Mercurial > repos > artbio > small_rna_map

annotate small_rna_map.py @ 8:2cc2948cfa34 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b6c6b4d92a8d839e59f7ac28cb169d25ca68ef0d
author artbio
date Sun, 23 Jul 2017 13:54:29 -0400
parents 35d3f8ac99cf
children
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
artbio
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1 import argparse
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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2 from collections import defaultdict
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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4 import numpy
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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6 import pysam
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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9 def Parser():
1ad5d040f85f planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit fa452d860cf550c7524df59e77b36fd39e3e2a45
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10 the_parser = argparse.ArgumentParser()
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11 the_parser.add_argument('--input', dest='input', required=True,
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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12 nargs='+', help='input BAM files')
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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13 the_parser.add_argument('--sample_name', dest='sample_name',
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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14 required=True, nargs='+', help='sample name')
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15 the_parser.add_argument('--output', action='store',
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16 type=str, help='output tabular file')
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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')
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19 args = the_parser.parse_args()
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20 return args
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23 class Map:
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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')
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28 self.chromosomes = dict(zip(self.bam_object.references,
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29 self.bam_object.lengths))
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30 self.map_dict = self.create_map(self.bam_object)
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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31 self.max = self.compute_max(self.map_dict)
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32 self.mean = self.compute_mean(self.map_dict)
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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33 self.median = self.compute_median(self.map_dict)
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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34 self.coverage = self.compute_coverage(self.map_dict)
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35 if computeSize:
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36 self.size = self.compute_size(self.map_dict)
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38 def create_map(self, bam_object):
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39 '''
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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40 Returns a map_dictionary {(chromosome,read_position,polarity):
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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41 [read_length, ...]}
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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42 '''
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43 map_dictionary = defaultdict(list)
2cc2948cfa34 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b6c6b4d92a8d839e59f7ac28cb169d25ca68ef0d
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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:
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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 not map_dictionary[(chrom, pos+1, 'R')]:
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55 map_dictionary[(chrom, pos+1, 'R')] = []
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56 if read.is_reverse:
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57 map_dictionary[(chrom, positions[-1]+1,
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58 'R')].append(read.query_alignment_length)
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59 else:
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60 map_dictionary[(chrom, positions[0]+1,
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61 'F')].append(read.query_alignment_length)
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62 return map_dictionary
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64 def compute_max(self, map_dictionary):
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65 '''
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66 takes a map_dictionary as input and returns
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67 a max_dictionary {(chromosome,read_position,polarity):
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68 max_of_number_of_read_at_any_position}
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69 '''
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70 merge_keylist = [(i[0], 0) for i in map_dictionary.keys()]
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71 max_dictionary = dict(merge_keylist)
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72 for key in map_dictionary:
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73 if len(map_dictionary[key]) > max_dictionary[key[0]]:
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74 max_dictionary[key[0]] = len(map_dictionary[key])
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75 return max_dictionary
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76
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77 def compute_mean(self, map_dictionary):
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78 '''
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79 takes a map_dictionary as input and returns
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80 a mean_dictionary {(chromosome,read_position,polarity):
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81 mean_value_of_reads}
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82 '''
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83 mean_dictionary = dict()
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84 for key in map_dictionary:
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85 if len(map_dictionary[key]) == 0:
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86 mean_dictionary[key] = 0
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87 else:
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88 mean_dictionary[key] = round(numpy.mean(map_dictionary[key]),
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89 1)
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90 return mean_dictionary
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91
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92 def compute_median(self, map_dictionary):
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93 '''
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94 takes a map_dictionary as input and returns
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95 a mean_dictionary {(chromosome,read_position,polarity):
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96 mean_value_of_reads}
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97 '''
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98 median_dictionary = dict()
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99 for key in map_dictionary:
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100 if len(map_dictionary[key]) == 0:
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101 median_dictionary[key] = 0
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102 else:
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103 median_dictionary[key] = numpy.median(map_dictionary[key])
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104 return median_dictionary
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105
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106 def compute_coverage(self, map_dictionary, quality=10):
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107 '''
8
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108 takes a map_dictionary as input and returns
