fml_gff3togtf: helper.py annotate

annotate helper.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 Common utility functions
c42c69aa81f8 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
c42c69aa81f8 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 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	7 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	8 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	9 import gzip
c42c69aa81f8 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 import bz2
c42c69aa81f8 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 import numpy
c42c69aa81f8 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 def 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	14 """
c42c69aa81f8 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 Initializing the gene structure
c42c69aa81f8 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 """
c42c69aa81f8 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
c42c69aa81f8 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 gene_det = [('id', 'f8'),
c42c69aa81f8 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 ('anno_id', numpy.dtype),
c42c69aa81f8 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 ('confgenes_id', numpy.dtype),
c42c69aa81f8 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 ('name', 'S25'),
c42c69aa81f8 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 ('source', 'S25'),
c42c69aa81f8 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 ('gene_info', numpy.dtype),
c42c69aa81f8 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 ('alias', 'S15'),
c42c69aa81f8 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 ('name2', numpy.dtype),
c42c69aa81f8 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 ('strand', 'S2'),
c42c69aa81f8 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 ('score', 'S15'),
c42c69aa81f8 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 ('chr', 'S15'),
c42c69aa81f8 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 ('chr_num', numpy.dtype),
c42c69aa81f8 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 ('paralogs', numpy.dtype),
c42c69aa81f8 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 ('start', 'f8'),
c42c69aa81f8 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 ('stop', 'f8'),
c42c69aa81f8 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 ('transcripts', numpy.dtype),
c42c69aa81f8 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 ('transcript_type', numpy.dtype),
c42c69aa81f8 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 ('transcript_info', numpy.dtype),
c42c69aa81f8 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 ('transcript_score', numpy.dtype),
c42c69aa81f8 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 ('transcript_status', numpy.dtype),
c42c69aa81f8 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 ('transcript_valid', numpy.dtype),
c42c69aa81f8 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 ('exons', numpy.dtype),
c42c69aa81f8 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 ('exons_confirmed', numpy.dtype),
c42c69aa81f8 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 ('cds_exons', numpy.dtype),
c42c69aa81f8 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 ('utr5_exons', numpy.dtype),
c42c69aa81f8 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 ('utr3_exons', numpy.dtype),
c42c69aa81f8 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 ('tis', numpy.dtype),
c42c69aa81f8 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 ('tis_conf', numpy.dtype),
c42c69aa81f8 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 ('tis_info', numpy.dtype),
c42c69aa81f8 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 ('cdsStop', numpy.dtype),
c42c69aa81f8 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 ('cdsStop_conf', numpy.dtype),
c42c69aa81f8 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 ('cdsStop_info', numpy.dtype),
c42c69aa81f8 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 ('tss', numpy.dtype),
c42c69aa81f8 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 ('tss_info', numpy.dtype),
c42c69aa81f8 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 ('tss_conf', numpy.dtype),
c42c69aa81f8 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 ('cleave', numpy.dtype),
c42c69aa81f8 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 ('cleave_info', numpy.dtype),
c42c69aa81f8 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 ('cleave_conf', numpy.dtype),
c42c69aa81f8 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 ('polya', numpy.dtype),
c42c69aa81f8 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 ('polya_info', numpy.dtype),
c42c69aa81f8 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 ('polya_conf', numpy.dtype),
c42c69aa81f8 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 ('is_alt', 'f8'),
c42c69aa81f8 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 ('is_alt_spliced', 'f8'),
c42c69aa81f8 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 ('is_valid', numpy.dtype),
c42c69aa81f8 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 ('transcript_complete', numpy.dtype),
c42c69aa81f8 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 ('is_complete', numpy.dtype),
c42c69aa81f8 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 ('is_correctly_gff3_referenced', 'S5'),
c42c69aa81f8 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 ('splicegraph', numpy.dtype) ]
c42c69aa81f8 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 gene_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	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 open_file(fname):
c42c69aa81f8 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 Open the file (supports .gz .bz2) and returns the handler
c42c69aa81f8 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 fname: input file name for reading
c42c69aa81f8 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 fname: 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
c42c69aa81f8 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 if os.path.splitext(fname)[1] == ".gz":
c42c69aa81f8 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 FH = gzip.open(fname, 'rb')
c42c69aa81f8 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 elif os.path.splitext(fname)[1] == ".bz2":
c42c69aa81f8 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 FH = bz2.BZ2File(fname, 'rb')
c42c69aa81f8 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 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	83 FH = open(fname, 'rU')
c42c69aa81f8 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 except Exception as error:
c42c69aa81f8 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 sys.exit(error)
c42c69aa81f8 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
c42c69aa81f8 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 return FH
c42c69aa81f8 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
c42c69aa81f8 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 def add_CDS_phase(strand, 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 """
c42c69aa81f8 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 Calculate CDS phase and add to the CDS exons
c42c69aa81f8 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
c42c69aa81f8 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 @args strand: feature strand 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	94 @type 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	95 @args cds: coding exon 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	96 @type cds: numpy array [[int, int, int]]
c42c69aa81f8 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 """
c42c69aa81f8 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
c42c69aa81f8 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 cds_region, cds_flag = [], 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	100 if 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	101 for cdspos in 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	102 if cds_flag == 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	103 cdspos = (cdspos[0], cdspos[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	104 diff = (cdspos[1]-(cdspos[0]-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	105 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	106 xy = 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	107 if diff == 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	108 cdspos = (cdspos[0], cdspos[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	109 elif diff == 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	110 cdspos = (cdspos[0], cdspos[1], 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	111 xy = 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	112 elif diff == 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	113 cdspos = (cdspos[0], cdspos[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	114 xy = 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	115 diff = ((cdspos[1]-(cdspos[0]-1))-xy)%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	116 cds_region.append(cdspos)
