Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.py @ 8:1827b74f872b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
author artbio
date Mon, 23 Oct 2017 08:29:39 -0400
parents 12c14642e6ac
children 3ea75c573429
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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1 import argparse
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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2 from collections import defaultdict
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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4 import numpy
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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6 import pysam
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9 def Parser():
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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10 the_parser = argparse.ArgumentParser()
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11 the_parser.add_argument('--inputs', dest='inputs', required=True,
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12 nargs='+', help='list of input BAM files')
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13 the_parser.add_argument('--minsize', dest='minsize', type=int,
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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14 default=0, help='minimal size of reads')
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
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15 the_parser.add_argument('--maxsize', dest='maxsize', type=int,
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
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16 default=10000, help='maximal size of reads')
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17 the_parser.add_argument('--sample_names', dest='sample_names',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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18 required=True, nargs='+',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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19 help='list of sample names')
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20 the_parser.add_argument('--outputs', nargs='+', action='store',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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21 help='list of two output paths (only two)')
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22 the_parser.add_argument('-M', '--plot_methods', nargs='+', action='store',
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23 help='list of 2 plot methods (only two) among:\
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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24 Counts, Max, Mean, Median, Coverage and Size')
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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25 args = the_parser.parse_args()
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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26 return args
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 class Map:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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artbio
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31 def __init__(self, bam_file, sample, minsize, maxsize):
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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32 self.sample_name = sample
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33 self.minsize = minsize
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
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34 self.maxsize = maxsize
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35 self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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36 self.chromosomes = dict(zip(self.bam_object.references,
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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37 self.bam_object.lengths))
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artbio
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38 self.map_dict = self.create_map(self.bam_object, self.minsize,
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
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39 self.maxsize)
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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40
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41 def create_map(self, bam_object, minsize, maxsize):
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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42 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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43 Returns a map_dictionary {(chromosome,read_position,polarity):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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44 [read_length, ...]}
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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45 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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46 map_dictionary = defaultdict(list)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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47 # get empty value for start and end of each chromosome
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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48 for chrom in self.chromosomes:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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49 map_dictionary[(chrom, 1, 'F')] = []
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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50 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
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51 for chrom in self.chromosomes:
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52 for read in bam_object.fetch(chrom):
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53 if (read.query_alignment_length >= minsize and
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54 read.query_alignment_length <= maxsize):
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55 positions = read.positions # a list of covered positions
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
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56 if read.is_reverse:
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57 map_dictionary[(chrom, positions[-1]+1, 'R')].append(
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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58 read.query_alignment_length)
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59 else:
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60 map_dictionary[(chrom, positions[0]+1, 'F')].append(
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
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61 read.query_alignment_length)
0
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62 return map_dictionary
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63
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64 def compute_readcount(self, map_dictionary, out):
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65 '''
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66 takes a map_dictionary as input and writes
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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67 a readmap_dictionary {(chromosome,read_position,polarity):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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68 number_of_reads}
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69 in an open file handler out
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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70 '''
2
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71 readmap_dictionary = dict()
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72 for key in map_dictionary:
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73 readmap_dictionary[key] = len(map_dictionary[key])
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74 self.write_table(readmap_dictionary, out)
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75
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76 def compute_max(self, map_dictionary, out):
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77 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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78 takes a map_dictionary as input and writes
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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79 a max_dictionary {(chromosome,read_position,polarity):
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80 max_of_number_of_read_at_any_position}
2
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81 Not clear this function is still required
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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82 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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83 merge_keylist = [(i[0], 0) for i in map_dictionary.keys()]
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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84 max_dictionary = dict(merge_keylist)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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85 for key in map_dictionary:
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86 if len(map_dictionary[key]) > max_dictionary[key[0]]:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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87 max_dictionary[key[0]] = len(map_dictionary[key])
2
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88 self.write_table(max_dictionary, out)
0
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89
2
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90 def compute_mean(self, map_dictionary, out):
0
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91 '''
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diff changeset
92 takes a map_dictionary as input and returns
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93 a mean_dictionary {(chromosome,read_position,polarity):
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94 mean_value_of_reads}
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95 '''
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96 mean_dictionary = dict()
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97 for key in map_dictionary:
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98 if len(map_dictionary[key]) == 0:
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99 mean_dictionary[key] = 0
