Mercurial > repos > jjohnson > ensembl_variant_report

annotate ensemblref.py @ 4:7fc91849ab21 draft default tip

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 4078a495c5569e9055b4eba33004fe609ee42aff"
author jjohnson
date Sat, 25 Jan 2020 15:22:46 -0500
parents 9f4ea174ce3d
children
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9f4ea174ce3d planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit e6aa05bbbee3cc7d98f16354fc41c674f439ff1b-dirty
jjohnson
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1 """
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jjohnson
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2 with gtf and twobit
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jjohnson
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3 get_bed(transcript_id)
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jjohnson
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4 """
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jjohnson
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5 from gtf_to_genes import gene, gene_utilities
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jjohnson
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6 from twobitreader import TwoBitFile
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jjohnson
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7 from Bio.Seq import reverse_complement, translate
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8 import logging
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9 logger = logging.getLogger("test")
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10
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11 class EnsemblRef(object):
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12
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13 def __init__(self,gtf_file,twobitfile,read_now=True):
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14 self.gtf_file = gtf_file
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15 self.twobitfile = twobitfile
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16 self.twobit = TwoBitFile(self.twobitfile)
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17 self.gene_dict = None
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18 self.transcript_idx = None
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19 self.name_idx = None
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20 if read_now:
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21 self.get_transcript_idx()
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22
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23
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24 def get_gene_dict(self):
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25 if self.gene_dict is None:
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26 gene_structures = gene.t_parse_gtf('test')
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27 self.gene_dict = gene_structures.get_genes(self.gtf_file,logger=logger)
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28 return self.gene_dict
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30
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31 def get_transcript_idx(self):
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32 if self.transcript_idx is None:
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33 self.transcript_idx = gene_utilities.index_transcripts(self.get_gene_dict(),by_prot_id=False)
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34 return self.transcript_idx
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35
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36
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37 def get_name_idx(self):
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38 if self.name_idx is None:
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39 self.name_idx = dict()
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40 for i,t in self.get_transcript_idx().items():
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41 for name in t.gene.names:
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42 self.name_idx[name] = t.gene
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43 for name in t.names:
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44 self.name_idx[name] = t
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45 if t.prot_id:
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46 self.name_idx[t.prot_id] = t
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47 return self.name_idx
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48
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49
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50 def get_gtf_transcript(self,name):
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51 idx = self.get_transcript_idx()
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52 if name in idx:
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53 return idx[name]
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54 else:
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55 nidx = self.get_name_idx()
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56 if name in nidx:
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57 return nidx[name]
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58 return None
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59
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60
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61 def transcript_is_coding(self,transcript_id):
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62 tx = self.get_transcript_idx()[transcript_id]
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63 return len(tx.start_codons) > 0
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64
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65
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66 def get_transcript_start_codon(self,transcript_id):
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67 tx = self.get_transcript_idx()[transcript_id]
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68 return tx.start_codons[0] if len(tx.start_codons) > 0 else None
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69
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70
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71 def get_bed_line(self,transcript_id,score=0,itemRgb='0,0,0',coding=False):
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72 tx = self.get_transcript_idx()[transcript_id]
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73 chrom = tx.gene.contig
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74 chromStart = tx.coding_beg if coding else tx.beg
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75 chromEnd = tx.coding_end if coding else tx.end
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76 name = transcript_id
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77 strand = '+' if tx.gene.strand else '-'
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78 thickStart = tx.coding_beg if tx.coding_beg else chromStart
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79 thickEnd = tx.coding_end if tx.coding_end else chromEnd
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80 exons = tx.get_coding_exons() if coding else tx.get_exons()
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81 blockCount = len(exons)
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82 if tx.gene.strand:
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83 strand = '+'
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84 blockSizes = [abs(e-s) for s,e in exons]
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85 blockStarts = [s - chromStart for s,e in exons]
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86 else:
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87 strand = '-'
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jjohnson
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diff changeset
88 blockSizes = [abs(e-s) for s,e in reversed(exons)]
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jjohnson
parents:
diff changeset
89 blockStarts = [s - chromStart for s,e in reversed(exons)]
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jjohnson
parents:
diff changeset
90 blockSizes = ','.join([str(x) for x in blockSizes])
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jjohnson
parents:
diff changeset
91 blockStarts = ','.join([str(x) for x in blockStarts])
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jjohnson
parents:
diff changeset
92 return '%s\t%d\t%d\t%s\t%s\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts)
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jjohnson
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93
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jjohnson
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94
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jjohnson
parents:
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95 def transcripts_in_range(self,chrom,startpos,endpos,strand=None):
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jjohnson
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diff changeset
96 spos = min(startpos,endpos) if endpos else startpos
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jjohnson
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97 epos = max(startpos,endpos) if endpos else startpos
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jjohnson
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98 transcripts = []
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jjohnson
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99 for i,t in self.get_transcript_idx().items():
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jjohnson
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100 if t.gene.contig == chrom and t.beg <= epos and spos <= t.end:
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jjohnson
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101 if strand and t.gene.strand != strand:
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jjohnson
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102 continue
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jjohnson
