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annotate small_rna_maps.py.bak @ 2:507383cce5a8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
author artbio
date Mon, 14 Aug 2017 05:52:34 -0400
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507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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diff changeset
1 import argparse
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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2 from collections import defaultdict
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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4 import numpy
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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6 import pysam
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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9 def Parser():
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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10 the_parser = argparse.ArgumentParser()
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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11 the_parser.add_argument('--input', dest='input', required=True,
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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12 nargs='+', help='input BAM files')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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13 the_parser.add_argument('--sample_name', dest='sample_name',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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14 required=True, nargs='+', help='sample name')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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15 the_parser.add_argument('--output', 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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16 type=str, help='output tabular file')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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17 the_parser.add_argument('-S', '--sizes', action='store',
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18 help='use to output read sizes dataframe')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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19 args = the_parser.parse_args()
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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20 return args
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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23 class Map:
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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25 def __init__(self, bam_file, sample, computeSize=False):
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26 self.sample_name = sample
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27 self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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28 self.chromosomes = dict(zip(self.bam_object.references,
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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29 self.bam_object.lengths))
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30 self.map_dict = self.create_map(self.bam_object)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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31 self.max = self.compute_max(self.map_dict)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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32 self.mean = self.compute_mean(self.map_dict)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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33 self.median = self.compute_median(self.map_dict)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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34 self.coverage = self.compute_coverage(self.map_dict)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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35 if computeSize:
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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36 self.size = self.compute_size(self.map_dict)
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37
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38 def create_map(self, bam_object):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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39 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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40 Returns a map_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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41 [read_length, ...]}
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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42 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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43 map_dictionary = defaultdict(list)
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44 # get empty value for start and end of each chromosome
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45 for chrom in self.chromosomes:
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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46 map_dictionary[(chrom, 1, 'F')] = []
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47 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
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48 for chrom in self.chromosomes:
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49 for read in bam_object.fetch(chrom):
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50 positions = read.positions # a list of covered positions
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51 for pos in positions:
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52 if not map_dictionary[(chrom, pos+1, 'F')]:
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53 map_dictionary[(chrom, pos+1, 'F')] = []
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54 if read.is_reverse:
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55 map_dictionary[(chrom, positions[-1]+1,
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56 'R')].append(read.query_alignment_length)
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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57 else:
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58 map_dictionary[(chrom, positions[0]+1,
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59 'F')].append(read.query_alignment_length)
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60 return map_dictionary
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61
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62 def compute_max(self, map_dictionary):
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63 '''
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64 takes a map_dictionary as input and returns
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65 a max_dictionary {(chromosome,read_position,polarity):
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66 max_of_number_of_read_at_any_position}
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67 '''
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68 merge_keylist = [(i[0], 0) for i in map_dictionary.keys()]
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69 max_dictionary = dict(merge_keylist)
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70 for key in map_dictionary:
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71 if len(map_dictionary[key]) > max_dictionary[key[0]]:
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72 max_dictionary[key[0]] = len(map_dictionary[key])
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73 return max_dictionary
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74
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75 def compute_mean(self, map_dictionary):
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76 '''
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77 takes a map_dictionary as input and returns
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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78 a mean_dictionary {(chromosome,read_position,polarity):
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79 mean_value_of_reads}
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80 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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81 mean_dictionary = dict()
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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82 for key in map_dictionary:
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83 if len(map_dictionary[key]) == 0:
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84 mean_dictionary[key] = 0
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85 else:
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86 mean_dictionary[key] = round(numpy.mean(map_dictionary[key]),
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87 1)
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88 return mean_dictionary
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89
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diff changeset
90 def compute_median(self, map_dictionary):
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91 '''
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artbio
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diff changeset
92 takes a map_dictionary as input and returns
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artbio
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93 a mean_dictionary {(chromosome,read_position,polarity):
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artbio
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94 mean_value_of_reads}
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diff changeset
95 '''
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artbio
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96 median_dictionary = dict()
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artbio
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97 for key in map_dictionary:
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artbio
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98 if len(map_dictionary[key]) == 0:
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artbio
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99 median_dictionary[key] = 0
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artbio
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100 else:
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artbio
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101 median_dictionary[key] = numpy.median(map_dictionary[key])
