Mercurial > repos > artbio > small_rna_signatures
comparison overlapping_reads.py @ 7:07771982ef9b draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit 7276b6b73aef7af4058ad2c1e34c4557e9cccbe0
author | artbio |
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date | Sun, 10 Sep 2017 13:50:40 -0400 |
parents | 4da23f009c9e |
children | 8d3ca9652a5b |
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6:4da23f009c9e | 7:07771982ef9b |
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86 return all_query_positions | 86 return all_query_positions |
87 | 87 |
88 def countpairs(self, uppers, lowers): | 88 def countpairs(self, uppers, lowers): |
89 query_range = self.query_range | 89 query_range = self.query_range |
90 target_range = self.target_range | 90 target_range = self.target_range |
91 uppers = [seq for seq in uppers if (len(seq) in query_range or len(seq) in target_range)] | 91 uppers = [seq for seq in uppers if (len(seq) in query_range or len(seq) |
92 in target_range)] | |
93 print(uppers) | |
92 uppers_expanded = [] | 94 uppers_expanded = [] |
93 for seq in uppers: | 95 for seq in uppers: |
94 expand = [seq for i in range(self.readdic[seq])] | 96 expand = [seq for i in range(self.readdic[seq])] |
95 uppers_expanded.extend(expand) | 97 uppers_expanded.extend(expand) |
98 print(uppers_expanded) | |
96 uppers = uppers_expanded | 99 uppers = uppers_expanded |
97 lowers = [seq for seq in lowers if (len(seq) in query_range or len(seq) in target_range)] | 100 lowers = [seq for seq in lowers if (len(seq) in query_range or len(seq) |
101 in target_range)] | |
98 lowers_expanded = [] | 102 lowers_expanded = [] |
99 for seq in lowers: | 103 for seq in lowers: |
100 expand = [seq for i in range(self.readdic[seq])] | 104 expand = [seq for i in range(self.readdic[seq])] |
101 lowers_expanded.extend(expand) | 105 lowers_expanded.extend(expand) |
102 lowers = lowers_expanded | 106 lowers = lowers_expanded |
117 target_range = self.target_range | 121 target_range = self.target_range |
118 overlap = self.overlap | 122 overlap = self.overlap |
119 stringresult = [] | 123 stringresult = [] |
120 header_template = '>%s|coord=%s|strand %s|size=%s|nreads=%s\n%s\n' | 124 header_template = '>%s|coord=%s|strand %s|size=%s|nreads=%s\n%s\n' |
121 total_pairs = 0 | 125 total_pairs = 0 |
122 print ('Chromosome\tNbre of pairs') | 126 print('Chromosome\tNbre of pairs') |
123 for chrom in sorted(self.chromosomes): | 127 for chrom in sorted(self.chromosomes): |
124 number_pairs = 0 | 128 number_pairs = 0 |
125 for pos in self.all_query_positions[chrom]: | 129 for pos in self.all_query_positions[chrom]: |
126 stringbuffer = [] | 130 stringbuffer = [] |
127 uppers = self.alignement_dic[chrom, pos, 'F'] | 131 uppers = self.alignement_dic[chrom, pos, 'F'] |
144 (chrom, pos+overlap-len(downread)+1, '-', | 148 (chrom, pos+overlap-len(downread)+1, '-', |
145 len(downread), self.readdic[downread], | 149 len(downread), self.readdic[downread], |
146 self.revcomp(downread))) | 150 self.revcomp(downread))) |
147 stringresult.extend(sorted(set(stringbuffer))) | 151 stringresult.extend(sorted(set(stringbuffer))) |
148 print('%s\t%s' % (chrom, number_pairs)) | 152 print('%s\t%s' % (chrom, number_pairs)) |
149 print('Total nbre of pairs that can be simultaneously formed\t%s' % total_pairs) | 153 print('Total nbre of pairs that can be simultaneously formed\t%s' |
154 % total_pairs) | |
150 F.write(''.join(stringresult)) | 155 F.write(''.join(stringresult)) |
151 | 156 |
152 def revcomp(self, sequence): | 157 def revcomp(self, sequence): |
153 antidict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"} | 158 antidict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"} |
154 revseq = sequence[::-1] | 159 revseq = sequence[::-1] |