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annotate windowSplitter.py @ 3:1011f028f09d draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
author devteam
date Wed, 03 Jun 2020 13:44:45 +0000
parents 4815516900d4
children
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1 #!/usr/bin/env python
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2 """
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3 Split into windows.
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4
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5 usage: %prog input size out_file
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6 -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
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7 """
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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8 from __future__ import print_function
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9
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10 import sys
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11
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12 from bx.cookbook import doc_optparse
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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13
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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14
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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15 # Default chrom, start, end, strand cols for a bed file
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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16 BED_DEFAULT_COLS = 0, 1, 2, 5
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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17
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18
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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19 def parse_cols_arg(cols):
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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20 """Parse a columns command line argument into a four-tuple"""
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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21 if cols:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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22 # Handle case where no strand column included - in this case, cols
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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23 # looks something like 1,2,3,
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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24 if cols.endswith(','):
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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25 cols += '0'
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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26 col_list = [int(x) - 1 for x in cols.split(",")]
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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27 return col_list
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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28 else:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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29 return BED_DEFAULT_COLS
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32 def main():
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33 # Parsing Command Line here
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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34 options, args = doc_optparse.parse(__doc__)
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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35
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36 try:
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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37 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg(options.cols)
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38 inp_file, winsize, out_file, makesliding, offset = args
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39 winsize = int(winsize)
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40 offset = int(offset)
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41 makesliding = int(makesliding)
3
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42 except Exception:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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43 sys.exit("Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset.")
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44
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45 skipped_lines = 0
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46 first_invalid_line = 0
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47 invalid_line = None
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48 if offset == 0:
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49 makesliding = 0
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50
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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51 with open(out_file, 'w') as fo, open(inp_file) as fi:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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52 for i, line in enumerate(fi):
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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53 line = line.strip()
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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54 if line and line[0:1] != "#":
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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55 try:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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56 elems = line.split('\t')
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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57 start = int(elems[start_col_1])
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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58 end = int(elems[end_col_1])
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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59 if makesliding == 0:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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60 numwin = (end - start) // winsize
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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61 else:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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62 numwin = (end - start) // offset
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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63 if numwin > 0:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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64 for _ in range(numwin):
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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65 elems_1 = elems
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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66 elems_1[start_col_1] = str(start)
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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67 elems_1[end_col_1] = str(start + winsize)
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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68 fo.write("%s\n" % '\t'.join(elems_1))
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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69 if makesliding == 0:
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70 start = start + winsize
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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71 else:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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72 start = start + offset
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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73 if start + winsize > end:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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74 break
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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75 except Exception:
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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76 skipped_lines += 1
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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77 if not invalid_line:
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78 first_invalid_line = i + 1
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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79 invalid_line = line
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80
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81 if makesliding == 1:
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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82 print('Window size=%d, Sliding=Yes, Offset=%d' % (winsize, offset))
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83 else:
3
1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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84 print('Window size=%d, Sliding=No' % (winsize))
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85 if skipped_lines > 0:
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1011f028f09d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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86 print('Skipped %d invalid lines starting with #%d: "%s"' % (skipped_lines, first_invalid_line, invalid_line))
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87
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88
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89 if __name__ == "__main__":
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90 main()