Add sequences from a Fasta file to a GFA file.

add_sequences_to_canu_gfa.py

#!/usr/bin/env python3
"""
Add sequences from a Fasta file to a GFA file.
"""

import argparse
import sys
import gfapy

op = argparse.ArgumentParser(description=__doc__)
op.add_argument("inputgfa")
op.add_argument("inputfasta")
op.add_argument("outputgfa")
op.add_argument("-v", "--verbose", action="store_true", help="verbose output")
op.add_argument("-V", '--version', action='version', version='%(prog)s 0.1')
opts = op.parse_args()

# note: to apply to Canu 1.6 (did not check for newer versions)
# the following fix to the GFA VN tag was necessary:
# sed -i s'/VN:Z:bogart\/edges/VN:Z:1.0/' canu.contigs.gfa

g = gfapy.Gfa.from_file(opts.inputgfa)

segment = None
slines = []
with open(opts.inputfasta) as f:
  for line in f:
    line = line.strip()
    if line.startswith(">"):
      if segment:
        segment.sequence = "".join(slines)
      sname = line[1:].split(" ")[0]
      if opts.verbose:
        sys.stderr.write("Processing segment {}...\n".format(sname))
      segment = g.segment(sname)
      if not segment:
        sys.stderr.write("ERROR: Segment with ID {}".format(sname)+
                         "found in Fasta but not in GFA file\n")
        exit(1)
      slines = []
    else:
      slines.append(line)
if segment:
  segment.sequence = "".join(slines)

g.to_file(opts.outputgfa)