c42c69aa81f8 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 cds_flag = 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	118 elif 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	119 cds.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	120 for cdspos in 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	121 if cds_flag == 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	122 cdspos = (cdspos[0], cdspos[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	123 diff = (cdspos[1]-(cdspos[0]-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	124 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	125 xy = 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	126 if diff == 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	127 cdspos = (cdspos[0], cdspos[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	128 elif diff == 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	129 cdspos = (cdspos[0], cdspos[1], 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	130 xy = 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	131 elif diff == 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	132 cdspos = (cdspos[0], cdspos[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	133 xy = 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	134 diff = ((cdspos[1]-(cdspos[0]-1))-xy)%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	135 cds_region.append(cdspos)
c42c69aa81f8 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 cds_flag = 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 cds_region.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	138 return cds_region
c42c69aa81f8 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 def buildUTR(cc, ec, 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	141 """
c42c69aa81f8 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 Build UTR regions from a given set of CDS and exon coordiantes of a 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	143
c42c69aa81f8 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 @args cc: coding exon 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	145 @type cc: numpy array [[int, int, int]]
c42c69aa81f8 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 @args ec: exon 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	147 @type ec: numpy array [[int, int]]
c42c69aa81f8 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 @args strand: feature strand 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	149 @type 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	150 """
c42c69aa81f8 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
c42c69aa81f8 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 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	153 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	154 if 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	155 cds_s = cc[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	156 for ex in ec:
c42c69aa81f8 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 ex[0] <= cds_s and cds_s <= ex[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	158 if ex[0] != cds_s:utr5.append((ex[0], cds_s-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	159 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	160 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	161 utr5.append(ex)
c42c69aa81f8 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 cds_e = cc[-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	163 for i in range(len(ec)):
c42c69aa81f8 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 i += 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	165 if ec[-i][0] <= cds_e and cds_e <= ec[-i][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	166 if ec[-i][1] != cds_e:utr3.append((cds_e +1, ec[-i][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	167 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	168 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	169 utr3.append(ec[-i])
c42c69aa81f8 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 utr3.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	171 elif 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	172 cds_s = cc[-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	173 for i in range(len(ec)):
c42c69aa81f8 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 i += 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	175 if ec[-i][0] <= cds_s and cds_s <= ec[-i][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	176 if ec[-i][1] != cds_s:utr5.append((cds_s+1, ec[-i][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	177 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	178 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	179 utr5.append(ec[-i])
c42c69aa81f8 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 utr5.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	181 cds_e = cc[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	182 for ex in ec:
c42c69aa81f8 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 if ex[0] <= cds_e and cds_e <= ex[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	184 if ex[0] != cds_e:utr3.append((ex[0], cds_e-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	185 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	186 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	187 utr3.append(ex)
c42c69aa81f8 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 return utr5, 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	189
c42c69aa81f8 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 def make_Exon_cod(strand_p, five_p_utr, cds_cod, three_p_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	191 """
c42c69aa81f8 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 Create exon cordinates from UTR's and CDS region
c42c69aa81f8 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
c42c69aa81f8 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 @args strand_p: feature strand 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	195 @type strand_p: +/-
c42c69aa81f8 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 @args five_p_utr: five prime utr exon 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	197 @type five_p_utr: numpy array [[int, int]]
c42c69aa81f8 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 @args cds_cod: coding exon 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	199 @type cds_cod: numpy array [[int, int, int]]
c42c69aa81f8 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 @args three_p_utr: three prime utr exon 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	201 @type three_p_utr: numpy array [[int, int]]
c42c69aa81f8 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 """
c42c69aa81f8 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 exon_pos = []
c42c69aa81f8 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 if strand_p == '+':
c42c69aa81f8 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 utr5_start, utr5_end = 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	207 if five_p_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	208 utr5_start, utr5_end = five_p_utr[-1][0], five_p_utr[-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	209 cds_5start, cds_5end = cds_cod[0][0], cds_cod[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	210 jun_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	211 if cds_5start-utr5_end == 0 or cds_5start-utr5_end == 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	212 jun_exon = [utr5_start, cds_5end]
c42c69aa81f8 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 if len(cds_cod) == 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	214 five_prime_flag = 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	215 if jun_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	216 five_p_utr = five_p_utr[:-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	217 five_prime_flag = 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	218 for utr5 in five_p_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	219 exon_pos.append(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	220 jun_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	221 utr3_start, utr3_end = 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	222 if three_p_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	223 utr3_start = three_p_utr[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	224 utr3_end = three_p_utr[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	225 if utr3_start-cds_5end == 0 or utr3_start-cds_5end == 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	226 jun_exon = [cds_5start, utr3_end]
