27 lines
1.1 KiB
Python
27 lines
1.1 KiB
Python
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#!/usr/bin/env python3
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import sys
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if len(sys.argv) != 3:
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sys.exit(f"python3 {sys.argv[0]} <input.fasta> <ID.list> > out.OrderByID.fasta")
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fasta_file, ids_file = sys.argv[1:]
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seqs = {}; current = None; chunks = []
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with open(fasta_file, encoding='utf-8', errors='replace') as fh:
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for line in fh:
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line = line.rstrip('\n')
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if line.startswith('>'):
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if current is not None:
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if current in seqs: sys.exit(f"erro {current} more than once in {fasta_file}")
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seqs[current] = ''.join(chunks)
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current = line[1:].split()[0]; chunks = []
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else:
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chunks.append(line)
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if current is not None:
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if current in seqs: sys.exit(f"erro {current} more than once in {fasta_file}")
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seqs[current] = ''.join(chunks)
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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 not f: continue
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name = f[0]
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if name in seqs: print(f">{name}\n{seqs[name]}")
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else: print(f"warning:{name} not in the {fasta_file} file", file=sys.stderr)
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