31 lines
1.2 KiB
Python
31 lines
1.2 KiB
Python
 
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#!/usr/bin/env python3
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import sys
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from collections import defaultdict
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if len(sys.argv) != 5:
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sys.exit(f"python3 {sys.argv[0]} <genome.len> <mcscanx.gff> <tandem.pair> <genelist> > out.mct")
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len_file, gff_file, tandem_file, ids_file = sys.argv[1:]
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lengths = {}
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with open(len_file, encoding='utf-8', errors='replace') as fh:
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for line in fh:
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f = line.split()
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if len(f) >= 2: lengths[f[0]] = float(f[1])
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ids = {}
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with open(ids_file, encoding='utf-8', errors='replace') as fh:
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for line in fh:
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f = line.split()
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if f: ids[f[0]] = 1
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bed = defaultdict(dict)
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with open(gff_file, encoding='utf-8', errors='replace') as fh:
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for line in fh:
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f = line.split()
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if len(f) >= 4 and f[1] in ids: bed[f[0]][int(f[2])] = f
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with open(tandem_file, encoding='utf-8', errors='replace') as fh:
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for line in fh:
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for gene in line.rstrip('\n').split(','):
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if gene in ids: ids[gene] = 'tandem'
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for chrom in sorted(bed):
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print(f"chrom {chrom} S=0 E={lengths[chrom]/1000000}")
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for pos in sorted(bed[chrom]):
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rec = bed[chrom][pos]; gid = rec[1]; mid = (int(rec[3]) + pos) / 2 / 1000000
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print(f"{gid} {mid} {'C2' if ids.get(gid) == 'tandem' else 'C4'}")
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