30 lines
1.2 KiB
Python
30 lines
1.2 KiB
Python
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#!/usr/bin/env python3
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import sys
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if len(sys.argv) != 4:
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sys.exit(f"python3 {sys.argv[0]} <geneID.list> <jcvi.anchors.new> <jcvi.anchors.simple> > out.highlight.simple")
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ids_file, anchors_file, simple_file = sys.argv[1:]
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ids = set()
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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.add(f[0])
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blocks = {}
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with open(anchors_file, encoding='utf-8', errors='replace') as fh:
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for block in fh.read().split('###'):
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block = block.strip()
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if not block: continue
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left=[]; right=[]; hit=False
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for line in block.splitlines():
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f = line.split()
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if len(f) < 2: continue
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if f[0] in ids or f[1] in ids: hit = True
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left.append(f[0]); right.append(f[1])
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if hit and left and right:
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blocks[' '.join(sorted([left[0], left[-1]]))] = ' '.join(sorted([right[0], right[-1]]))
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with open(simple_file, encoding='utf-8', errors='replace') as fh:
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for line in fh:
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raw = line.rstrip('\n'); f = raw.split(); flag = False
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if len(f) >= 4:
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flag = blocks.get(' '.join(sorted([f[0], f[1]]))) == ' '.join(sorted([f[2], f[3]]))
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print(('r*' if flag else '') + raw)
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