Mercurial > repos > yating-l > ucsc_trix_index_generator
comparison extractHeaders.py @ 0:3de4fbd488a1 draft default tip
planemo upload commit 81955d80a45c04ad4874f19f43c36ca608b3735e
| author | yating-l |
|---|---|
| date | Wed, 16 May 2018 17:33:35 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:3de4fbd488a1 |
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| 1 #!/usr/bin/python | |
| 2 """ Extract headers from Fasta file and write the headers to a Tabular file """ | |
| 3 | |
| 4 import sys | |
| 5 | |
| 6 def extractHeaders(fasta_file, tab_file): | |
| 7 | |
| 8 with open(tab_file, 'w') as out: | |
| 9 with open(fasta_file, 'r') as f: | |
| 10 lines = f.readlines() | |
| 11 for l in lines: | |
| 12 if '>' in l: | |
| 13 l = l.split() | |
| 14 name = l[0].replace('>', '').rstrip() | |
| 15 desc = ''.join(l[1:]).rstrip() | |
| 16 out.write(name + '\t' + desc + '\n') | |
| 17 | |
| 18 | |
| 19 | |
| 20 def main(argv): | |
| 21 input_file = argv[1] | |
| 22 output_file = argv[2] | |
| 23 extractHeaders(input_file, output_file) | |
| 24 | |
| 25 if __name__ == "__main__": | |
| 26 main(sys.argv) |