27 lines
606 B
Python
27 lines
606 B
Python
#!/usr/bin/env/ python3
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import os
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import sys
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annot_file = sys.argv[1]
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gene_symbol = sys.argv[2]
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transcript = sys.argv[3]
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var_conseq = ["missense", "frameshift", "stop_gained", "splice_donor", "splice_acceptor", "inframe_insertion", "inframe_deletion", "start_lost", "stop_lost"]
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for line in open(annot_file, "r"):
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line = line.strip()
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if line.startswith("#"):
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pass
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else:
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for i in var_conseq:
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pattern = i + "|" + gene_symbol + "|" + transcript
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if pattern in line:
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print(line)
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else:
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pass
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