Mercurial > repos > artbio > small_rna_signatures

annotate overlapping_reads.py @ 14:5150d641d515 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c
author artbio
date Thu, 06 Apr 2023 23:00:54 +0000
parents 124f404b0fe7
children
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6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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diff changeset
1 import argparse
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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2 from collections import defaultdict
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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4 import pysam
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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7 def Parser():
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8 the_parser = argparse.ArgumentParser()
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9 the_parser.add_argument(
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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10 '--input', action="store", type=str, help="bam alignment file")
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11 the_parser.add_argument(
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12 '--minquery', type=int,
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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13 help="Minimum readsize of query reads (nt) - must be an integer")
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14 the_parser.add_argument(
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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15 '--maxquery', type=int,
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16 help="Maximum readsize of query reads (nt) - must be an integer")
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17 the_parser.add_argument(
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18 '--mintarget', type=int,
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19 help="Minimum readsize of target reads (nt) - must be an integer")
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20 the_parser.add_argument(
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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21 '--maxtarget', type=int,
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22 help="Maximum readsize of target reads (nt) - must be an integer")
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23 the_parser.add_argument(
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24 '--overlap', type=int,
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25 help="Overlap analyzed (nt) - must be an integer")
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26 the_parser.add_argument(
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27 '--output', action="store", type=str,
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28 help="Pairable sequences")
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29 args = the_parser.parse_args()
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30 return args
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33 class Map:
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35 def __init__(self, bam_file, output, minquery=23, maxquery=29,
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36 mintarget=23, maxtarget=29, overlap=10):
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37 self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
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38 self.output = output
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39 self.query_range = range(minquery, maxquery + 1)
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40 self.target_range = range(mintarget, maxtarget + 1)
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41 self.overlap = overlap
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42 self.chromosomes = dict(zip(self.bam_object.references,
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43 self.bam_object.lengths))
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44 self.alignement_dic = self.index_alignments(self.bam_object)
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45 self.all_query_positions = self.query_positions(self.bam_object,
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46 overlap=self.overlap)
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47 self.readdic = self.make_readdic(self.bam_object)
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48 self.pairing()
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49
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50 def make_readdic(self, bam_object):
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51 readdic = defaultdict(int)
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52 for read in bam_object.fetch():
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53 readdic[read.query_sequence] += 1
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54 return readdic
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55
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56 def index_alignments(self, bam_object):
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57 '''
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58 dic[(chrom, pos, polarity)]: [readseq1, readseq2, ...]
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59 the list value is further converted in set
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60 '''
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61 dic = defaultdict(list)
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62 for chrom in self.chromosomes:
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63 for read in bam_object.fetch(chrom):
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64 if read.is_reverse:
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65 coord = read.reference_end-1
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66 pol = 'R'
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67 else:
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68 coord = read.reference_start
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69 pol = 'F'
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70 dic[(chrom, coord, pol)].append(read.query_sequence)
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71 for key in dic:
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72 dic[key] = set(dic[key])
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73 return dic
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74
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75 def query_positions(self, bam_object, overlap):
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76 all_query_positions = defaultdict(list)
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77 for genomicKey in list(self.alignement_dic):
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78 chrom, coord, pol = genomicKey
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79 if pol == 'F' and len(self.alignement_dic[(chrom,
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80 coord+overlap-1,
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81 'R')]) > 0:
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82 all_query_positions[chrom].append(coord)
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83 for chrom in all_query_positions:
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84 all_query_positions[chrom] = sorted(
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85 list(set(all_query_positions[chrom])))
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86 return all_query_positions
1
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87
6
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88 def countpairs(self, uppers, lowers):
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89 query_range = self.query_range
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90 target_range = self.target_range
7
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91 uppers = [seq for seq in uppers if (len(seq) in query_range or len(seq)
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92 in target_range)]
6
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93 uppers_expanded = []
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94 for seq in uppers:
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95 expand = [seq for i in range(self.readdic[seq])]
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96 uppers_expanded.extend(expand)
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97 uppers = uppers_expanded
7
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98 lowers = [seq for seq in lowers if (len(seq) in query_range or len(seq)
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99 in target_range)]
6
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100 lowers_expanded = []
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101 for seq in lowers:
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102 expand = [seq for i in range(self.readdic[seq])]
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103 lowers_expanded.extend(expand)
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104 lowers = lowers_expanded
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105 paired = []
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106 for upread in uppers:
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107 for downread in lowers:
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108 if (len(upread) in query_range and len(downread) in
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109 target_range) or (len(upread) in target_range and
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diff changeset
110 len(downread) in query_range):
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111 paired.append(upread)
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112 lowers.remove(downread)
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113 break
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114 return len(paired)
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115
5
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116 def pairing(self):
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117 F = open(self.output, 'w')
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118 query_range = self.query_range
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119 target_range = self.target_range
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120 overlap = self.overlap
3
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121 stringresult = []
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122 header_template = '>%s|coord=%s|strand %s|size=%s|nreads=%s\n%s\n'
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123 total_pairs = 0
3
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124 for chrom in sorted(self.chromosomes):
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125 number_pairs = 0
5
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126 for pos in self.all_query_positions[chrom]:
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127 stringbuffer = []
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128 uppers = self.alignement_dic[chrom, pos, 'F']
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129 lowers = self.alignement_dic[chrom, pos+overlap-1, 'R']
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130 number_pairs += self.countpairs(uppers, lowers)
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131 total_pairs += number_pairs
5
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132 if uppers and lowers:
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133 for upread in uppers:
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134 for downread in lowers:
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135 if (len(upread) in query_range and len(downread) in
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diff changeset
136 target_range) or (len(upread) in target_range
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137 and len(downread) in
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138 query_range):
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139 stringbuffer.append(
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140 header_template %
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141 (chrom, pos+1, '+', len(upread),
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142 self.readdic[upread], upread))
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143 stringbuffer.append(
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144 header_template %
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145 (chrom, pos+overlap-len(downread)+1, '-',
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146 len(downread), self.readdic[downread],
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147 self.revcomp(downread)))
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148 stringresult.extend(sorted(set(stringbuffer)))
3
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149 F.write(''.join(stringresult))
1
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150
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151 def revcomp(self, sequence):
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152 antidict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"}
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153 revseq = sequence[::-1]
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154 return "".join([antidict[i] for i in revseq])
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155
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156
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157 if __name__ == "__main__":
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158 args = Parser()
5
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159 mapobj = Map(args.input, args.output, args.minquery, args.maxquery,
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160 args.mintarget, args.maxtarget, args.overlap)