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109 a coverage_dictionary {(chromosome,read_position,polarity):
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110 coverage}
5
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111 '''
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112 coverage_dictionary = dict()
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113 for chrom in self.chromosomes:
8
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114 coverage_dictionary[(chrom, 1, 'F')] = 0
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115 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
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116
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117 for key in map_dictionary:
5
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118 coverage = self.bam_object.count_coverage(
8
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119 reference=key[0],
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120 start=key[1]-1,
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121 end=key[1],
5
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122 quality_threshold=quality)
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123 """ Add the 4 coverage values """
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124 coverage = [sum(x) for x in zip(*coverage)]
8
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125 coverage_dictionary[key] = coverage[0]
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126 # coverage_dictionary[(key[0], key[1], 'R')] = coverage
5
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127 return coverage_dictionary
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128
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129 def compute_size(self, map_dictionary):
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130 '''
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131 Takes a map_dictionary and returns a dictionary of sizes:
7
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132 {chrom: {polarity: {size: nbre of reads}}}
5
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133 '''
6
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134 size_dictionary = defaultdict(lambda: defaultdict(
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135 lambda: defaultdict( int )))
7
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136 # to track empty chromosomes
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137 for chrom in self.chromosomes:
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138 if self.bam_object.count(chrom) == 0:
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139 size_dictionary[chrom]['F'][10] = 0
5
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140 for key in map_dictionary:
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141 for size in map_dictionary[key]:
6
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142 size_dictionary[key[0]][key[2]][size] += 1
5
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143 return size_dictionary
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144
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145 def write_size_table(self, out):
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146 '''
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147 Dataset, Chromosome, Polarity, Size, Nbr_reads
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148 out is an *open* file handler
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149 '''
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150 for chrom in sorted(self.size):
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151 sizes = self.size[chrom]['F'].keys()
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152 sizes.extend(self.size[chrom]['R'].keys())
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153 for polarity in sorted(self.size[chrom]):
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154 for size in range(min(sizes), max(sizes)+1):
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155 try:
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156 line = [self.sample_name, chrom, polarity, size,
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157 self.size[chrom][polarity][size]]
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diff changeset
158 except KeyError:
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159 line = [self.sample_name, chrom, polarity, size, 0]
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160 line = [str(i) for i in line]
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161 out.write('\t'.join(line) + '\n')
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162
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163 def write_table(self, out):
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164 '''
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165 Dataset, Chromosome, Chrom_length, Coordinate, Nbr_reads
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166 Polarity, Max, Mean, Median, Coverage
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167 out is an *open* file handler
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168 '''
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169 for key in sorted(self.map_dict):
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170 line = [self.sample_name, key[0], self.chromosomes[key[0]],
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171 key[1], len(self.map_dict[key]), key[2], self.max[key[0]],
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172 self.mean[key], self.median[key], self.coverage[key]]
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173 line = [str(i) for i in line]
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diff changeset
174 out.write('\t'.join(line) + '\n')
0
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175
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176
5
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177 def main(inputs, samples, file_out, size_file_out=''):
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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178 F = open(file_out, 'w')
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179 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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180 "Nbr_reads", "Polarity", "Max", "Mean", "Median", "Coverage"]
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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181 F.write('\t'.join(header) + '\n')
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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182 if size_file_out:
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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183 Fs = open(size_file_out, 'w')
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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184 header = ["Dataset", "Chromosome", "Polarity", "Size", "Nbr_reads"]
d65045e976e6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit b673d39fbe79f5164ba6489b33cfa78ac238ee09
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185 Fs.write('\t'.join(header) + '\n')
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186 for file, sample in zip(inputs, samples):
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187 mapobj = Map(file, sample, computeSize=True)
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188 mapobj.write_table(F)
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189 mapobj.write_size_table(Fs)
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190 Fs.close()
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191 else:
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192 for file, sample in zip(inputs, samples):
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193 mapobj = Map(file, sample, computeSize=False)
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194 mapobj.write_table(F)
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195 F.close()
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196
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197
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198 if __name__ == "__main__":
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199 args = Parser()
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200 # if identical sample names
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201 if len(set(args.sample_name)) != len(args.sample_name):
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202 args.sample_name = [name + '_' + str(i) for
2e0dc6032a98 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_map commit 93f212712d9846c7aaa389de60babb332d38363e
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203 i, name in enumerate(args.sample_name)]
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204 main(args.input, args.sample_name, args.output, args.sizes)