Mercurial > repos > artbio > small_rna_signatures

annotate overlapping_reads.py @ 12:aa5e2c64dff8 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6806c0677e53d52164707faeb36947987f5c500a
author artbio
date Sat, 22 Oct 2022 23:49:52 +0000
parents 8d3ca9652a5b
children 124f404b0fe7
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6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
artbio
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1 import argparse
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
artbio
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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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6
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():
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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8 the_parser = argparse.ArgumentParser()
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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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")
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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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")
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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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,
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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16 help="Maximum readsize of query reads (nt) - must be an integer")
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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17 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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18 '--mintarget', 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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19 help="Minimum readsize of target reads (nt) - must be an integer")
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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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,
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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22 help="Maximum readsize of target reads (nt) - must be an integer")
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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23 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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24 '--overlap', 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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25 help="Overlap analyzed (nt) - must be an integer")
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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26 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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27 '--output', action="store", type=str,
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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28 help="Pairable sequences")
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29 args = the_parser.parse_args()
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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30 return args
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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33 class Map:
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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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):
1
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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)
a7fd04208764 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 24d44a9b7ec9db4dce3d839b597eea2b1be34adb
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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,
6f1378738798 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 6133bb114c76a795fa12a4a11edb1a8b80fd104d
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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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artbio
parents: 1
diff changeset
86 return all_query_positions
1
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artbio
parents:
diff changeset
87
6
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artbio
parents: 5
diff changeset
88 def countpairs(self, uppers, lowers):
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artbio
parents: 5
diff changeset
89 query_range = self.query_range
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artbio
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diff changeset
90 target_range = self.target_range
7
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artbio
parents: 6
diff changeset
91 uppers = [seq for seq in uppers if (len(seq) in query_range or len(seq)
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artbio
parents: 6
diff changeset
92 in target_range)]
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artbio
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diff changeset
93 print(uppers)
6
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artbio
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diff changeset
94 uppers_expanded = []
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artbio
parents: 5
diff changeset
95 for seq in uppers:
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artbio
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diff changeset
96 expand = [seq for i in range(self.readdic[seq])]
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artbio
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diff changeset
97 uppers_expanded.extend(expand)
7
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diff changeset
98 print(uppers_expanded)
6
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diff changeset
99 uppers = uppers_expanded
7
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artbio
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diff changeset
100 lowers = [seq for seq in lowers if (len(seq) in query_range or len(seq)
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artbio
parents: 6
diff changeset
101 in target_range)]
6
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diff changeset
102 lowers_expanded = []
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artbio
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diff changeset
103 for seq in lowers:
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artbio
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diff changeset
104 expand = [seq for i in range(self.readdic[seq])]
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artbio
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diff changeset
105 lowers_expanded.extend(expand)
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artbio
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diff changeset
106 lowers = lowers_expanded
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artbio
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diff changeset
107 paired = []
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artbio
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diff changeset
108 for upread in uppers:
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artbio
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diff changeset
109 for downread in lowers:
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artbio
parents: 5
diff changeset
110 if (len(upread) in query_range and len(downread) in
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artbio
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diff changeset
111 target_range) or (len(upread) in target_range and
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artbio
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diff changeset
112 len(downread) in query_range):
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diff changeset
113 paired.append(upread)
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artbio
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diff changeset
114 lowers.remove(downread)
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artbio
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diff changeset
115 break
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116 return len(paired)
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diff changeset
117
5
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diff changeset
118 def pairing(self):
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119 F = open(self.output, 'w')
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120 query_range = self.query_range
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121 target_range = self.target_range
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122 overlap = self.overlap
3
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123 stringresult = []
5
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124 header_template = '>%s|coord=%s|strand %s|size=%s|nreads=%s\n%s\n'
6
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125 total_pairs = 0
7
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126 print('Chromosome\tNbre of pairs')
3
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127 for chrom in sorted(self.chromosomes):
6
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128 number_pairs = 0
5
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129 for pos in self.all_query_positions[chrom]:
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130 stringbuffer = []
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131 uppers = self.alignement_dic[chrom, pos, 'F']
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132 lowers = self.alignement_dic[chrom, pos+overlap-1, 'R']
6
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133 number_pairs += self.countpairs(uppers, lowers)
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134 total_pairs += number_pairs
5
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diff changeset
135 if uppers and lowers:
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diff changeset
136 for upread in uppers:
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diff changeset
137 for downread in lowers:
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diff changeset
138 if (len(upread) in query_range and len(downread) in
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diff changeset
139 target_range) or (len(upread) in target_range
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diff changeset
140 and len(downread) in
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diff changeset
141 query_range):
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142 stringbuffer.append(
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diff changeset
143 header_template %
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144 (chrom, pos+1, '+', len(upread),
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diff changeset
145 self.readdic[upread], upread))
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diff changeset
146 stringbuffer.append(
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diff changeset
147 header_template %
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diff changeset
148 (chrom, pos+overlap-len(downread)+1, '-',
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diff changeset
149 len(downread), self.readdic[downread],
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diff changeset
150 self.revcomp(downread)))
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diff changeset
151 stringresult.extend(sorted(set(stringbuffer)))
6
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152 print('%s\t%s' % (chrom, number_pairs))
7
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diff changeset
153 print('Total nbre of pairs that can be simultaneously formed\t%s'
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diff changeset
154 % total_pairs)
3
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diff changeset
155 F.write(''.join(stringresult))
1
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diff changeset
156
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diff changeset
157 def revcomp(self, sequence):
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diff changeset
158 antidict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"}
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diff changeset
159 revseq = sequence[::-1]
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diff changeset
160 return "".join([antidict[i] for i in revseq])
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diff changeset
161
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diff changeset
162
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163 if __name__ == "__main__":
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diff changeset
164 args = Parser()
5
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diff changeset
165 mapobj = Map(args.input, args.output, args.minquery, args.maxquery,
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diff changeset
166 args.mintarget, args.maxtarget, args.overlap)