Mercurial > repos > artbio > small_rna_signatures
comparison overlapping_reads.py @ 4:20d28cfdeefe draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit cfdc08418887bfe4a35588cd78d0a2b6ffa6e19e
| author | artbio |
|---|---|
| date | Fri, 08 Sep 2017 04:44:22 -0400 |
| parents | 4d9682bd3a6b |
| children | a7fd04208764 |
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| 3:4d9682bd3a6b | 4:20d28cfdeefe |
|---|---|
| 49 all_query_positions = defaultdict(list) | 49 all_query_positions = defaultdict(list) |
| 50 for chrom in self.chromosomes: | 50 for chrom in self.chromosomes: |
| 51 for read in bam_object.fetch(chrom): | 51 for read in bam_object.fetch(chrom): |
| 52 if not read.is_reverse: | 52 if not read.is_reverse: |
| 53 all_query_positions[chrom].append( | 53 all_query_positions[chrom].append( |
| 54 read.get_reference_positions(full_length=True)[0]) | 54 read.reference_start) |
| 55 else: | 55 else: |
| 56 all_query_positions[chrom].append( | 56 all_query_positions[chrom].append( |
| 57 read.get_reference_positions(full_length=True)[-1]) | 57 read.reference_end) |
| 58 all_query_positions[chrom] = sorted( | 58 all_query_positions[chrom] = sorted( |
| 59 list(set(all_query_positions[chrom]))) | 59 list(set(all_query_positions[chrom]))) |
| 60 return all_query_positions | 60 return all_query_positions |
| 61 | 61 |
| 62 def direct_pairing(self, minquery, maxquery, mintarget, maxtarget, | 62 def direct_pairing(self, minquery, maxquery, mintarget, maxtarget, |
| 75 start=pos, end=pos+overlap-1) | 75 start=pos, end=pos+overlap-1) |
| 76 iterreads_4 = self.bam_object.fetch(chrom, | 76 iterreads_4 = self.bam_object.fetch(chrom, |
| 77 start=pos, end=pos+overlap-1) | 77 start=pos, end=pos+overlap-1) |
| 78 # 1 | 78 # 1 |
| 79 for queryread in iterreads_1: | 79 for queryread in iterreads_1: |
| 80 if queryread.get_reference_positions( | 80 if queryread.reference_start == pos and \ |
| 81 full_length=True)[0] == pos and \ | |
| 82 queryread.query_alignment_length in query_range \ | 81 queryread.query_alignment_length in query_range \ |
| 83 and not queryread.is_reverse: | 82 and not queryread.is_reverse: |
| 84 for targetread in iterreads_2: | 83 for targetread in iterreads_2: |
| 85 if (targetread. | 84 if (targetread. |
| 86 get_reference_positions(full_length=True)[-1] | 85 get_reference_positions()[-1] |
| 87 == queryread.get_reference_positions( | 86 == queryread.get_reference_positions( |
| 88 full_length=True)[overlap-1] and | 87 )[overlap-1] and |
| 89 targetread.query_alignment_length in | 88 targetread.query_alignment_length in |
| 90 target_range and targetread.is_reverse): | 89 target_range and targetread.is_reverse): |
| 91 targetreadseq = self.revcomp( | 90 targetreadseq = self.revcomp( |
| 92 targetread.query_sequence) | 91 targetread.query_sequence) |
| 93 stringresult.append( | 92 stringresult.append( |
| 94 '>%s|%s|%s|%s|n=%s\n%s\n' % | 93 '>%s|%s|%s|%s|n=%s\n%s\n' % |
| 95 (chrom, queryread.get_reference_positions( | 94 (chrom, queryread.reference_start+1, |
| 96 full_length=True)[0]+1, | |
| 97 'F', queryread.query_alignment_length, | 95 'F', queryread.query_alignment_length, |
| 98 self.readdic[queryread.query_sequence], | 96 self.readdic[queryread.query_sequence], |
| 99 queryread.query_sequence)) | 97 queryread.query_sequence)) |
| 100 stringresult.append( | 98 stringresult.append( |
| 101 '>%s|%s|%s|%s|n=%s\n%s\n' % | 99 '>%s|%s|%s|%s|n=%s\n%s\n' % |
| 102 (chrom, targetread.get_reference_positions( | 100 (chrom, targetread.reference_start+1, |
| 103 full_length=True)[0]+1, | |
| 104 'R', targetread.query_alignment_length, | 101 'R', targetread.query_alignment_length, |
| 105 self.readdic[targetread.query_sequence], | 102 self.readdic[targetread.query_sequence], |
| 106 targetreadseq)) | 103 targetreadseq)) |
| 107 # 2 | 104 # 2 |
| 108 for queryread in iterreads_3: | 105 for queryread in iterreads_3: |
| 109 if queryread.get_reference_positions( | 106 if queryread.reference_end-1 == pos+overlap-1 and \ |
| 110 full_length=True)[-1] == pos+overlap-1 and \ | |
| 111 queryread.query_alignment_length in query_range \ | 107 queryread.query_alignment_length in query_range \ |
| 112 and queryread.is_reverse: | 108 and queryread.is_reverse: |
| 113 for targetread in iterreads_4: | 109 for targetread in iterreads_4: |
| 114 if (targetread. | 110 if (targetread. |
| 115 get_reference_positions(full_length=True)[0] | 111 reference_start |
| 116 == pos and targetread.query_alignment_length | 112 == pos and targetread.query_alignment_length |
| 117 in target_range and not | 113 in target_range and not |
| 118 targetread.is_reverse): | 114 targetread.is_reverse): |
| 119 queryreadseq = self.revcomp( | 115 queryreadseq = self.revcomp( |
| 120 queryread.query_sequence) | 116 queryread.query_sequence) |
| 121 targetreadseq = targetread.query_sequence | 117 targetreadseq = targetread.query_sequence |
| 122 stringresult.append( | 118 stringresult.append( |
| 123 '>%s|%s|%s|%s|n=%s\n%s\n' % | 119 '>%s|%s|%s|%s|n=%s\n%s\n' % |
| 124 (chrom, queryread.get_reference_positions( | 120 (chrom, queryread.reference_start+1, 'R', |
| 125 full_length=True)[0]+1, 'R', | |
| 126 queryread.query_alignment_length, | 121 queryread.query_alignment_length, |
| 127 self.readdic[queryread.query_sequence], | 122 self.readdic[queryread.query_sequence], |
| 128 queryreadseq)) | 123 queryreadseq)) |
| 129 stringresult.append( | 124 stringresult.append( |
| 130 '>%s|%s|%s|%s|n=%s\n%s\n' % | 125 '>%s|%s|%s|%s|n=%s\n%s\n' % |
| 131 (chrom, targetread.get_reference_positions( | 126 (chrom, targetread.reference_start+1, |
| 132 full_length=True)[0]+1, | |
| 133 'F', targetread.query_alignment_length, | 127 'F', targetread.query_alignment_length, |
| 134 self.readdic[targetread.query_sequence], | 128 self.readdic[targetread.query_sequence], |
| 135 targetreadseq)) | 129 targetreadseq)) |
| 136 stringresult = sorted(set(stringresult), | 130 stringresult = sorted(set(stringresult), |
| 137 key=lambda x: stringresult.index(x)) | 131 key=lambda x: stringresult.index(x)) |