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100 else:
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101 mean_dictionary[key] = round(numpy.mean(map_dictionary[key]),
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102 1)
2
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103 self.write_table(mean_dictionary, out)
0
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104
2
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105 def compute_median(self, map_dictionary, out):
0
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106 '''
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107 takes a map_dictionary as input and returns
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108 a mean_dictionary {(chromosome,read_position,polarity):
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109 mean_value_of_reads}
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110 '''
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111 median_dictionary = dict()
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112 for key in map_dictionary:
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113 if len(map_dictionary[key]) == 0:
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114 median_dictionary[key] = 0
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115 else:
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116 median_dictionary[key] = numpy.median(map_dictionary[key])
2
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117 self.write_table(median_dictionary, out)
0
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118
2
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119 def compute_coverage(self, map_dictionary, out, quality=10):
0
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120 '''
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121 takes a map_dictionary as input and returns
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122 a coverage_dictionary {(chromosome,read_position,polarity):
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123 coverage}
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124 '''
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125 coverage_dictionary = dict()
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126 for chrom in self.chromosomes:
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127 coverage_dictionary[(chrom, 1, 'F')] = 0
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128 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
4
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129 for read in self.bam_object.fetch(chrom):
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130 positions = read.positions # a list of covered positions
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131 for pos in positions:
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132 if not map_dictionary[(chrom, pos+1, 'F')]:
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133 map_dictionary[(chrom, pos+1, 'F')] = []
0
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134 for key in map_dictionary:
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135 coverage = self.bam_object.count_coverage(
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136 reference=key[0],
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137 start=key[1]-1,
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138 end=key[1],
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139 quality_threshold=quality)
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140 """ Add the 4 coverage values """
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141 coverage = [sum(x) for x in zip(*coverage)]
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142 coverage_dictionary[key] = coverage[0]
2
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143 self.write_table(coverage_dictionary, out)
0
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144
2
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145 def compute_size(self, map_dictionary, out):
0
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146 '''
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147 Takes a map_dictionary and returns a dictionary of sizes:
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148 {chrom: {polarity: {size: nbre of reads}}}
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149 '''
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150 size_dictionary = defaultdict(lambda: defaultdict(
1
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151 lambda: defaultdict(int)))
0
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152 # to track empty chromosomes
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153 for chrom in self.chromosomes:
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154 if self.bam_object.count(chrom) == 0:
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155 size_dictionary[chrom]['F'][10] = 0
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156 for key in map_dictionary:
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157 for size in map_dictionary[key]:
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158 size_dictionary[key[0]][key[2]][size] += 1
2
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159 self.write_size_table(size_dictionary, out)
0
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160
2
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161 def write_table(self, mapdict, out):
0
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162 '''
2
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163 Generic writer
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164 Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
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165 <some mapped value>
0
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166 out is an *open* file handler
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167 '''
2
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168 for key in sorted(mapdict):
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169 line = [self.sample_name, key[0], self.chromosomes[key[0]],
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170 key[1], key[2], mapdict[key]]
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171 line = [str(i) for i in line]
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172 out.write('\t'.join(line) + '\n')
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173
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174 def write_size_table(self, sizedic, out):
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175 '''
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176 Generic writer of summary values
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177 Dataset, Chromosome, Chrom_length, <some category>, <some value>
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178 out is an *open* file handler
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179 '''
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180 for chrom in sorted(sizedic):
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181 sizes = sizedic[chrom]['F'].keys()
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182 sizes.extend(sizedic[chrom]['R'].keys())
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183 for polarity in sorted(sizedic[chrom]):
0
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184 for size in range(min(sizes), max(sizes)+1):
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185 try:
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186 line = [self.sample_name, chrom, polarity, size,
2
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187 sizedic[chrom][polarity][size]]
0
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188 except KeyError:
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189 line = [self.sample_name, chrom, polarity, size, 0]
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190 line = [str(i) for i in line]
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191 out.write('\t'.join(line) + '\n')
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192
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193
8
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194 def main(inputs, samples, methods, outputs, minsize, maxsize):
2
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195 for method, output in zip(methods, outputs):
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196 F = open(output, 'w')
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197 if method == 'Size':
5
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198 header = ["Dataset", "Chromosome", "Polarity", method, "Counts"]
2
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199 else:
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200 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
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201 "Polarity", method]
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202 F.write('\t'.join(header) + '\n')
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203 for input, sample in zip(inputs, samples):
8
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204 mapobj = Map(input, sample, minsize, maxsize)
3
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205 token = {"Counts": mapobj.compute_readcount,
2
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206 "Max": mapobj.compute_max,
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207 "Mean": mapobj.compute_mean,
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208 "Median": mapobj.compute_median,
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209 "Coverage": mapobj.compute_coverage,
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210 "Size": mapobj.compute_size}
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211 token[method](mapobj.map_dict, F)
0
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212 F.close()
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213
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214
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215 if __name__ == "__main__":
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216 args = Parser()
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217 # if identical sample names
2
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218 if len(set(args.sample_names)) != len(args.sample_names):
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219 args.sample_names = [name + '_' + str(i) for
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220 i, name in enumerate(args.sample_names)]
8
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221 main(args.inputs, args.sample_names, args.plot_methods, args.outputs,
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222 args.minsize, args.maxsize)