--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GFFtools-GX/helper.py	Wed Jun 11 16:29:25 2014 -0400
@@ -0,0 +1,332 @@
+#!/usr/bin/env python
+"""
+Common utility functions
+"""
+
+import os 
+import re
+import sys 
+import gzip 
+import bz2
+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_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