fml_gff3togtf: GFFParser.py annotate

annotate GFFParser.py @ 11:5c6f33e20fcc default tip

requirement tag added

author	vipints <vipin@cbio.mskcc.org>
date	Fri, 24 Apr 2015 18:04:27 -0400
parents	c42c69aa81f8
children

rev	line source
10 c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	1 #!/usr/bin/env python
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	2 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	3 Extract genome annotation from a GFF (a tab delimited format for storing sequence features and annotations) file.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	4
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	5 Requirements:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	6 Numpy :- http://numpy.org/
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	7
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	8 Copyright (C)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	9
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	10 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society, Tubingen, Germany.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	11 2012-2015 Memorial Sloan Kettering Cancer Center, New York City, USA.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	12 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	13
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	14 import re
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	15 import os
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	16 import sys
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	17 import urllib
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	18 import numpy as np
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	19 import helper as utils
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	20 from collections import defaultdict
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	21
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	22 def attribute_tags(col9):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	23 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	24 Split the key-value tags from the attribute column, it takes column number 9 from GTF/GFF file
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	25
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	26 @args col9: attribute column from GFF file
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	27 @type col9: str
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	28 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	29 info = defaultdict(list)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	30 is_gff = False
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	31
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	32 if not col9:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	33 return is_gff, info
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	34
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	35 # trim the line ending semi-colon ucsc may have some white-space
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	36 col9 = col9.rstrip(';\| ')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	37 # attributes from 9th column
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	38 atbs = col9.split(" ; ")
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	39 if len(atbs) == 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	40 atbs = col9.split("; ")
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	41 if len(atbs) == 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	42 atbs = col9.split(";")
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	43 # check the GFF3 pattern which has key value pairs like:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	44 gff3_pat = re.compile("\w+=")
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	45 # sometime GTF have: gene_id uc002zkg.1;
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	46 gtf_pat = re.compile("\s?\w+\s")
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	47
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	48 key_vals = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	49
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	50 if gff3_pat.match(atbs[0]): # gff3 pattern
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	51 is_gff = True
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	52 key_vals = [at.split('=') for at in atbs]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	53 elif gtf_pat.match(atbs[0]): # gtf pattern
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	54 for at in atbs:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	55 key_vals.append(at.strip().split(" ",1))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	56 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	57 # to handle attribute column has only single value
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	58 key_vals.append(['ID', atbs[0]])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	59 # get key, val items
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	60 for item in key_vals:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	61 key, val = item
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	62 # replace the double qoutes from feature identifier
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	63 val = re.sub('"', '', val)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	64 # replace the web formating place holders to plain text format
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	65 info[key].extend([urllib.unquote(v) for v in val.split(',') if v])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	66
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	67 return is_gff, info
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	68
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	69 def spec_features_keywd(gff_parts):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	70 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	71 Specify the feature key word according to the GFF specifications
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	72
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	73 @args gff_parts: attribute field key
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	74 @type gff_parts: str
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	75 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	76 for t_id in ["transcript_id", "transcriptId", "proteinId"]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	77 try:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	78 gff_parts["info"]["Parent"] = gff_parts["info"][t_id]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	79 break
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	80 except KeyError:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	81 pass
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	82 for g_id in ["gene_id", "geneid", "geneId", "name", "gene_name", "genename"]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	83 try:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	84 gff_parts["info"]["GParent"] = gff_parts["info"][g_id]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	85 break
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	86 except KeyError:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	87 pass
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	88 ## TODO key words
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	89 for flat_name in ["Transcript", "CDS"]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	90 if gff_parts["info"].has_key(flat_name):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	91 # parents
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	92 if gff_parts['type'] in [flat_name] or re.search(r'transcript', gff_parts['type'], re.IGNORECASE):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	93 if not gff_parts['id']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	94 gff_parts['id'] = gff_parts['info'][flat_name][0]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	95 #gff_parts["info"]["ID"] = [gff_parts["id"]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	96 # children
