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changeset 9:0c769b205d18 draft

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Deleted selected files
author brigidar
date Fri, 09 Oct 2015 11:52:37 -0400
parents 53f1f83e80a1
children 82186605ba75
files helper.py
diffstat 1 files changed, 0 insertions(+), 333 deletions(-) [+]
line wrap: on
line diff
--- a/helper.py	Fri Oct 09 11:52:31 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,333 +0,0 @@
-#!/usr/bin/env python
-"""
-Common utility functions
-"""
-
-import os 
-import re
-import sys 
-import bz2
-import gzip 
-import numpy 
-
-def init_gene():
-    """
-    Initializing the gene structure 
-    """
-
-    gene_det = [('id', 'f8'), 
-            ('anno_id', numpy.dtype), 
-            ('confgenes_id', numpy.dtype),
-            ('name', 'S25'),
-            ('source', 'S25'),
-            ('gene_info', numpy.dtype),
-            ('alias', 'S15'),
-            ('name2', numpy.dtype),
-            ('strand', 'S2'), 
-            ('score', 'S15'), 
-            ('chr', 'S15'), 
-            ('chr_num', numpy.dtype),
-            ('paralogs', numpy.dtype),
-            ('start', 'f8'),
-            ('stop', 'f8'), 
-            ('transcripts', numpy.dtype),
-            ('transcript_type', numpy.dtype),
-            ('transcript_info', numpy.dtype),
-            ('transcript_score', numpy.dtype),
-            ('transcript_status', numpy.dtype),
-            ('transcript_valid', numpy.dtype),
-            ('exons', numpy.dtype),
-            ('exons_confirmed', numpy.dtype),
-            ('cds_exons', numpy.dtype),
-            ('utr5_exons', numpy.dtype),
-            ('utr3_exons', numpy.dtype),
-            ('tis', numpy.dtype),
-            ('tis_conf', numpy.dtype),
-            ('tis_info', numpy.dtype),
-            ('cdsStop', numpy.dtype),
-            ('cdsStop_conf', numpy.dtype),
-            ('cdsStop_info', numpy.dtype),
-            ('tss', numpy.dtype),
-            ('tss_info', numpy.dtype),
-            ('tss_conf', numpy.dtype),
-            ('cleave', numpy.dtype),
-            ('cleave_info', numpy.dtype),
-            ('cleave_conf', numpy.dtype),
-            ('polya', numpy.dtype),
-            ('polya_info', numpy.dtype),
-            ('polya_conf', numpy.dtype),
-            ('is_alt', 'f8'), 
-            ('is_alt_spliced', 'f8'), 
-            ('is_valid',  numpy.dtype),
-            ('transcript_complete', numpy.dtype),
-            ('is_complete', numpy.dtype),
-            ('is_correctly_gff3_referenced', 'S5'),
-            ('splicegraph', numpy.dtype) ]
-
-    return gene_det
-
-def open_file(fname):
-    """
-    Open the file (supports .gz .bz2) and returns the handler
-
-    @args fname: input file name for reading 
-    @type fname: str
-    """
-
-    try:
-        if os.path.splitext(fname)[1] == ".gz":
-            FH = gzip.open(fname, 'rb')
-        elif os.path.splitext(fname)[1] == ".bz2":
-            FH = bz2.BZ2File(fname, 'rb')
-        else:
-            FH = open(fname, 'rU')
-    except Exception as error:
-        sys.exit(error)
-
-    return FH
-
-def add_CDS_phase(strand, cds):
-    """
-    Calculate CDS phase and add to the CDS exons
-
-    @args strand: feature strand information 
-    @type strand: +/- 
-    @args cds: coding exon coordinates 
-    @type cds: numpy array [[int, int, int]]
-    """
-
-    cds_region, cds_flag = [], 0 
-    if strand == '+':
-        for cdspos in cds:
-            if cds_flag == 0:
-                cdspos = (cdspos[0], cdspos[1], 0)
-                diff = (cdspos[1]-(cdspos[0]-1))%3
-            else:
-                xy = 0
-                if diff == 0: 
-                    cdspos = (cdspos[0], cdspos[1], 0)
-                elif diff == 1: 
-                    cdspos = (cdspos[0], cdspos[1], 2)
-                    xy = 2
-                elif diff == 2: 
-                    cdspos = (cdspos[0], cdspos[1], 1)
-                    xy = 1
-                diff = ((cdspos[1]-(cdspos[0]-1))-xy)%3
-            cds_region.append(cdspos)
-            cds_flag = 1 
-    elif strand == '-':
-        cds.reverse()
