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More consistent formatting #57

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merged 1 commit into from
Nov 27, 2023
Merged

More consistent formatting #57

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51 changes: 26 additions & 25 deletions scripts/chain_invert.py
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Original file line number Diff line number Diff line change
@@ -1,34 +1,35 @@
'''
"""
Switch the source and target reference of a chain file
'''
"""
import argparse
import sys
import re
import sys


def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument(
'-c', '--chain', required=True,
help='Path to the input chain file.'
"-c", "--chain", required=True, help="Path to the input chain file."
)
parser.add_argument(
'-o', '--out', default='',
help='Path to the output verbose chain file. [empty string]'
"-o",
"--out",
default="",
help="Path to the output verbose chain file. [empty string]",
)
args = parser.parse_args()
return args


def invert(in_fn: str, out_fn: str) -> None:
f = open(in_fn, 'r')
fo = open(out_fn, 'w')
f = open(in_fn, "r")
fo = open(out_fn, "w")
for line in f:
if not line:
continue
line = line.rstrip()
fields = re.split(r'[\s\t]+', line)
if fields[0] == 'chain':
fields = re.split(r"[\s\t]+", line)
if fields[0] == "chain":
source = fields[2]
source_len = int(fields[3])
s_start = int(fields[5])
Expand All @@ -39,41 +40,41 @@ def invert(in_fn: str, out_fn: str) -> None:
d_start = int(fields[10])
d_end = int(fields[11])
changed = fields[:2] + fields[7:12] + fields[2:7] + [fields[12]]
if strand == '-':
if strand == "-":
changed[5] = str(dest_len - d_end)
changed[6] = str(dest_len - d_start)
changed[10] = str(source_len - s_end)
changed[11] = str(source_len - s_start)
changed[4] = '+'
changed[9] = '-'
changed_str = ' '.join(changed)
print(f'{changed_str}', file=fo)
changed[4] = "+"
changed[9] = "-"
changed_str = " ".join(changed)
print(f"{changed_str}", file=fo)
chain_list = []
elif len(fields) == 3:
l = int(fields[0])
ds = int(fields[1])
dd = int(fields[2])
changed = [fields[0], fields[2], fields[1]]
changed_str = ' '.join(changed)
if strand == '+':
changed_str = " ".join(changed)
if strand == "+":
chain_list += [fields[0], fields[2], fields[1]]
else:
chain_list += [fields[0], fields[1], fields[2]]
elif len(fields) == 1 and fields[0] != '':
elif len(fields) == 1 and fields[0] != "":
l = int(fields[0])
chain_list.append(fields[0])
if strand == '-':
if strand == "-":
chain_list = chain_list[::-1]
for i in range(int(len(chain_list) / 3)):
p = ' '.join(chain_list[i*3: (i+1)*3])
p = " ".join(chain_list[i * 3 : (i + 1) * 3])
print(p, file=fo)
print(chain_list[-1], file=fo)
print('', file=fo)
print("", file=fo)


if __name__ == '__main__':
if __name__ == "__main__":
args = parse_args()

print('Input chain:', args.chain, file=sys.stderr)
print('Output chain (verbose):', args.out, file=sys.stderr)
print("Input chain:", args.chain, file=sys.stderr)
print("Output chain (verbose):", args.out, file=sys.stderr)
invert(in_fn=args.chain, out_fn=args.out)
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