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	97 elif gff_parts["type"] in ["intron", "exon", "three_prime_UTR",
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	98 "coding_exon", "five_prime_UTR", "CDS", "stop_codon",
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	99 "start_codon"]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	100 gff_parts["info"]["Parent"] = gff_parts["info"][flat_name]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	101 break
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	102 return gff_parts
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	103
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	104 def Parse(ga_file):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	105 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	106 Parsing GFF/GTF file based on feature relationship, it takes the input file.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	107
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	108 @args ga_file: input file name
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	109 @type ga_file: str
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	110 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	111 child_map = defaultdict(list)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	112 parent_map = dict()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	113
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	114 ga_handle = utils.open_file(ga_file)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	115
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	116 for rec in ga_handle:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	117 rec = rec.strip('\n\r')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	118
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	119 # skip empty line fasta identifier and commented line
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	120 if not rec or rec[0] in ['#', '>']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	121 continue
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	122 # skip the genome sequence
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	123 if not re.search('\t', rec):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	124 continue
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	125
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	126 parts = rec.split('\t')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	127 assert len(parts) >= 8, rec
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	128
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	129 # process the attribute column (9th column)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	130 ftype, tags = attribute_tags(parts[-1])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	131 if not tags: # skip the line if no attribute column.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	132 continue
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	133
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	134 # extract fields
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	135 if parts[1]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	136 tags["source"] = parts[1]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	137 if parts[7]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	138 tags["phase"] = parts[7]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	139
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	140 gff_info = dict()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	141 gff_info['info'] = dict(tags)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	142 gff_info["is_gff3"] = ftype
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	143 gff_info['chr'] = parts[0]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	144 gff_info['score'] = parts[5]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	145
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	146 if parts[3] and parts[4]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	147 gff_info['location'] = [int(parts[3]) ,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	148 int(parts[4])]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	149 gff_info['type'] = parts[2]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	150 gff_info['id'] = tags.get('ID', [''])[0]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	151 if parts[6] in ['?', '.']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	152 parts[6] = None
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	153 gff_info['strand'] = parts[6]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	154
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	155 # key word according to the GFF spec.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	156 # is_gff3 flag is false check this condition and get the attribute fields
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	157 if not ftype:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	158 gff_info = spec_features_keywd(gff_info)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	159
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	160 # link the feature relationships
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	161 if gff_info['info'].has_key('Parent'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	162 for p in gff_info['info']['Parent']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	163 if p == gff_info['id']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	164 gff_info['id'] = ''
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	165 break
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	166 rec_category = 'child'
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	167 elif gff_info['id']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	168 rec_category = 'parent'
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	169 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	170 rec_category = 'record'
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	171
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	172 # depends on the record category organize the features
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	173 if rec_category == 'child':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	174 for p in gff_info['info']['Parent']:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	175 # create the data structure based on source and feature id
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	176 child_map[(gff_info['chr'], gff_info['info']['source'], p)].append(
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	177 dict( type = gff_info['type'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	178 location = gff_info['location'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	179 strand = gff_info['strand'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	180 score = gff_info['score'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	181 ID = gff_info['id'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	182 gene_id = gff_info['info'].get('GParent', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	183 ))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	184 elif rec_category == 'parent':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	185 parent_map[(gff_info['chr'], gff_info['info']['source'], gff_info['id'])] = dict(
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	186 type = gff_info['type'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	187 location = gff_info['location'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	188 strand = gff_info['strand'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	189 score = gff_info['score'],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	190 name = tags.get('Name', [''])[0])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	191 elif rec_category == 'record':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	192 #TODO how to handle plain records?