-        for cdspos in cds: 
-            if cds_flag == 0:
-                cdspos = (cdspos[0], cdspos[1], 0)
-                diff = (cdspos[1]-(cdspos[0]-1))%3
-            else:  
-                xy = 0 
-                if diff == 0: 
-                    cdspos = (cdspos[0], cdspos[1], 0)
-                elif diff == 1:
-                    cdspos = (cdspos[0], cdspos[1], 2)
-                    xy = 2
-                elif diff == 2: 
-                    cdspos = (cdspos[0], cdspos[1], 1)
-                    xy = 1
-                diff = ((cdspos[1]-(cdspos[0]-1))-xy)%3
-            cds_region.append(cdspos)
-            cds_flag = 1
-        cds_region.reverse()
-    return cds_region
-
-def buildUTR(cc, ec, strand):
-    """
-    Build UTR regions from a given set of CDS and exon coordiantes of a gene
-
-    @args cc: coding exon coordinates 
-    @type cc: numpy array [[int, int, int]]
-    @args ec: exon coordinates 
-    @type ec: numpy array [[int, int]]
-    @args strand: feature strand information 
-    @type strand: +/- 
-    """
-
-    utr5 = []
-    utr3 = []
-    if strand == '+':
-        cds_s = cc[0][0]
-        for ex in ec:
-            if ex[0] <= cds_s and cds_s <= ex[1]:
-                if ex[0] != cds_s:utr5.append((ex[0], cds_s-1))
-                break
-            else:
-                utr5.append(ex)
-        cds_e = cc[-1][1]
-        for i in range(len(ec)):
-            i += 1
-            if ec[-i][0] <= cds_e and cds_e <= ec[-i][1]:
-                if ec[-i][1] != cds_e:utr3.append((cds_e +1, ec[-i][1]))
-                break
-            else:
-                utr3.append(ec[-i]) 
-        utr3.reverse()
-    elif strand == '-':
-        cds_s = cc[-1][1]
-        for i in range(len(ec)):
-            i += 1
-            if ec[-i][0] <= cds_s and cds_s <= ec[-i][1]:
-                if ec[-i][1] != cds_s:utr5.append((cds_s+1, ec[-i][1]))
-                break
-            else:
-                utr5.append(ec[-i])
-        utr5.reverse()
-        cds_e = cc[0][0] 
-        for ex in ec:
-            if ex[0] <= cds_e and cds_e <= ex[1]:
-                if ex[0] != cds_e:utr3.append((ex[0], cds_e-1))
-                break
-            else:
-                utr3.append(ex)
-    return utr5, utr3
-
-def make_Exon_cod(strand_p, five_p_utr, cds_cod, three_p_utr):
-    """
-    Create exon cordinates from UTR's and CDS region
-
-    @args strand_p: feature strand information 
-    @type strand_p: +/- 
-    @args five_p_utr: five prime utr exon coordinates 
-    @type five_p_utr: numpy array [[int, int]]
-    @args cds_cod: coding exon coordinates 
-    @type cds_cod: numpy array [[int, int, int]]
-    @args three_p_utr: three prime utr exon coordinates 
-    @type three_p_utr: numpy array [[int, int]]
-    """
-
-    exon_pos = []
-    if strand_p == '+':        
-        utr5_start, utr5_end = 0, 0
-        if five_p_utr != []:
-            utr5_start, utr5_end = five_p_utr[-1][0], five_p_utr[-1][1] 
-        cds_5start, cds_5end = cds_cod[0][0], cds_cod[0][1]
-        jun_exon = []
-        if cds_5start-utr5_end == 0 or cds_5start-utr5_end == 1:
-            jun_exon = [utr5_start, cds_5end]    
-        if len(cds_cod) == 1:
-            five_prime_flag = 0
-            if jun_exon != []:
-                five_p_utr = five_p_utr[:-1]
-                five_prime_flag = 1
-            for utr5 in five_p_utr:
-                exon_pos.append(utr5)
-            jun_exon = []
-            utr3_start, utr3_end = 0, 0
-            if three_p_utr != []: 
-                utr3_start = three_p_utr[0][0]
-                utr3_end = three_p_utr[0][1]
-            if utr3_start-cds_5end == 0 or utr3_start-cds_5end == 1:
-                jun_exon = [cds_5start, utr3_end]
-            three_prime_flag = 0
-            if jun_exon != []: 
-                cds_cod = cds_cod[:-1]
-                three_p_utr = three_p_utr[1:]
-                three_prime_flag = 1
-            if five_prime_flag == 1 and three_prime_flag == 1:
-                exon_pos.append([utr5_start, utr3_end])
-            if five_prime_flag == 1 and three_prime_flag == 0:
