Mercurial > repos > jjohnson > ensembl_variant_report

annotate ensemblref.py @ 3:bfc8ceb44c5f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
author jjohnson
date Fri, 06 Jan 2017 17:40:24 -0500
parents c3a9e63e8c51
children 9e83cc05d384
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
1 """
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
2 with gtf and twobit
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
3 get_bed(transcript_id)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
4 """
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
5 from gtf_to_genes import gene, gene_utilities
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
6 from twobitreader import TwoBitFile
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
7 from Bio.Seq import reverse_complement, translate
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
8 import logging
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
9 logger = logging.getLogger("test")
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
10
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
11 class EnsemblRef(object):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
12
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
13 def __init__(self,gtf_file,twobitfile,read_now=True):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
14 self.gtf_file = gtf_file
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
15 self.twobitfile = twobitfile
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
16 self.twobit = TwoBitFile(self.twobitfile)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
17 self.gene_dict = None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
18 self.transcript_idx = None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
19 self.name_idx = None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
20 if read_now:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
21 self.get_transcript_idx()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
22
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
23
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
24 def get_gene_dict(self):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
25 if self.gene_dict is None:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
26 gene_structures = gene.t_parse_gtf('test')
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
27 self.gene_dict = gene_structures.get_genes(self.gtf_file,logger=logger)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
28 return self.gene_dict
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
29
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
30
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
31 def get_transcript_idx(self):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
32 if self.transcript_idx is None:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
33 self.transcript_idx = gene_utilities.index_transcripts(self.get_gene_dict(),by_prot_id=False)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
34 return self.transcript_idx
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
35
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
36
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
37 def get_name_idx(self):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
38 if self.name_idx is None:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
39 self.name_idx = dict()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
40 for i,t in self.get_transcript_idx().items():
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
41 for name in t.gene.names:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
42 self.name_idx[name] = t.gene
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
43 for name in t.names:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
44 self.name_idx[name] = t
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
45 if t.prot_id:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
46 self.name_idx[t.prot_id] = t
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
47 return self.name_idx
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
48
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
49
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
50 def get_gtf_transcript(self,transcript_id):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
51 idx = self.get_transcript_idx()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
52 return idx[transcript_id] if transcript_id in idx else None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
53
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
54
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
55 def transcript_is_coding(self,transcript_id):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
56 tx = self.get_transcript_idx()[transcript_id]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
57 return len(tx.start_codons) > 0
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
58
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
59
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
60 def get_transcript_start_codon(self,transcript_id):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
61 tx = self.get_transcript_idx()[transcript_id]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
62 return tx.start_codons[0] if len(tx.start_codons) > 0 else None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
63
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
64
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
65 def get_bed_line(self,transcript_id,coding=False):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
66 tx = self.get_transcript_idx()[transcript_id]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
67 chrom = tx.gene.contig
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
68 chromStart = tx.coding_beg if coding else tx.beg
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
69 chromEnd = tx.coding_end if coding else tx.end
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
70 name = transcript_id
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
71 score = 0
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
72 strand = '+' if tx.gene.strand else '-'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
73 thickStart = tx.coding_beg if tx.coding_beg else chromStart
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
74 thickEnd = tx.coding_end if tx.coding_end else chromEnd
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
75 itemRgb = '0,0,0'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
76 exons = tx.get_coding_exons() if coding else tx.get_exons()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
77 blockCount = len(exons)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
78 if tx.gene.strand:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
79 strand = '+'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
80 blockSizes = [abs(e-s) for s,e in exons]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
81
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
82 def get_bed_line(self,transcript_id,coding=False):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
83 tx = self.get_transcript_idx()[transcript_id]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
84 chrom = tx.gene.contig
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
85 chromStart = tx.coding_beg if coding else tx.beg
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
86 chromEnd = tx.coding_end if coding else tx.end
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
87 name = transcript_id
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
88 score = 0
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
89 strand = '+' if tx.gene.strand else '-'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
90 thickStart = tx.coding_beg if tx.coding_beg else chromStart
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
91 thickEnd = tx.coding_end if tx.coding_end else chromEnd
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
92 itemRgb = '0,0,0'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
93 exons = tx.get_coding_exons() if coding else tx.get_exons()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
94 blockCount = len(exons)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
95 if tx.gene.strand:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
96 strand = '+'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
97 blockSizes = [abs(e-s) for s,e in exons]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
