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07f_consensus_contigs.py
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07f_consensus_contigs.py
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#-----------------------------------------------------------+
# |
# template.py - Python template |
# |
#-----------------------------------------------------------+
# |
# AUTHOR: Vikas Gupta |
# CONTACT: [email protected] |
# STARTED: 09/06/2013 |
# UPDATED: 09/06/2013 |
# |
# DESCRIPTION: |
# Short script to convert and copy the wheat BACs |
# Run this in the parent dir that the HEX* dirs exist |
# |
# LICENSE: |
# GNU General Public License, Version 3 |
# http://www.gnu.org/licenses/gpl.html |
# |
#-----------------------------------------------------------+
# Example:
# python ~/script/python/100b_fasta2flat.py -i 02_Stegodyphous_cdna.refined.fa.orf.tr_longest_frame
### import modules
import os,sys,getopt, re
import threading
from multiprocessing import Process, Queue, Manager
from threading import Thread
import classGene
### global variables
global infile
### make a logfile
import datetime
now = datetime.datetime.now()
o = open(str(now.strftime("%Y-%m-%d_%H%M."))+'logfile','w')
def get_size(file):
size = {}
for line in open(file,'r'):
line = line.strip()
if len(line) > 0:
if line[0] != '#':
token = line.split('\t')
if token[0] not in size:
size[token[0]] = int(token[4])
else:
if int(token[4]) > size[token[0]]:
size[token[0]] = int(token[4])
size_sorted={}
for w in sorted(size, key=size.get, reverse=False):
size_sorted[w]=size[w]
return size_sorted
### write logfile
def logfile(infile):
o.write("Program used: \t\t%s" % "100b_fasta2flat.py"+'\n')
o.write("Program was run at: \t%s" % str(now.strftime("%Y-%m-%d_%H%M"))+'\n')
o.write("Infile used: \t\t%s" % infile+'\n')
def help():
print '''
python 100b_fasta2flat.py -i <infile>
'''
sys.exit(2)
def temp(file):
num_lines = sum(1 for line in open(file))
return num_lines
### main argument to
def options(argv):
global infile, threads, gaps
infile = ''
threads = 2
try:
opts, args = getopt.getopt(argv,"hi:t:g:",["infile=","threads=","gaps="])
except getopt.GetoptError:
help()
for opt, arg in opts:
if opt == '-h':
help()
elif opt in ("-i", "--infile"):
infile = arg
elif opt in ("-t", "--threads"):
threads = int(arg)
elif opt in ("-g", "--gaps"):
gaps = int(arg)
logfile(infile)
def merge_contigs():
first_line = True
block_start = True
for line in open(infile,'r'):
line = line.strip()
tokens = line.split('\t')
contig = tokens[0]
st = int(tokens[1])
en = int(tokens[2])
g_id = tokens[3].replace('ID=','')
score = tokens[4]
strand = tokens[5]
if first_line == False:
if contig == last_contig:
### check if new contig overlaps
if bl_en + gaps > st:
if en > bl_en:
bl_en = en
bl_id += '_' + g_id
else:
block_start = True
print last_contig + '\t' + str(bl_st) + '\t' + str(bl_en) + '\t' + 'id=' + bl_id+ '\t' + str(bl_score) + '\t' + str(bl_strand)
else:
block_start = True
print last_contig + '\t' + str(bl_st) + '\t' + str(bl_en) + '\t' + 'id=' + bl_id + '\t' + str(bl_score) + '\t' + str(bl_strand)
### check if new block starts
if block_start == True:
bl_st = st
bl_en = en
bl_id = g_id
bl_contig = contig
bl_score = score
bl_strand = strand
block_start = False
first_line = False
last_contig = contig
last_en = en
### print the last line
print last_contig + '\t' + str(bl_st) + '\t' + str(bl_en) + '\t' + 'id=' + bl_id+ '\t' + str(bl_score) + '\t' + str(bl_strand)
if __name__ == "__main__":
options(sys.argv[1:])
start_time = datetime.datetime.now()
print >> sys.stderr, "Input file must be sorted"
print >> sys.stderr, "Running temp script: " + str(datetime.datetime.now())
print >> sys.stderr, "Input count: " + str(temp(infile))
merge_contigs()
print >> sys.stderr, "Output count: " + str(temp(infile))
print >> sys.stderr, "Completed temp script: " + str(datetime.datetime.now())
print >> sys.stderr, "Time take to complete: " + str(datetime.datetime.now() - start_time)