c42c69aa81f8 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 three_prime_flag = 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	228 if jun_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	229 cds_cod = cds_cod[:-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	230 three_p_utr = three_p_utr[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 three_prime_flag = 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	232 if five_prime_flag == 1 and three_prime_flag == 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	233 exon_pos.append([utr5_start, utr3_end])
c42c69aa81f8 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 if five_prime_flag == 1 and three_prime_flag == 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	235 exon_pos.append([utr5_start, cds_5end])
c42c69aa81f8 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 cds_cod = cds_cod[:-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 if five_prime_flag == 0 and three_prime_flag == 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	238 exon_pos.append([cds_5start, utr3_end])
c42c69aa81f8 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 for cds in cds_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	240 exon_pos.append(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	241 for utr3 in three_p_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	242 exon_pos.append(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	243 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	244 if jun_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	245 five_p_utr = five_p_utr[:-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	246 cds_cod = cds_cod[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	247 for utr5 in five_p_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	248 exon_pos.append(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	249 exon_pos.append(jun_exon) if jun_exon != [] 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	250 jun_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	251 utr3_start, utr3_end = 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	252 if three_p_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	253 utr3_start = three_p_utr[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	254 utr3_end = three_p_utr[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	255 cds_3start = cds_cod[-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	256 cds_3end = cds_cod[-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	257 if utr3_start-cds_3end == 0 or utr3_start-cds_3end == 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	258 jun_exon = [cds_3start, utr3_end]
c42c69aa81f8 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 if jun_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	260 cds_cod = cds_cod[:-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	261 three_p_utr = three_p_utr[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	262 for cds in cds_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	263 exon_pos.append(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	264 exon_pos.append(jun_exon) if jun_exon != [] 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	265 for utr3 in three_p_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	266 exon_pos.append(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	267 elif strand_p == '-':
c42c69aa81f8 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 utr3_start, utr3_end = 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	269 if three_p_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	270 utr3_start = three_p_utr[-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	271 utr3_end = three_p_utr[-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	272 cds_3start = cds_cod[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	273 cds_3end = cds_cod[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	274 jun_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	275 if cds_3start-utr3_end == 0 or cds_3start-utr3_end == 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	276 jun_exon = [utr3_start, cds_3end]
c42c69aa81f8 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 if len(cds_cod) == 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	278 three_prime_flag = 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	279 if jun_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	280 three_p_utr = three_p_utr[:-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	281 three_prime_flag = 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	282 for utr3 in three_p_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	283 exon_pos.append(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	284 jun_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	285 (utr5_start, utr5_end) = (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	286 if five_p_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	287 utr5_start = five_p_utr[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	288 utr5_end = five_p_utr[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	289 if utr5_start-cds_3end == 0 or utr5_start-cds_3end == 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	290 jun_exon = [cds_3start, utr5_end]
c42c69aa81f8 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 five_prime_flag = 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	292 if jun_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	293 cds_cod = cds_cod[:-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	294 five_p_utr = five_p_utr[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	295 five_prime_flag = 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	296 if three_prime_flag == 1 and five_prime_flag == 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	297 exon_pos.append([utr3_start, utr5_end])
c42c69aa81f8 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 if three_prime_flag == 1 and five_prime_flag == 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	299 exon_pos.append([utr3_start, cds_3end])
c42c69aa81f8 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 cds_cod = cds_cod[:-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	301 if three_prime_flag == 0 and five_prime_flag == 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	302 exon_pos.append([cds_3start, utr5_end])
c42c69aa81f8 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 for cds in cds_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	304 exon_pos.append(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	305 for utr5 in five_p_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	306 exon_pos.append(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	307 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	308 if jun_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	309 three_p_utr = three_p_utr[:-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	310 cds_cod = cds_cod[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 for utr3 in three_p_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	312 exon_pos.append(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	313 if jun_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	314 exon_pos.append(jun_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	315 jun_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	316 (utr5_start, utr5_end) = (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	317 if five_p_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	318 utr5_start = five_p_utr[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	319 utr5_end = five_p_utr[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	320 cds_5start = cds_cod[-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	321 cds_5end = cds_cod[-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	322 if utr5_start-cds_5end == 0 or utr5_start-cds_5end == 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	323 jun_exon = [cds_5start, utr5_end]
c42c69aa81f8 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 jun_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 cds_cod = cds_cod[:-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 five_p_utr = five_p_utr[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	327 for cds in cds_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	328 exon_pos.append(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	329 if jun_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	330 exon_pos.append(jun_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	331 for utr5 in five_p_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	332 exon_pos.append(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	333 return exon_pos

Mercurial > repos > vipints > fml_gff3togtf

annotate helper.py @ 11:5c6f33e20fcc default tip