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artbio
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102 return median_dictionary
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artbio
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103
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104 def compute_coverage(self, map_dictionary, quality=10):
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105 '''
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artbio
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106 takes a map_dictionary as input and returns
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artbio
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107 a coverage_dictionary {(chromosome,read_position,polarity):
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artbio
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108 coverage}
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artbio
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109 '''
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artbio
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110 coverage_dictionary = dict()
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111 for chrom in self.chromosomes:
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artbio
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112 coverage_dictionary[(chrom, 1, 'F')] = 0
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artbio
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113 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
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114 for key in map_dictionary:
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115 coverage = self.bam_object.count_coverage(
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116 reference=key[0],
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artbio
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117 start=key[1]-1,
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118 end=key[1],
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119 quality_threshold=quality)
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120 """ Add the 4 coverage values """
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121 coverage = [sum(x) for x in zip(*coverage)]
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artbio
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122 coverage_dictionary[key] = coverage[0]
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123 # coverage_dictionary[(key[0], key[1], 'R')] = coverage
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124 return coverage_dictionary
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125
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126 def compute_size(self, map_dictionary):
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127 '''
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artbio
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128 Takes a map_dictionary and returns a dictionary of sizes:
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129 {chrom: {polarity: {size: nbre of reads}}}
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130 '''
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artbio
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131 size_dictionary = defaultdict(lambda: defaultdict(
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132 lambda: defaultdict(int)))
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133 # to track empty chromosomes
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134 for chrom in self.chromosomes:
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135 if self.bam_object.count(chrom) == 0:
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136 size_dictionary[chrom]['F'][10] = 0
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137 for key in map_dictionary:
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138 for size in map_dictionary[key]:
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artbio
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139 size_dictionary[key[0]][key[2]][size] += 1
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140 return size_dictionary
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141
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142 def write_size_table(self, out):
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143 '''
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144 Dataset, Chromosome, Polarity, Size, Nbr_reads
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artbio
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145 out is an *open* file handler
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146 '''
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artbio
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147 for chrom in sorted(self.size):
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148 sizes = self.size[chrom]['F'].keys()
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diff changeset
149 sizes.extend(self.size[chrom]['R'].keys())
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150 for polarity in sorted(self.size[chrom]):
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151 for size in range(min(sizes), max(sizes)+1):
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diff changeset
152 try:
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artbio
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153 line = [self.sample_name, chrom, polarity, size,
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diff changeset
154 self.size[chrom][polarity][size]]
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diff changeset
155 except KeyError:
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artbio
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diff changeset
156 line = [self.sample_name, chrom, polarity, size, 0]
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diff changeset
157 line = [str(i) for i in line]
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artbio
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diff changeset
158 out.write('\t'.join(line) + '\n')
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159
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diff changeset
160 def write_table(self, out):
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161 '''
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artbio
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diff changeset
162 Dataset, Chromosome, Chrom_length, Coordinate, Nbr_reads
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artbio
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diff changeset
163 Polarity, Max, Mean, Median, Coverage
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artbio
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diff changeset
164 out is an *open* file handler
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diff changeset
165 '''
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artbio
parents:
diff changeset
166 for key in sorted(self.map_dict):
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artbio
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167 line = [self.sample_name, key[0], self.chromosomes[key[0]],
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artbio
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diff changeset
168 key[1], len(self.map_dict[key]), key[2], self.max[key[0]],
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artbio
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diff changeset
169 self.mean[key], self.median[key], self.coverage[key]]
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artbio
parents:
diff changeset
170 line = [str(i) for i in line]
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artbio
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diff changeset
171 out.write('\t'.join(line) + '\n')
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172
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173
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diff changeset
174 def main(inputs, samples, file_out, size_file_out=''):
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artbio
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diff changeset
175 F = open(file_out, 'w')
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artbio
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176 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
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artbio
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diff changeset
177 "Nbr_reads", "Polarity", "Max", "Mean", "Median", "Coverage"]
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178 F.write('\t'.join(header) + '\n')
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diff changeset
179 if size_file_out:
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180 Fs = open(size_file_out, 'w')
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181 header = ["Dataset", "Chromosome", "Polarity", "Size", "Nbr_reads"]
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182 Fs.write('\t'.join(header) + '\n')
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183 for file, sample in zip(inputs, samples):
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184 mapobj = Map(file, sample, computeSize=True)
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185 mapobj.write_table(F)
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186 mapobj.write_size_table(Fs)
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187 Fs.close()
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188 else:
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189 for file, sample in zip(inputs, samples):
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190 mapobj = Map(file, sample, computeSize=False)
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191 mapobj.write_table(F)
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192 F.close()
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193
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194
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195 if __name__ == "__main__":
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196 args = Parser()
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197 # if identical sample names
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198 if len(set(args.sample_name)) != len(args.sample_name):
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199 args.sample_name = [name + '_' + str(i) for
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200 i, name in enumerate(args.sample_name)]
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201 main(args.input, args.sample_name, args.output, args.sizes)