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annotate tabpad.py @ 2:a40bbd70b8b1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 2948f114101aeefa951f47df8ee3b25656d9680e
author iuc
date Thu, 09 Mar 2023 21:00:52 +0000
parents b6c5e7343617
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
iuc
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1 #!/usr/bin/env python
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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2
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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3 import argparse
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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4 import re
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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5
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6
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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7 def padfile(infile, outfile, fieldcnt=None):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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8 with open(infile, 'r') as fh:
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9 out = open(outfile, 'w')
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10 commentlines = []
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11 tabs = '\t' * fieldcnt if fieldcnt is not None else None
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13 def pad_line(txtline, tabs=None):
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14 line = txtline.rstrip('\r\n')
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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15 fields = line.split('\t')
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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16 if not tabs:
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17 tabs = '\t' * len(fields)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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18 out.write('%s%s\n' % (line, tabs[len(fields):]))
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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19
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20 for i, txtline in enumerate(fh):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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21 if txtline.lstrip().startswith('#'):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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22 commentlines.append(txtline)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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23 else:
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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24 if commentlines:
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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25 for i in range(len(commentlines) - 1):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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26 out.write(commentlines[i])
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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27 pad_line(commentlines[-1], tabs=tabs)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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28 commentlines = []
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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29 pad_line(txtline, tabs=tabs)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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30 out.close()
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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32
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33 def fieldcount(infile):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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34 fieldcnt = 0
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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35 with open(infile, 'r') as fh:
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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36 for i, line in enumerate(fh):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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37 fieldcnt = max(fieldcnt, len(line.rstrip('\r\n').split('\t')))
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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38 return fieldcnt
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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39
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40
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41 def tsvname(infile):
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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42 return re.sub('.txt$', '', infile) + '.tsv'
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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43
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44
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45 def __main__():
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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46 parser = argparse.ArgumentParser(
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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47 description='Pad a file with TABS for equal field size across lines')
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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48 parser.add_argument(
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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49 '-i', '--input', help='input file')
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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50 parser.add_argument(
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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51 '-o', '--output', help='output file')
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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52 parser.add_argument(
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53 'files', nargs='*', help='.txt files')
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54 args = parser.parse_args()
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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55
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56 if args.input:
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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57 outfile = args.output if args.output else tsvname(args.input)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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58 fieldcnt = fieldcount(args.input)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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59 padfile(args.input, outfile, fieldcnt=fieldcnt)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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60 for infile in args.files:
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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61 outfile = tsvname(infile)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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62 fieldcnt = fieldcount(infile)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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63 padfile(infile, outfile, fieldcnt=fieldcnt)
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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64
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65
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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66 if __name__ == "__main__":
b6c5e7343617 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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67 __main__()