98 blockStarts = [s - chromStart for s,e in exons]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
99 else:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
100 strand = '-'
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
101 blockSizes = [abs(e-s) for s,e in reversed(exons)]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
102 blockStarts = [s - chromStart for s,e in reversed(exons)]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
103 blockSizes = ','.join([str(x) for x in blockSizes])
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
104 blockStarts = ','.join([str(x) for x in blockStarts])
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
105 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)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
106
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
107
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
108 def transcripts_in_range(self,chrom,startpos,endpos,strand=None):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
109 spos = min(startpos,endpos) if endpos else startpos
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
110 epos = max(startpos,endpos) if endpos else startpos
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
111 transcripts = []
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
112 for i,t in self.get_transcript_idx().items():
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
113 if t.gene.contig == chrom and t.beg <= epos and spos <= t.end:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
114 if strand and t.gene.strand != strand:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
115 continue
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
116 transcripts.append(t)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
117 return transcripts
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
118
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
119
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
120 def genes_in_range(self,chrom,startpos,endpos,strand=None,gene_types=None):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
121 spos = min(startpos,endpos) if endpos else startpos
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
122 epos = max(startpos,endpos) if endpos else startpos
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
123 gene_dict = self.get_gene_dict()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
124 gtypes = set(gene_types) & set(gene_dict.keys()) if gene_types else set(gene_dict.keys())
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
125 genes = []
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
126 for gt in gtypes:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
127 for gene in gene_dict[gt]:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
128 if gene.contig == chrom and gene.beg <= epos and spos <= gene.end:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
129 if strand and gene.strand != strand:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
130 continue
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
131 genes.append(gene)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
132 return genes
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
133
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
134
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
135 def get_sequence(self,chrom,start,end):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
136 if self.twobit:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
137 if chrom in self.twobit:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
138 return self.twobit[chrom][start:end]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
139 contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
140 if contig in self.twobit:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
141 return self.twobit[contig][start:end]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
142 return None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
143
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
144
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
145 def sequence_sizes(self):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
146 return self.twobit.sequence_sizes()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
147
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
148
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
149 def get_transcript_seq(self,transcript_id,coding=False):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
150 tx = self.get_transcript_idx()[transcript_id]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
151 chrom = tx.gene.contig
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
152 exonbnds = tx.get_coding_exons() if coding else tx.get_exons()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
153 if tx.gene.strand:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
154 seqs = [self.get_sequence(chrom,s,e) for s,e in exonbnds]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
155 else:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
156 seqs = [reverse_complement(self.get_sequence(chrom,s,e)) for s,e in exonbnds]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
157 return ''.join(seqs)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
158
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
159
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
160 def get_cdna(self,transcript_id):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
161 return self.get_transcript_seq(transcript_id,coding=False)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
162
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
163
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
164 def get_cds(self,transcript_id):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
165 return self.get_transcript_seq(transcript_id,coding=True)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
166
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
167
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
168 def genome_to_transcript_pos(self,transcript_id,genome_pos,coding=False):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
169 tx = self.get_transcript_idx()[transcript_id]
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
170 if not tx.beg <= genome_pos < tx.end:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
171 return None
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
172 exonbnds = tx.get_coding_exons() if coding else tx.get_exons()
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
173 cdna_pos = 0
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
174 if tx.gene.strand:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
175 for s,e in exonbnds:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
176 if s <= genome_pos < e:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
177 cdna_pos += genome_pos - s
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
178 break
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
179 else:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
180 cdna_pos += e - s
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
181 else:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
182 for s,e in exonbnds:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
183 if s <= genome_pos < e:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
184 cdna_pos += e - genome_pos - 1
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
185 break
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
186 else:
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
187 cdna_pos += e - s
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
188 return cdna_pos
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
189
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
190
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
191 def genome_to_cdna_pos(self,transcript_id,genome_pos):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
192 return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=False)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
193
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
194
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
195 def genome_to_cds_pos(self,transcript_id,genome_pos):
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
196 return self.genome_to_transcript_pos(transcript_id,genome_pos,coding=True)
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
197
c3a9e63e8c51 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
jjohnson
parents:
diff changeset
198