Mercurial > repos > galaxyp > gffcompare_to_bed

annotate gffcompare_to_bed.py @ 3:ba5368c19dbd draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 98ac160e172e3a404163c1af8e2d5ae42a2b425d"
author galaxyp
date Wed, 13 Jan 2021 20:59:52 +0000
parents 9a4cfc910674
children
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7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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1 #!/usr/bin/env python
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2017, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13 """
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14
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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15 import argparse
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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16 import sys
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17
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18
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19 class BedEntry(object):
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20 def __init__(self, chrom=None, chromStart=None, chromEnd=None,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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21 name=None, score=None, strand=None,
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22 thickStart=None, thickEnd=None, itemRgb=None,
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23 blockCount=None, blockSizes=None, blockStarts=None):
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24 self.chrom = chrom
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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25 self.chromStart = int(chromStart)
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26 self.chromEnd = int(chromEnd)
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27 self.name = name
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28 self.score = int(score) if score is not None else 0
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29 self.strand = '-' if str(strand).startswith('-') else '+'
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30 self.thickStart = int(thickStart) if thickStart else self.chromStart
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31 self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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32 self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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33 self.blockCount = int(blockCount)
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34 if isinstance(blockSizes, str):
0
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35 self.blockSizes = [int(x) for x in blockSizes.split(',')]
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36 elif isinstance(blockSizes, list):
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37 self.blockSizes = [int(x) for x in blockSizes]
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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38 else:
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39 self.blockSizes = blockSizes
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40 if isinstance(blockStarts, str):
0
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41 self.blockStarts = [int(x) for x in blockStarts.split(',')]
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42 elif isinstance(blockStarts, list):
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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43 self.blockStarts = [int(x) for x in blockStarts]
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44 else:
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45 self.blockStarts = blockStarts
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46
3
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47 def sort_exons(self):
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48 sorted_list = [i for i in sorted(zip(self.blockStarts,self.blockSizes))]
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49 self.blockStarts = [i[0] for i in sorted_list]
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50 self.blockSizes = [i[1] for i in sorted_list]
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51
0
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52 def __str__(self):
3
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53 self.sort_exons()
0
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54 return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (
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55 self.chrom, self.chromStart, self.chromEnd,
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56 self.name, self.score, self.strand,
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57 self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount,
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58 ','.join([str(x) for x in self.blockSizes]),
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59 ','.join([str(x) for x in self.blockStarts]))
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60
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61
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62 def __main__():
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63 parser = argparse.ArgumentParser(
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64 description='Retrieve Ensembl cDNAs and three frame translate')
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65 parser.add_argument(
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66 'input',
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67 help='GFFCompare annotated GTF file, (-) for stdin')
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68 parser.add_argument(
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69 'output',
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70 help='BED file, (-) for stdout')
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71 parser.add_argument(
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72 '-C', '--class_code', action='append', default=[],
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73 help='Restrict output to gffcompare class codes')
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74 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
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75 args = parser.parse_args()
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76
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77 # print >> sys.stderr, "args: %s" % args
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78 input_rdr = open(args.input, 'r') if args.input != '-' else sys.stdin
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79 output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
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80
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81 def write_bed_entry(bed):
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82 if bed.blockCount == 0:
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83 bed.blockCount = 1
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84 output_wtr.write("%s\n" % str(bed))
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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85
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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86 class_codes = [c.strip() for codes in args.class_code
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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87 for c in codes.split(',')] if args.class_code else None
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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88 bed = None
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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89 class_code = None
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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90 for i, line in enumerate(input_rdr):
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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91 if line.startswith('#'):
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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92 continue
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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93 fields = line.rstrip('\r\n').split('\t')
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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94 if len(fields) != 9:
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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95 continue
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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96 (seqname, source, feature, start, end,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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97 score, strand, frame, attributes) = fields
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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98 attribute = {i[0]: i[1].strip('"') for i in [j.strip().split(' ')
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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99 for j in attributes.rstrip(';').split(';')]}
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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100 if feature == 'transcript':
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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101 if args.debug:
2
9a4cfc910674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
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102 sys.stderr.write("%s\t%s\n" % ('\t'.join([seqname, source,
9a4cfc910674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
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103 feature, start, end, score, strand, frame]),
9a4cfc910674 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
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104 attribute))
0
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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105 if bed is not None:
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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106 write_bed_entry(bed)
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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107 bed = None
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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108 class_code = attribute['class_code'].strip('"')\
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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109 if 'class_code' in attribute else None
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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110 if class_codes and class_code not in class_codes:
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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111 continue
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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112 chromStart = int(start) - 1
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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113 chromEnd = int(end)
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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114 cat = '_' + class_code if class_code and class_code != '=' else ''
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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115 bed = BedEntry(chrom=seqname,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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116 chromStart=chromStart, chromEnd=chromEnd,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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117 name=attribute['transcript_id'] + cat,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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118 strand=strand,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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119 blockCount=0,
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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120 blockSizes=[chromEnd - chromStart],
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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121 blockStarts=[0])
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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122 elif feature == 'exon' and bed is not None:
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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123 chromStart = int(start) - 1
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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124 chromEnd = int(end)
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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125 blockSize = chromEnd - chromStart
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
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126 if bed.blockCount == 0:
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galaxyp
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127 bed.blockSizes = []
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galaxyp
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128 bed.blockStarts = []
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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129 bed.blockSizes.append(blockSize)
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galaxyp
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130 bed.blockStarts.append(chromStart - bed.chromStart)
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
galaxyp
parents:
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131 bed.blockCount += 1
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132 if bed is not None:
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galaxyp
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133 write_bed_entry(bed)
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134
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135
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galaxyp
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136 if __name__ == "__main__":
7e572e148175 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe
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137 __main__()