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annotate tabpad.py @ 0:2feaf3d2805b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
author iuc
date Tue, 10 Dec 2019 21:02:47 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2feaf3d2805b "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
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2
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3 import argparse
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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4 import re
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5
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6
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7 def padfile(infile, outfile, fieldcnt=None):
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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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12
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13 def pad_line(txtline, tabs=None):
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14 line = txtline.rstrip('\r\n')
2feaf3d2805b "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')
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16 if not tabs:
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17 tabs = '\t' * len(fields)
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18 out.write('%s%s\n' % (line, tabs[len(fields):]))
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19
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20 for i, txtline in enumerate(fh):
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21 if txtline.lstrip().startswith('#'):
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22 commentlines.append(txtline)
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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23 else:
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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24 if commentlines:
2feaf3d2805b "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):
2feaf3d2805b "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])
2feaf3d2805b "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)
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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28 commentlines = []
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29 pad_line(txtline, tabs=tabs)
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30 out.close()
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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31
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32
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33 def fieldcount(infile):
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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34 fieldcnt = 0
2feaf3d2805b "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:
2feaf3d2805b "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):
2feaf3d2805b "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')))
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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38 return fieldcnt
2feaf3d2805b "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):
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42 return re.sub('.txt$', '', infile) + '.tsv'
2feaf3d2805b "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__():
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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46 parser = argparse.ArgumentParser(
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47 description='Pad a file with TABS for equal field size across lines')
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48 parser.add_argument(
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49 '-i', '--input', help='input file')
2feaf3d2805b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a"
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50 parser.add_argument(
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51 '-o', '--output', help='output file')
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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()
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55
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56 if args.input:
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57 outfile = args.output if args.output else tsvname(args.input)
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58 fieldcnt = fieldcount(args.input)
2feaf3d2805b "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)
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60 for infile in args.files:
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61 outfile = tsvname(infile)
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62 fieldcnt = fieldcount(infile)
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63 padfile(infile, outfile, fieldcnt=fieldcnt)
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64
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65
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66 if __name__ == "__main__":
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67 __main__()