Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.py @ 20:de7fbcb1348c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
author artbio
date Sun, 25 Nov 2018 06:56:40 -0500
parents f33afecac67a
children e75a10eba0a6
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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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diff changeset
1 import argparse
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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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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4 import numpy
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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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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,
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14 default=0, help='minimal size of reads')
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15 the_parser.add_argument('--maxsize', dest='maxsize', type=int,
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16 default=10000, help='maximal size of reads')
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17 the_parser.add_argument('--cluster', dest='cluster', type=int,
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18 default=0, help='clustering distance')
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19 the_parser.add_argument('--sample_names', dest='sample_names',
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20 required=True, nargs='+',
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21 help='list of sample names')
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22 the_parser.add_argument('--bed', dest='bed', required=False,
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23 help='Name of bed output must be specified\
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24 if --cluster option used')
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25 the_parser.add_argument('--bed_skipsize', dest='bed_skipsize',
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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26 required=False, type=int, default=1,
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27 help='Skip clusters of size equal or less than\
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28 specified integer in the bed output. \
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29 Default = 0, not skipping')
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30 the_parser.add_argument('--bed_skipdensity', dest='bed_skipdensity',
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31 required=False, type=float, default=0,
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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32 help='Skip clusters of density equal or less than\
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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33 specified float number in the bed output. \
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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34 Default = 0, not skipping')
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35 the_parser.add_argument('--bed_skipcounts', dest='bed_skipcounts',
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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36 required=False, type=int, default=1,
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37 help='Skip clusters of size equal or less than\
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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38 specified integer in the bed output. \
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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39 Default = 0, not skipping')
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40 the_parser.add_argument('--outputs', nargs='+', action='store',
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41 help='list of two output paths (only two)')
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42 the_parser.add_argument('-M', '--plot_methods', nargs='+', action='store',
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43 help='list of 2 plot methods (only two) among:\
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44 Counts, Max, Mean, Median, Coverage and Size')
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45 the_parser.add_argument('--nostrand', action='store_true',
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46 help='Consider reads regardless their polarity')
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47
0
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48 args = the_parser.parse_args()
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49 return args
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52 class Map:
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53
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54 def __init__(self, bam_file, sample, minsize, maxsize, cluster, nostrand):
0
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55 self.sample_name = sample
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56 self.minsize = minsize
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57 self.maxsize = maxsize
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58 self.cluster = cluster
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59 if not nostrand:
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60 self.nostrand = False
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61 else:
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62 self.nostrand = True
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63 self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
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64 self.chromosomes = dict(zip(self.bam_object.references,
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65 self.bam_object.lengths))
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66 self.map_dict = self.create_map(self.bam_object, self.minsize,
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67 self.maxsize, self.nostrand)
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68 if self.cluster:
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69 self.map_dict = self.tile_map(self.map_dict, self.cluster)
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70
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71 def create_map(self, bam_object, minsize, maxsize, nostrand=False):
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72 '''
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73 Returns a map_dictionary {(chromosome,read_position,polarity):
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74 [read_length, ...]}
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75 '''
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76 map_dictionary = defaultdict(list)
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77 for chrom in self.chromosomes:
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78 # get empty value for start and end of each chromosome
0
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79 map_dictionary[(chrom, 1, 'F')] = []
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80 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
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81 if not nostrand:
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82 for read in bam_object.fetch(chrom):
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83 positions = read.positions # a list of covered positions
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84 if read.is_reverse:
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85 map_dictionary[(chrom, positions[-1]+1, 'R')].append(
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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86 read.query_alignment_length)
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87 else:
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88 map_dictionary[(chrom, positions[0]+1, 'F')].append(
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89 read.query_alignment_length)
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90 else:
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91 for read in bam_object.fetch(chrom):
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92 positions = read.positions # a list of covered positions
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93 if read.is_reverse:
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94 map_dictionary[(chrom, positions[-1]+1, 'F')].append(
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95 read.query_alignment_length)
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96 else:
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97 map_dictionary[(chrom, positions[0]+1, 'F')].append(
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98 read.query_alignment_length)
0
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99 return map_dictionary
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100
9
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101 def grouper(self, iterable, clust_distance):
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102 prev = None
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103 group = []
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104 for item in iterable:
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105 if not prev or item - prev <= clust_distance:
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106 group.append(item)
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107 else:
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108 yield group
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109 group = [item]
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110 prev = item
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111 if group:
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112 yield group
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113
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114 def tile_map(self, map_dic, clust_distance):
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115 '''
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116 takes a map_dictionary {(chromosome,read_position,polarity):
16
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117 [read_length, ...]}
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118 and returns a map_dictionary with structure:
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119 {(chromosome,read_position,polarity):
20
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120 [*counts*, [start_clust, end_clust]]}
9
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121 '''
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122 clustered_dic = defaultdict(list)
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123 for chrom in self.chromosomes:
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124 F_chrom_coord = []
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125 R_chrom_coord = []
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126 for key in map_dic:
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127 if key[0] == chrom and key[2] == 'F':
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128 F_chrom_coord.append(key[1])
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129 elif key[0] == chrom and key[2] == 'R':
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130 R_chrom_coord.append(key[1])
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131 F_chrom_coord = list(set(F_chrom_coord))
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132 R_chrom_coord = list(set(R_chrom_coord))
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133 F_chrom_coord.sort()
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134 R_chrom_coord.sort()
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135 F_clust_values = [i for i in self.grouper(F_chrom_coord,
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136 clust_distance)]
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137 F_clust_keys = [(i[-1]+i[0])/2 for i in F_clust_values]
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138 R_clust_values = [i for i in self.grouper(R_chrom_coord,
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139 clust_distance)]
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140 R_clust_keys = [(i[-1]+i[0])/2 for i in R_clust_values]
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141 # now 2 dictionnaries (F and R) with structure:
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142 # {centered_coordinate: [coord1, coord2, coord3, ..]}
9
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143 F_clust_dic = dict(zip(F_clust_keys, F_clust_values))
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144 R_clust_dic = dict(zip(R_clust_keys, R_clust_values))
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145 for centcoor in F_clust_dic:
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146 accumulator = []
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147 for coor in F_clust_dic[centcoor]:
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148 accumulator.extend(map_dic[(chrom, coor, 'F')])
16
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149 clustered_dic[(chrom, centcoor, 'F')] = [len(accumulator), [
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150 F_clust_dic[centcoor][0],
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151 F_clust_dic[centcoor][-1]]]
9
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152 for centcoor in R_clust_dic:
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153 accumulator = []
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154 for coor in R_clust_dic[centcoor]:
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155 accumulator.extend(map_dic[(chrom, coor, 'R')])
16
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156 clustered_dic[(chrom, centcoor, 'R')] = [len(accumulator), [
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157 R_clust_dic[centcoor][0],
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158 R_clust_dic[centcoor][-1]]]
9
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159 return clustered_dic
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160
3
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161 def compute_readcount(self, map_dictionary, out):
2
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162 '''
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163 takes a map_dictionary as input and writes
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164 a readmap_dictionary {(chromosome,read_position,polarity):
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165 number_of_reads}
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166 in an open file handler out
0
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167 '''
2
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168 readmap_dictionary = dict()
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169 for key in map_dictionary:
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170 readmap_dictionary[key] = len(map_dictionary[key])
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171 self.write_table(readmap_dictionary, out)
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172
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173 def compute_max(self, map_dictionary, out):
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174 '''
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175 takes a map_dictionary as input and writes
0
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176 a max_dictionary {(chromosome,read_position,polarity):
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177 max_of_number_of_read_at_any_position}
2
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178 Not clear this function is still required
0
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179 '''
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180 merge_keylist = [(i[0], 0) for i in map_dictionary.keys()]
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181 max_dictionary = dict(merge_keylist)
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182 for key in map_dictionary:
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183 if len(map_dictionary[key]) > max_dictionary[key[0]]:
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184 max_dictionary[key[0]] = len(map_dictionary[key])
2
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185 self.write_table(max_dictionary, out)
0
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186
2
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187 def compute_mean(self, map_dictionary, out):
0
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188 '''
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189 takes a map_dictionary as input and returns
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190 a mean_dictionary {(chromosome,read_position,polarity):
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191 mean_value_of_reads}
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192 '''
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193 mean_dictionary = dict()
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194 for key in map_dictionary:
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195 if len(map_dictionary[key]) == 0:
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196 mean_dictionary[key] = 0
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197 else:
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198 mean_dictionary[key] = round(numpy.mean(map_dictionary[key]),
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199 1)
2
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200 self.write_table(mean_dictionary, out)
0
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201
2
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202 def compute_median(self, map_dictionary, out):
0
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203 '''
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204 takes a map_dictionary as input and returns
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205 a mean_dictionary {(chromosome,read_position,polarity):
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206 mean_value_of_reads}
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207 '''
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artbio
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208 median_dictionary = dict()
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209 for key in map_dictionary:
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210 if len(map_dictionary[key]) == 0:
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211 median_dictionary[key] = 0
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212 else:
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213 median_dictionary[key] = numpy.median(map_dictionary[key])
2
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214 self.write_table(median_dictionary, out)
0
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215
16
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216 def compute_coverage(self, map_dictionary, out, quality=15):
0
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217 '''
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218 takes a map_dictionary as input and returns
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219 a coverage_dictionary {(chromosome,read_position,polarity):
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220 coverage}
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221 '''
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222 coverage_dictionary = dict()
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223 for chrom in self.chromosomes:
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224 coverage_dictionary[(chrom, 1, 'F')] = 0
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225 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
4
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226 for read in self.bam_object.fetch(chrom):
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diff changeset
227 positions = read.positions # a list of covered positions
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228 for pos in positions:
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229 if not map_dictionary[(chrom, pos+1, 'F')]:
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230 map_dictionary[(chrom, pos+1, 'F')] = []
0
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231 for key in map_dictionary:
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232 coverage = self.bam_object.count_coverage(
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233 reference=key[0],
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234 start=key[1]-1,
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235 end=key[1],
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236 quality_threshold=quality)
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237 """ Add the 4 coverage values """
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238 coverage = [sum(x) for x in zip(*coverage)]
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239 coverage_dictionary[key] = coverage[0]
2
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240 self.write_table(coverage_dictionary, out)
0
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241
2
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242 def compute_size(self, map_dictionary, out):
0
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243 '''
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244 Takes a map_dictionary and returns a dictionary of sizes:
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245 {chrom: {polarity: {size: nbre of reads}}}
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246 '''
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247 size_dictionary = defaultdict(lambda: defaultdict(
1
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248 lambda: defaultdict(int)))
0
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249 # to track empty chromosomes
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250 for chrom in self.chromosomes:
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251 if self.bam_object.count(chrom) == 0:
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252 size_dictionary[chrom]['F'][10] = 0
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253 for key in map_dictionary:
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254 for size in map_dictionary[key]:
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255 size_dictionary[key[0]][key[2]][size] += 1
2
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256 self.write_size_table(size_dictionary, out)
0
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257
2
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258 def write_table(self, mapdict, out):
0
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259 '''
16
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diff changeset
260 Writer of a tabular file
2
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diff changeset
261 Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
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artbio
parents: 1
diff changeset
262 <some mapped value>
0
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artbio
parents:
diff changeset
263 out is an *open* file handler
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artbio
parents:
diff changeset
264 '''
2
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artbio
parents: 1
diff changeset
265 for key in sorted(mapdict):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
266 line = [self.sample_name, key[0], self.chromosomes[key[0]],
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
267 key[1], key[2], mapdict[key]]
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
268 line = [str(i) for i in line]
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
269 out.write('\t'.join(line) + '\n')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
270
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
271 def write_size_table(self, sizedic, out):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
272 '''
16
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artbio
parents: 15
diff changeset
273 Writer of a tabular file
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
274 Dataset, Chromosome, Chrom_length, <category (size)>, <some value>
2
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
275 out is an *open* file handler
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
276 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
277 for chrom in sorted(sizedic):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
278 sizes = sizedic[chrom]['F'].keys()
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
279 sizes.extend(sizedic[chrom]['R'].keys())
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
280 for polarity in sorted(sizedic[chrom]):
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
281 for size in range(min(sizes), max(sizes)+1):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
282 try:
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artbio
parents:
diff changeset
283 line = [self.sample_name, chrom, polarity, size,
2
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
284 sizedic[chrom][polarity][size]]
0
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artbio
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diff changeset
285 except KeyError:
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artbio
parents:
diff changeset
286 line = [self.sample_name, chrom, polarity, size, 0]
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artbio
parents:
diff changeset
287 line = [str(i) for i in line]
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artbio
parents:
diff changeset
288 out.write('\t'.join(line) + '\n')
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
289
20
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artbio
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diff changeset
290 def write_cluster_table(self, clustered_dic, out, bedpath):
16
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291 '''
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artbio
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diff changeset
292 Writer of a tabular file
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artbio
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diff changeset
293 Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
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artbio
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diff changeset
294 <some mapped value>
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artbio
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diff changeset
295 out is an *open* file handler
18
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artbio
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diff changeset
296 bed is an a file handler internal to the function
16
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artbio
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297 '''
20
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artbio
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298 def filterCluster(size, count, density):
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artbio
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299 if size < args.bed_skipsize:
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artbio
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diff changeset
300 return False
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artbio
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301 if count < args.bed_skipcounts:
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artbio
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diff changeset
302 return False
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artbio
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diff changeset
303 if density <= args.bed_skipdensity:
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artbio
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diff changeset
304 return False
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artbio
parents: 19
diff changeset
305 return True
18
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artbio
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diff changeset
306 bed = open(bedpath, 'w')
20
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artbio
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diff changeset
307 clusterid = 0
16
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artbio
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diff changeset
308 for key in sorted(clustered_dic):
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artbio
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diff changeset
309 start = clustered_dic[key][1][0]
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artbio
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diff changeset
310 end = clustered_dic[key][1][1]
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artbio
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diff changeset
311 size = end - start + 1
20
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artbio
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diff changeset
312 read_count = clustered_dic[key][0]
18
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artbio
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diff changeset
313 if self.nostrand:
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artbio
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diff changeset
314 polarity = '.'