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	193 c = 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	194 ga_handle.close()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	195
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	196 # depends on file type create parent feature
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	197 if not ftype:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	198 parent_map, child_map = create_missing_feature_type(parent_map, child_map)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	199
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	200 # connecting parent child relations
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	201 # essentially the parent child features are here from any type of GTF/GFF2/GFF3 file
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	202 gene_mat = format_gene_models(parent_map, child_map)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	203
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	204 return gene_mat
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	205
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	206 def format_gene_models(parent_nf_map, child_nf_map):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	207 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	208 Genarate GeneObject based on the parsed file contents
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	209
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	210 @args parent_nf_map: parent features with source and chromosome information
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	211 @type parent_nf_map: collections defaultdict
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	212 @args child_nf_map: transctipt and exon information are encoded
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	213 @type child_nf_map: collections defaultdict
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	214 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	215
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	216 g_cnt = 0
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	217 gene = np.zeros((len(parent_nf_map),), dtype = utils.init_gene())
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	218
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	219 for pkey, pdet in parent_nf_map.items():
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	220 # considering only gene features
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	221 #if not re.search(r'gene', pdet.get('type', '')):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	222 # continue
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	223
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	224 # infer the gene start and stop if not there in the
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	225 if not pdet.get('location', []):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	226 GNS, GNE = [], []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	227 # multiple number of transcripts
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	228 for L1 in child_nf_map[pkey]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	229 GNS.append(L1.get('location', [])[0])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	230 GNE.append(L1.get('location', [])[1])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	231 GNS.sort()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	232 GNE.sort()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	233 pdet['location'] = [GNS[0], GNE[-1]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	234
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	235 orient = pdet.get('strand', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	236 gene[g_cnt]['id'] = g_cnt +1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	237 gene[g_cnt]['chr'] = pkey[0]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	238 gene[g_cnt]['source'] = pkey[1]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	239 gene[g_cnt]['name'] = pkey[-1]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	240 gene[g_cnt]['start'] = pdet.get('location', [])[0]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	241 gene[g_cnt]['stop'] = pdet.get('location', [])[1]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	242 gene[g_cnt]['strand'] = orient
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	243 gene[g_cnt]['score'] = pdet.get('score','')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	244
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	245 # default value
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	246 gene[g_cnt]['is_alt_spliced'] = gene[g_cnt]['is_alt'] = 0
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	247 if len(child_nf_map[pkey]) > 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	248 gene[g_cnt]['is_alt_spliced'] = gene[g_cnt]['is_alt'] = 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	249
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	250 # complete sub-feature for all transcripts
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	251 dim = len(child_nf_map[pkey])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	252 TRS = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	253 TR_TYP = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	254 EXON = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	255 UTR5 = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	256 UTR3 = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	257 CDS = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	258 TISc = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	259 TSSc = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	260 CLV = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	261 CSTOP = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	262 TSTAT = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	263 TSCORE = np.zeros((dim,), dtype=np.object)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	264
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	265 # fetching corresponding transcripts
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	266 for xq, Lv1 in enumerate(child_nf_map[pkey]):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	267
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	268 TID = Lv1.get('ID', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	269 TRS[xq]= np.array([TID])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	270
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	271 TYPE = Lv1.get('type', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	272 TR_TYP[xq] = np.array('')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	273 TR_TYP[xq] = np.array(TYPE) if TYPE else TR_TYP[xq]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	274
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	275 orient = Lv1.get('strand', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	276 tr_score = Lv1.get('score', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	277
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	278 # fetching different sub-features
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	279 child_feat = defaultdict(list)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	280 for Lv2 in child_nf_map[(pkey[0], pkey[1], TID)]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	281 E_TYP = Lv2.get('type', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	282 child_feat[E_TYP].append(Lv2.get('location'))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	283
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	284 # make general ascending order of coordinates
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	285 if orient == '-':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	286 for etype, excod in child_feat.items():
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	287 if len(excod) > 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	288 if excod[0][0] > excod[-1][0]:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	289 excod.reverse()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	290 child_feat[etype] = excod
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	291
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	292 # make exon coordinate from cds and utr regions
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	293 if not child_feat.get('exon'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	294 if child_feat.get('CDS'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	295 exon_cod = utils.make_Exon_cod( orient,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	296 NonetoemptyList(child_feat.get('five_prime_UTR')),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	297 NonetoemptyList(child_feat.get('CDS')),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	298 NonetoemptyList(child_feat.get('three_prime_UTR')))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	299 child_feat['exon'] = exon_cod
