Mercurial > repos > galaxyp > bed_to_protein_map

annotate bed_to_protein_map.py @ 1:f270ac79c0a1 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
author galaxyp
date Tue, 07 Apr 2020 15:30:33 +0000
parents 7b2642f6c004
children
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0
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
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1 #!/usr/bin/env python
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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2 """
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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3 #
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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6 # Copyright 2017, Regents of the University of Minnesota
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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7 #------------------------------------------------------------------------------
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8 # Author:
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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9 #
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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10 # James E Johnson
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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11 #
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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12 #------------------------------------------------------------------------------
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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13 """
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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14
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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15 import argparse
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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16 import sys
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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17
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18
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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19 def __main__():
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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20 parser = argparse.ArgumentParser(
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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21 description='Convert BED file to protein mapping')
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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22 parser.add_argument(
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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23 'input',
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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24 help='A BED file (12 column)')
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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25 parser.add_argument(
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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26 'output',
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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27 help='Output file (-) for stdout')
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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28 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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29 args = parser.parse_args()
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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30
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31 input_rdr = open(args.input, 'r') if args.input != '-' else sys.stdin
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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32 output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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33
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34 try:
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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35 for linenum, line in enumerate(input_rdr):
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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36 if args.debug:
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f270ac79c0a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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37 sys.stderr.write("%d: %s\n" % (linenum, line))
0
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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38 if line.startswith('#'):
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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39 continue
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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40 if line.strip() == '':
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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41 continue
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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42 fields = line.rstrip('\r\n').split('\t')
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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43 if len(fields) < 12:
1
f270ac79c0a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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44 sys.stderr.write("%d: %s\n" % (linenum, line))
0
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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45 continue
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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46 (chrom, _chromStart, _chromEnd, name, score, strand,
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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47 _thickStart, _thickEnd, itemRgb,
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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48 _blockCount, blockSizes, blockStarts) = fields[0:12]
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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49 chromStart = int(_chromStart)
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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50 thickStart = int(_thickStart)
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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51 thickEnd = int(_thickEnd)
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52 blockCount = int(_blockCount)
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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53 blockSizes = [int(x) for x in blockSizes.split(',')]
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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54 blockStarts = [int(x) for x in blockStarts.split(',')]
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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55 if strand == '+':
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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56 cds_start = 0
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57 cds_end = 0
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58 for i in range(blockCount):
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59 start = chromStart + blockStarts[i]
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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60 end = start + blockSizes[i]
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61 if end < thickStart:
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62 continue
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63 if start > thickEnd:
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64 break
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65 if start < thickStart:
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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66 start = thickStart
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67 if end > thickEnd:
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68 end = thickEnd
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69 cds_end = cds_start + (end - start)
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70 output_wtr.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n'
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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71 % (name, chrom, start, end,
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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72 strand, cds_start, cds_end))
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73 cds_start = cds_end
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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74 elif strand == '-':
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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75 cds_start = 0
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76 cds_end = 0
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77 for i in reversed(range(blockCount)):
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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78 start = chromStart + blockStarts[i]
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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79 end = start + blockSizes[i]
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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80 if end < thickStart:
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81 break
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
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82 if start > thickEnd:
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
83 continue
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
84 if start < thickStart:
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
85 start = thickStart
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
86 if end > thickEnd:
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
87 end = thickEnd
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
88 cds_end = cds_start + (end - start)
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
89 output_wtr.write('%s\t%s\t%d\t%d\t%s\t%d\t%d\n'
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
90 % (name, chrom, start, end,
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
91 strand, cds_start, cds_end))
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
92 cds_start = cds_end
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
93 pass
1
f270ac79c0a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
94 except Exception as e:
f270ac79c0a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
95 sys.stderr.write("failed: %s\n" % e)
0
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
96 exit(1)
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
97
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
98
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
99 if __name__ == "__main__":
7b2642f6c004 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map commit 2d39f681f77eedc840c17aebe4ddc8f66c8a7c62
galaxyp
parents:
diff changeset
100 __main__()