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rename_fasta.py
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rename_fasta.py
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#!/usr/bin/env python
import argparse
import csv
import sys
import re
import os
def _parse_name(seq):
"""Parse a fasta header and remove > and new lines.
If [metadata is True] then parse the prophage metadata from
the header.
Current metadata: phage-circular and prophage-<start>:<end>
"""
if not seq:
return seq
clean = seq.replace(">", "").replace("\n", "")
phage_data = clean.split("|")
seq_name = phage_data[0]
phage_circular = "phage-circular" if "phage-circular" in seq else ""
metadata = []
if phage_circular:
metadata.append(phage_circular)
if len(phage_data) == 1:
return seq_name.strip(), metadata
for phage_metadata in phage_data[1:]:
match = re.search(r"prophage-\d+:\d+", phage_metadata)
if match:
metadata.append(match[0])
return seq_name.strip(), metadata
def rename(args):
"""Rename a multi-fasta fasta entries with <name>.<counter> and store the
mapping between new and old files in tsv (args.map)
"""
print("Renaming " + args.input)
with open(args.input, "r") as fasta_in:
with open(args.output, "w") as fasta_out, open(args.map, "w") as map_tsv:
count = 1
tsv_map = csv.writer(map_tsv, delimiter="\t")
tsv_map.writerow(["original", "renamed"])
for line in fasta_in:
if line.startswith(">"):
fasta_out.write(f">{args.prefix}{count}\n")
name, _ = _parse_name(line)
tsv_map.writerow([name, f"{args.prefix}{count}"])
count += 1
else:
fasta_out.write(line)
print(f"Wrote {count} sequences to {args.output}.")
def restore(args):
"""Restore a multi-fasta fasta using the mapping file.
VirSorter metadata is preserved.
"""
if not args.input:
print("File not provided. Skipping")
return
if not os.path.exists(args.input):
print("File " + args.input + " doesn't exist. Skipping")
return
print("Restoring " + args.input)
mapping = {}
with open(args.map, "r") as map_tsv:
for m in csv.DictReader(map_tsv, delimiter="\t"):
mapping[m["renamed"]] = m["original"]
with open(args.input, "r") as fasta_in:
with open(args.output, "w") as fasta_out:
for line in fasta_in:
if line.startswith(">"):
mod, metadata = _parse_name(line)
# prophage metada removal
original = mapping.get(mod, None)
if not original:
print(
f"Missing sequence in mapping for {mod}. Header: {line}",
file=sys.stderr,
)
original = mod
if len(metadata):
fasta_out.write(f">{original}|{'|'.join(metadata)}\n")
else:
fasta_out.write(f">{original}\n")
else:
fasta_out.write(line)
def main():
"""Multi fasta rename and restore."""
parser = argparse.ArgumentParser(
description="Rename multi fastas and restore the names tools."
)
parser.add_argument(
"-i", "--input", help="indicate input FASTA file", required=False
)
parser.add_argument(
"-m",
"--map",
help="Map current names with the renames",
type=str,
default="fasta_map.tsv",
)
parser.add_argument(
"-o", "--output", help="indicate output FASTA file", required=True
)
subparser = parser.add_subparsers()
rename_parser = subparser.add_parser("rename")
rename_parser.add_argument(
"--prefix",
help="string pre fasta count, i.e. default is seq such as seq1, seq2...",
type=str,
default="seq",
)
rename_parser.set_defaults(func=rename)
restore_parser = subparser.add_parser("restore")
restore_parser.set_defaults(func=restore)
args = parser.parse_args()
args.func(args)
if __name__ == "__main__":
main()