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	300 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	301 # TODO only UTR's
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	302 # searching through keys to find a pattern describing exon feature
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	303 ex_key_pattern = [k for k in child_feat if k.endswith("exon")]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	304 if ex_key_pattern:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	305 child_feat['exon'] = child_feat[ex_key_pattern[0]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	306
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	307 # stop_codon are seperated from CDS, add the coordinates based on strand
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	308 if child_feat.get('stop_codon'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	309 if orient == '+':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	310 if child_feat.get('stop_codon')[0][0] - child_feat.get('CDS')[-1][1] == 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	311 child_feat['CDS'][-1] = [child_feat.get('CDS')[-1][0], child_feat.get('stop_codon')[0][1]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	312 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	313 child_feat['CDS'].append(child_feat.get('stop_codon')[0])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	314 elif orient == '-':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	315 if child_feat.get('CDS')[0][0] - child_feat.get('stop_codon')[0][1] == 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	316 child_feat['CDS'][0] = [child_feat.get('stop_codon')[0][0], child_feat.get('CDS')[0][1]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	317 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	318 child_feat['CDS'].insert(0, child_feat.get('stop_codon')[0])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	319
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	320 # transcript signal sites
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	321 TIS, cdsStop, TSS, cleave = [], [], [], []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	322 cds_status, exon_status, utr_status = 0, 0, 0
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	323
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	324 if child_feat.get('exon'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	325 TSS = [child_feat.get('exon')[-1][1]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	326 TSS = [child_feat.get('exon')[0][0]] if orient == '+' else TSS
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	327 cleave = [child_feat.get('exon')[0][0]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	328 cleave = [child_feat.get('exon')[-1][1]] if orient == '+' else cleave
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	329 exon_status = 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	330
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	331 if child_feat.get('CDS'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	332 if orient == '+':
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	333 TIS = [child_feat.get('CDS')[0][0]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	334 cdsStop = [child_feat.get('CDS')[-1][1]-3]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	335 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	336 TIS = [child_feat.get('CDS')[-1][1]]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	337 cdsStop = [child_feat.get('CDS')[0][0]+3]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	338 cds_status = 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	339 # cds phase calculation
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	340 child_feat['CDS'] = utils.add_CDS_phase(orient, child_feat.get('CDS'))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	341
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	342 # sub-feature status
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	343 if child_feat.get('three_prime_UTR') or child_feat.get('five_prime_UTR'):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	344 utr_status =1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	345
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	346 if utr_status == cds_status == exon_status == 1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	347 t_status = 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	348 else:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	349 t_status = 0
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	350
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	351 # add sub-feature # make array for export to different out
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	352 TSTAT[xq] = t_status
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	353 EXON[xq] = np.array(child_feat.get('exon'), np.float64)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	354 UTR5[xq] = np.array(NonetoemptyList(child_feat.get('five_prime_UTR')))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	355 UTR3[xq] = np.array(NonetoemptyList(child_feat.get('three_prime_UTR')))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	356 CDS[xq] = np.array(NonetoemptyList(child_feat.get('CDS')))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	357 TISc[xq] = np.array(TIS)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	358 CSTOP[xq] = np.array(cdsStop)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	359 TSSc[xq] = np.array(TSS)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	360 CLV[xq] = np.array(cleave)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	361 TSCORE[xq] = tr_score
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	362
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	363 # add sub-features to the parent gene feature
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	364 gene[g_cnt]['transcript_status'] = TSTAT
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	365 gene[g_cnt]['transcripts'] = TRS
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	366 gene[g_cnt]['exons'] = EXON
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	367 gene[g_cnt]['utr5_exons'] = UTR5
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	368 gene[g_cnt]['cds_exons'] = CDS
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	369 gene[g_cnt]['utr3_exons'] = UTR3
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	370 gene[g_cnt]['transcript_type'] = TR_TYP
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	371 gene[g_cnt]['tis'] = TISc
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	372 gene[g_cnt]['cdsStop'] = CSTOP
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	373 gene[g_cnt]['tss'] = TSSc
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	374 gene[g_cnt]['cleave'] = CLV
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	375 gene[g_cnt]['transcript_score'] = TSCORE
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	376
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	377 gene[g_cnt]['gene_info'] = dict( ID = pkey[-1],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	378 Name = pdet.get('name'),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	379 Source = pkey[1])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	380 # few empty fields // TODO fill this:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	381 gene[g_cnt]['anno_id'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	382 gene[g_cnt]['confgenes_id'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	383 gene[g_cnt]['alias'] = ''
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	384 gene[g_cnt]['name2'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	385 gene[g_cnt]['chr_num'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	386 gene[g_cnt]['paralogs'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	387 gene[g_cnt]['transcript_valid'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	388 gene[g_cnt]['exons_confirmed'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	389 gene[g_cnt]['tis_conf'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	390 gene[g_cnt]['tis_info'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	391 gene[g_cnt]['cdsStop_conf'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	392 gene[g_cnt]['cdsStop_info'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	393 gene[g_cnt]['tss_info'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	394 gene[g_cnt]['tss_conf'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	395 gene[g_cnt]['cleave_info'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	396 gene[g_cnt]['cleave_conf'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	397 gene[g_cnt]['polya_info'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	398 gene[g_cnt]['polya_conf'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	399 gene[g_cnt]['is_valid'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	400 gene[g_cnt]['transcript_complete'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	401 gene[g_cnt]['is_complete'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	402 gene[g_cnt]['is_correctly_gff3_referenced'] = ''
