Mercurial > repos > iuc > read_it_and_keep
comparison trim_reference.py @ 0:554aa2a63f04 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep commit 4b41e2742ba5f9c957e13a188ca49e60e16ae13b"
| author | iuc |
|---|---|
| date | Fri, 28 Jan 2022 18:47:34 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:554aa2a63f04 |
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| 1 #!/usr/bin/env python | |
| 2 | |
| 3 from __future__ import print_function | |
| 4 | |
| 5 import argparse | |
| 6 import sys | |
| 7 | |
| 8 if __name__ == '__main__': | |
| 9 parser = argparse.ArgumentParser() | |
| 10 parser.add_argument('input_file', type=argparse.FileType()) | |
| 11 parser.add_argument('output_file', type=argparse.FileType('w'), nargs='?', default=sys.stdout) | |
| 12 args = parser.parse_args() | |
| 13 lines = args.input_file.readlines() | |
| 14 i = len(lines) - 1 | |
| 15 trimmed = False | |
| 16 # step backwards through the lines, removing all As until we find a non-A nucleotide | |
| 17 while not trimmed: | |
| 18 line = lines[i].upper().rstrip() | |
| 19 for j in range(len(line) - 1, -1, -1): | |
| 20 # walk backwards through the line, checking for a non-A (and non-space) character | |
| 21 if line[j] not in ['A', ' ']: | |
| 22 lines[i] = line[:j + 1] + '\n' | |
| 23 trimmed = True | |
| 24 break | |
| 25 else: | |
| 26 # we processed the whole line - all As - so we don't include this line in the output | |
| 27 i -= 1 | |
| 28 args.output_file.write(''.join(lines[:i + 1])) |