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artbio
parents: 17
diff changeset
315 elif key[2] == 'F':
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artbio
parents: 17
diff changeset
316 polarity = '+'
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artbio
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diff changeset
317 else:
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artbio
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diff changeset
318 polarity = '-'
20
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artbio
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diff changeset
319 density = float(read_count) / size
16
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artbio
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diff changeset
320 line = [self.sample_name, key[0], self.chromosomes[key[0]],
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
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diff changeset
321 key[1], key[2], read_count,
16
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artbio
parents: 15
diff changeset
322 str(start) + "-" + str(end), str(size), str(density)]
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artbio
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diff changeset
323 line = [str(i) for i in line]
20
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artbio
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diff changeset
324 out.write('\t'.join(line) + '\n')
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
325 if filterCluster(size, read_count, density):
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artbio
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diff changeset
326 clusterid += 1
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
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diff changeset
327 name = 'cluster_' + str(clusterid)
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
328 bedline = [key[0], str(start-1), str(end), name,
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
329 str(read_count), polarity, str(density)]
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
parents: 17
diff changeset
330 bed.write('\t'.join(bedline) + '\n')
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
331 print("number of reported clusters:", clusterid)
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
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diff changeset
332 bed.close()
16
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artbio
parents: 15
diff changeset
333
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff changeset
334
17
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
artbio
parents: 16
diff changeset
335 def main(inputs, samples, methods, outputs, minsize, maxsize, cluster,
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
336 nostrand, bedfile=None, bed_skipsize=0):
2
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artbio
parents: 1
diff changeset
337 for method, output in zip(methods, outputs):
16
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artbio
parents: 15
diff changeset
338 out = open(output, 'w')
2
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artbio
parents: 1
diff changeset
339 if method == 'Size':
5
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artbio
parents: 4
diff changeset
340 header = ["Dataset", "Chromosome", "Polarity", method, "Counts"]
16
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
341 elif cluster:
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
342 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
343 "Polarity", method, "Start-End", "Cluster Size",
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
344 "density"]
2
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artbio
parents: 1
diff changeset
345 else:
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artbio
parents: 1
diff changeset
346 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
347 "Polarity", method]
16
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artbio
parents: 15
diff changeset
348 out.write('\t'.join(header) + '\n')
2
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artbio
parents: 1
diff changeset
349 for input, sample in zip(inputs, samples):
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350 mapobj = Map(input, sample, minsize, maxsize, cluster, nostrand)
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351 token = {"Counts": mapobj.compute_readcount,
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352 "Max": mapobj.compute_max,
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353 "Mean": mapobj.compute_mean,
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354 "Median": mapobj.compute_median,
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355 "Coverage": mapobj.compute_coverage,
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356 "Size": mapobj.compute_size,
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357 "cluster": mapobj.write_cluster_table}
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358 if cluster:
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359 token["cluster"](mapobj.map_dict, out, bedfile)
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parents: 15
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360 else:
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361 token[method](mapobj.map_dict, out)
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362 out.close()
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363
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364
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365 if __name__ == "__main__":
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366 args = Parser()
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367 # if identical sample names
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368 if len(set(args.sample_names)) != len(args.sample_names):
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369 args.sample_names = [name + '_' + str(i) for
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370 i, name in enumerate(args.sample_names)]
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371 main(args.inputs, args.sample_names, args.plot_methods, args.outputs,
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372 args.minsize, args.maxsize, args.cluster, args.nostrand, args.bed)