.add_argument('-o', '--output_file', type=str, required=True, help='Path to an output file to be created' )
parser.add_argument('-t', '--feature_type', type=str, required=False, help='Only update features of a given type (gff column 3)' )
parser.add_argument('-k', '--key', type=str, required=True, help='Which column 9 key/attribute to update values for?' )
parser.add_argument('-a', '--appended_text', type=str, required=True, help='Text to append' )
args = parser.parse_args()
# protect the user
if args.input_file == args.output_file:
raise Exception("ERROR: Don't set --input_file and --output_file to be the same thing. Bad things will happen. Bad Things.")
ofh = open(args.output_file, 'wt')
replacement_count = 0
for line in open(args.input_file):
line = line.rstrip()
cols = line.split("\t")
if len(cols) == 9:
if args.feature_type is None or args.feature_type == cols[2]:
col9 = gff.column_9_dict(cols[8])
if args.key in col9:
col9[args.key] = "{0}{1}".format(col9[args.key], args.appended_text)
cols[8] = gff.build_column_9_from_dict(col9)
replacement_count += 1
ofh.write("{0}\t{1}\n".format("\t".join(cols[0:8]), cols[8]))
else:
ofh.write("{0}\n".format(line))
else:
ofh.write("{0}\n".format(line))
print("INFO: Made {0} replacements in the file".format(replacement_count))
def main():
parser = argparse.ArgumentParser(
description=
'Updates 9th-column key/value pairs in GFF file using a batch-update file'
)
## output file to be written
parser.add_argument('-i',
'--input_file',
type=str,
required=True,
help='A GFF3 file')
parser.add_argument('-u',
'--update_file',
type=str,
required=True,
help='A two-column file (FeatureID, value)')
parser.add_argument('-a',
'--attribute',
type=str,
required=True,
help='The attribute value to update')
parser.add_argument('-o',
'--output_file',
type=str,
required=True,
help='Path to an output file to be created')
parser.add_argument(
'-k',
'--key',
type=str,
required=False,
default='ID',
help='Which key in the 9th column helps identify the row to be updated?'
)
parser.add_argument(
'-t',
'--type',
type=str,
required=False,
help='Filter rows updated based on the 3rd (type) column')
args = parser.parse_args()
# protect the user
if args.input_file == args.output_file:
raise Exception(
"ERROR: Don't set --input_file and --output_file to be the same thing. Bad things will happen. Bad Things."
)
outfh = open(args.output_file, 'wt')
# first read in the values to be updated
changes = dict()
for line in open(args.update_file):
cols = line.rstrip().split("\t")
if len(cols) != 2:
print(
"WARNING: Skipping the following update line because two columns were expected:\n{0}"
.format(line))
continue
changes[cols[0]] = cols[1]
for line in open(args.input_file):
cols = line.rstrip().split("\t")
if len(cols) == 9:
if args.type is None or args.type == cols[2]:
atts = gff.column_9_dict(cols[8])
if args.key in atts and atts[args.key] in changes:
atts[args.attribute] = changes[atts[args.key]]
cols[8] = gff.build_column_9_from_dict(atts)
outfh.write("\t".join(cols) + "\n")
def main():
parser = argparse.ArgumentParser( description='Updates 9th-column key/value pairs in GFF file using a batch-update file')
parser.add_argument('-i', '--input_file', type=str, required=True, help='A GFF3 file' )
parser.add_argument('-o', '--output_file', type=str, required=True, help='Path to an output file to be created' )
parser.add_argument('-t', '--type', type=str, required=False, help='Filter rows updated based on the 3rd (type) column' )
args = parser.parse_args()
outfh = open(args.output_file, 'wt')
chr_lst = {}
cdsexon_count = {}
for line in open(args.input_file):
cols = line.rstrip().split("\t")
if len(cols) == 9:
if args.type is None or args.type == cols[2]:
#init. incrementeur for a new chromosome
chr = cols[0]
if not chr in chr_lst:
chr_lst[chr] = None
incr = 0
#first feature must be "gene", init. first gene by 000010
feature = cols[2]
if feature == 'gene':
incr += 10
#split col 9
atts = gff.column_9_dict(cols[8])
if 'Name' in atts:
atts.pop('Name')
#change values
if feature == 'gene':
old_id = atts['ID']
gene_id = chr + '_' + format(incr, '06d')
atts['ID'] = gene_id
new_id = gene_id
print(old_id, new_id)
# assume no isoforms
elif feature in ['mRNA', 'tRNA']:
mRNA_id = gene_id + '.1'
atts['ID'] = mRNA_id
atts['Parent'] = gene_id
cdsexon_count[mRNA_id] = 1
elif feature in ['CDS','exon']:
cdsexon_id = mRNA_id + '.' + str(cdsexon_count[mRNA_id])
atts['Parent'] = mRNA_id
atts['ID'] = cdsexon_id
if feature == 'CDS':
atts['ID'] = 'CDS:' + cdsexon_id
# allow exon / cds switch position
if not cdsexon_id in cdsexon_count:
cdsexon_count[cdsexon_id] = None
else:
cdsexon_count[mRNA_id] += 1
cols[8] = gff.build_column_9_from_dict(atts)
outfh.write("\t".join(cols) + "\n")