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	403 gene[g_cnt]['splicegraph'] = []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	404 g_cnt += 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	405
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	406 ## deleting empty gene records from the main array
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	407 XPFLG=0
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	408 for XP, ens in enumerate(gene):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	409 if ens[0]==0:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	410 XPFLG=1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	411 break
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	412
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	413 if XPFLG==1:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	414 XQC = range(XP, len(gene)+1)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	415 gene = np.delete(gene, XQC)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	416
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	417 return gene
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	418
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	419 def NonetoemptyList(XS):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	420 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	421 Convert a None type to empty list
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	422
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	423 @args XS: None type
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	424 @type XS: str
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	425 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	426 return [] if XS is None else XS
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	427
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	428 def create_missing_feature_type(p_feat, c_feat):
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	429 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	430 GFF/GTF file defines only child features. This function tries to create
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	431 the parent feature from the information provided in the attribute column.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	432
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	433 example:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	434 chr21 hg19_knownGene exon 9690071 9690100 0.000000 + . gene_id "uc002zkg.1"; transcript_id "uc002zkg.1";
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	435 chr21 hg19_knownGene exon 9692178 9692207 0.000000 + . gene_id "uc021wgt.1"; transcript_id "uc021wgt.1";
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	436 chr21 hg19_knownGene exon 9711935 9712038 0.000000 + . gene_id "uc011abu.2"; transcript_id "uc011abu.2";
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	437
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	438 This function gets the parsed feature annotations.
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	439
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	440 @args p_feat: Parent feature map
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	441 @type p_feat: collections defaultdict
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	442 @args c_feat: Child feature map
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	443 @type c_feat: collections defaultdict
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	444 """
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	445
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	446 child_n_map = defaultdict(list)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	447 for fid, det in c_feat.items():
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	448 # get the details from grand child
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	449 GID = STRD = SCR = None
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	450 SPOS, EPOS = [], []
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	451 TYP = dict()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	452 for gchild in det:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	453 GID = gchild.get('gene_id', [''])[0]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	454 SPOS.append(gchild.get('location', [])[0])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	455 EPOS.append(gchild.get('location', [])[1])
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	456 STRD = gchild.get('strand', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	457 SCR = gchild.get('score', '')
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	458 if gchild.get('type', '') == "gene": ## gencode GTF file has this problem
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	459 continue
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	460 TYP[gchild.get('type', '')] = 1
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	461 SPOS.sort()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	462 EPOS.sort()
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	463
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	464 # infer transcript type
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	465 transcript_type = 'transcript'
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	466 transcript_type = 'mRNA' if TYP.get('CDS', '') or TYP.get('cds', '') else transcript_type
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	467
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	468 # gene id and transcript id are same
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	469 transcript_id = fid[-1]
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	470 if GID == transcript_id:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	471 transcript_id = 'Transcript:' + str(GID)
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	472
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	473 # level -1 feature type
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	474 p_feat[(fid[0], fid[1], GID)] = dict( type = 'gene',
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	475 location = [], ## infer location based on multiple transcripts
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	476 strand = STRD,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	477 name = GID )
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	478 # level -2 feature type
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	479 child_n_map[(fid[0], fid[1], GID)].append(
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	480 dict( type = transcript_type,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	481 location = [SPOS[0], EPOS[-1]],
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	482 strand = STRD,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	483 score = SCR,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	484 ID = transcript_id,
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	485 gene_id = '' ))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	486 # reorganizing the grand child
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	487 for gchild in det:
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	488 child_n_map[(fid[0], fid[1], transcript_id)].append(
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	489 dict( type = gchild.get('type', ''),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	490 location = gchild.get('location'),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	491 strand = gchild.get('strand'),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	492 ID = gchild.get('ID'),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	493 score = gchild.get('score'),
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	494 gene_id = '' ))
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	495 return p_feat, child_n_map
c42c69aa81f8 fixed manually the upload of version 2.1.0 - deleted accidentally added files to the repo vipints <vipin@cbio.mskcc.org> parents: diff changeset	496

Mercurial > repos > vipints > fml_gff3togtf

annotate GFFParser.py @ 11:5c6f33e20fcc default tip