-                exon_pos.append([utr5_start, cds_5end])
-                cds_cod = cds_cod[:-1]
-            if five_prime_flag == 0 and three_prime_flag == 1:
-                exon_pos.append([cds_5start, utr3_end])
-            for cds in cds_cod:
-                exon_pos.append(cds)
-            for utr3 in three_p_utr:
-                exon_pos.append(utr3)
-        else:    
-            if jun_exon != []:
-                five_p_utr = five_p_utr[:-1]
-                cds_cod = cds_cod[1:]
-            for utr5 in five_p_utr:
-                exon_pos.append(utr5)
-            exon_pos.append(jun_exon) if jun_exon != [] else ''
-            jun_exon = []
-            utr3_start, utr3_end = 0, 0
-            if three_p_utr != []:
-                utr3_start = three_p_utr[0][0]
-                utr3_end = three_p_utr[0][1]
-            cds_3start = cds_cod[-1][0]
-            cds_3end = cds_cod[-1][1]
-            if utr3_start-cds_3end == 0 or utr3_start-cds_3end == 1:       
-                jun_exon = [cds_3start, utr3_end]
-            if jun_exon != []:
-                cds_cod = cds_cod[:-1]
-                three_p_utr = three_p_utr[1:]
-            for cds in cds_cod:
-                exon_pos.append(cds)
-            exon_pos.append(jun_exon) if jun_exon != [] else ''
-            for utr3 in three_p_utr:
-                exon_pos.append(utr3)
-    elif strand_p == '-':
-        utr3_start, utr3_end = 0, 0        
-        if three_p_utr != []:
-            utr3_start = three_p_utr[-1][0]
-            utr3_end = three_p_utr[-1][1]
-        cds_3start = cds_cod[0][0]
-        cds_3end = cds_cod[0][1]
-        jun_exon = []
-        if cds_3start-utr3_end == 0 or cds_3start-utr3_end == 1:
-            jun_exon = [utr3_start, cds_3end]  
-        if len(cds_cod) == 1:    
-            three_prime_flag = 0
-            if jun_exon != []:
-                three_p_utr = three_p_utr[:-1]
-                three_prime_flag = 1
-            for utr3 in three_p_utr:
-                exon_pos.append(utr3)
-            jun_exon = []
-            (utr5_start, utr5_end) = (0, 0)
-            if five_p_utr != []:
-                utr5_start = five_p_utr[0][0]
-                utr5_end = five_p_utr[0][1]
-            if utr5_start-cds_3end == 0 or utr5_start-cds_3end == 1:
-                jun_exon = [cds_3start, utr5_end]
-            five_prime_flag = 0
-            if jun_exon != []:
-                cds_cod = cds_cod[:-1]
-                five_p_utr = five_p_utr[1:]
-                five_prime_flag = 1
-            if three_prime_flag == 1 and five_prime_flag == 1:
-                exon_pos.append([utr3_start, utr5_end])
-            if three_prime_flag == 1 and five_prime_flag == 0:
-                exon_pos.append([utr3_start, cds_3end])
-                cds_cod = cds_cod[:-1]
-            if three_prime_flag == 0 and five_prime_flag == 1:
-                exon_pos.append([cds_3start, utr5_end])        
-            for cds in cds_cod:
-                exon_pos.append(cds)
-            for utr5 in five_p_utr:
-                exon_pos.append(utr5)
-        else:
-            if jun_exon != []:
-                three_p_utr = three_p_utr[:-1]
-                cds_cod = cds_cod[1:]
-            for utr3 in three_p_utr:
-                exon_pos.append(utr3)   
-            if jun_exon != []:
-                exon_pos.append(jun_exon)
-            jun_exon = []
-            (utr5_start, utr5_end) = (0, 0)
-            if five_p_utr != []:
-                utr5_start = five_p_utr[0][0]
-                utr5_end = five_p_utr[0][1]    
-            cds_5start = cds_cod[-1][0]
-            cds_5end = cds_cod[-1][1]
-            if utr5_start-cds_5end == 0 or utr5_start-cds_5end == 1:
-                jun_exon = [cds_5start, utr5_end]
-            if jun_exon != []:
-                cds_cod = cds_cod[:-1]
-                five_p_utr = five_p_utr[1:]
-            for cds in cds_cod:
-                exon_pos.append(cds)
-            if jun_exon != []:
-                exon_pos.append(jun_exon)    
-            for utr5 in five_p_utr:
-                exon_pos.append(utr5)
-    return exon_pos