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103 transcripts.append(t)
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jjohnson
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104 return transcripts
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jjohnson
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105
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106
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jjohnson
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107 def genes_in_range(self,chrom,startpos,endpos,strand=None,gene_types=None):
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108 spos = min(startpos,endpos) if endpos else startpos
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jjohnson
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109 epos = max(startpos,endpos) if endpos else startpos
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jjohnson
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110 gene_dict = self.get_gene_dict()
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jjohnson
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111 gtypes = set(gene_types) & set(gene_dict.keys()) if gene_types else set(gene_dict.keys())
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jjohnson
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112 genes = []
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jjohnson
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113 for gt in gtypes:
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114 for gene in gene_dict[gt]:
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jjohnson
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115 if gene.contig == chrom and gene.beg <= epos and spos <= gene.end:
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diff changeset
116 if strand and gene.strand != strand:
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jjohnson
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117 continue
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jjohnson
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118 genes.append(gene)
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jjohnson
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119 return genes
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120
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121
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jjohnson
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122 def get_sequence(self,chrom,start,end):
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jjohnson
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123 if self.twobit:
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jjohnson
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124 if chrom in self.twobit:
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jjohnson
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125 return self.twobit[chrom][start:end]
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126 contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom
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jjohnson
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127 if contig in self.twobit:
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jjohnson
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128 return self.twobit[contig][start:end]
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129 return None
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130
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131
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jjohnson
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132 def sequence_sizes(self):
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jjohnson
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133 return self.twobit.sequence_sizes()
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134
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135
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jjohnson
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136 def get_transcript_seq(self,transcript_id,coding=False):
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jjohnson
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137 tx = self.get_transcript_idx()[transcript_id]
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jjohnson
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diff changeset
138 chrom = tx.gene.contig
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jjohnson
parents:
diff changeset
139 exonbnds = tx.get_coding_exons() if coding else tx.get_exons()
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jjohnson
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140 if tx.gene.strand:
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jjohnson
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diff changeset
141 seqs = [self.get_sequence(chrom,s,e) for s,e in exonbnds]
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jjohnson
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142 else:
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jjohnson
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diff changeset
143 seqs = [reverse_complement(self.get_sequence(chrom,s,e)) for s,e in exonbnds]
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jjohnson
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144 return ''.join(seqs)
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diff changeset
145
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146
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jjohnson
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147 def get_cdna(self,transcript_id):
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jjohnson
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148 return self.get_transcript_seq(transcript_id,coding=False)
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149
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jjohnson
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150
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jjohnson
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151 def get_cds(self,transcript_id):
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jjohnson
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152 return self.get_transcript_seq(transcript_id,coding=True)
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153
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jjohnson
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154
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jjohnson
parents:
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155 def genome_to_transcript_pos(self,transcript_id,genome_pos,coding=False):
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jjohnson
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diff changeset
156 tx = self.get_transcript_idx()[transcript_id]
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jjohnson
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diff changeset
157 if not tx.beg <= genome_pos < tx.end:
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jjohnson
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158 return None
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jjohnson
parents:
diff changeset
159 exonbnds = tx.get_coding_exons() if coding else tx.get_exons()
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jjohnson
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diff changeset
160 cdna_pos = 0
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jjohnson
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diff changeset
161 if tx.gene.strand:
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jjohnson
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162 for s,e in exonbnds:
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jjohnson
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diff changeset
163 if s <= genome_pos < e:
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jjohnson
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164 cdna_pos += genome_pos - s
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jjohnson
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diff changeset
165 break
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166 else:
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jjohnson
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167 cdna_pos += e - s
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jjohnson
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168 else:
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jjohnson
parents:
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169 for s,e in exonbnds:
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jjohnson
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170 if s <= genome_pos < e:
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jjohnson
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171 cdna_pos += e - genome_pos - 1
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jjohnson
parents:
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172 break
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jjohnson
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173 else:
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jjohnson
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174 cdna_pos += e - s
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175 return cdna_pos
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176
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177
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178 def genome_to_cdna_pos(self,transcript_id,genome_pos):
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179 return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=False)
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180
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181
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182 def genome_to_cds_pos(self,transcript_id,genome_pos):
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183 return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=True)
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184
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185