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#!/usr/bin/python3
from operator import itemgetter
import os
from os import path
import sys
from Bio import SeqIO
import common
import subprocess
def print_usage():
print("Usage: split_bins.py <contigs> <binning info> <output directory> [-g]")
contigs = sys.argv[1]
sample, _ = path.splitext(path.basename(contigs))
out_dir = sys.argv[3]
glue = False
if len(sys.argv) > 4 and sys.argv[4]:
glue = True
binning = common.load_annotation(sys.argv[2], False)
if glue:
glue_binning = dict()
for split, bins in binning.items():
contig_bins = glue_binning.setdefault(common.extract_id(split), {})
for bin in bins:
contig_bins.setdefault(bin, 0)
contig_bins[bin] += 1
if path.isdir(out_dir):
subprocess.call("rm -f {}/*.fasta".format(out_dir), shell=True)
else:
os.mkdir(out_dir)
for seq in SeqIO.parse(contigs, "fasta"):
if glue:
bins = []
bin_freq = glue_binning.get(common.extract_id(seq.id))
if bin_freq:
bins = [max(bin_freq.items(), key=itemgetter(1))[0]]
else:
bins = binning.get(seq.id, [])
for cag in bins:
filename = cag + ".fasta"
with open(path.join(out_dir, filename), "a") as output:
SeqIO.write(seq, output, "fasta")
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