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125_pileup2bed.py
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125_pileup2bed.py
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#-----------------------------------------------------------+
# |
# 125_pileup2bed.py - Script to convert from Pileup to Bed format |
# |
#-----------------------------------------------------------+
# |
# 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
### global variables
global ifile
### make a logfile
import datetime
now = datetime.datetime.now()
o = open(str(now.strftime("%Y-%m-%d_%H%M."))+'logfile','w')
### 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 <ifile>
'''
sys.exit(2)
### main argument to
def options(argv):
global ifile
ifile = ''
try:
opts, args = getopt.getopt(argv,"hi:",["ifile="])
except getopt.GetoptError:
help()
for opt, arg in opts:
if opt == '-h':
help()
elif opt in ("-i", "--ifile"):
ifile = arg
logfile(ifile)
def pileup2bed():
last_chr = ''
last_start = 0
last_end = 0
first_line = True
name = '.'
score = '0'
for line in open(ifile, 'r'):
if not line.startswith('#'):
line = line.strip()
token = line.split('\t')
chro = token[0]
pos = int(token[1])
if first_line == False:
if last_chr != chro and last_chr !='':
print str(last_chr) + '\t' + str(last_start) + '\t' + str(last_end+1) + '\t'+ name + '\t' + score
last_chr = chro
last_start = pos
elif pos > last_end + 1 and last_chr !='':
print str(last_chr) + '\t' + str(last_start) + '\t' + str(last_end+1) +'\t'+ name + '\t' + score
last_start = pos
if last_chr == '':
last_start = pos
last_chr = chro
last_end = pos
first_line = False
print str(last_chr) + '\t' + str(last_start) + '\t' + str(last_end + 1) +'\t'+ name + '\t' + score
if __name__ == "__main__":
options(sys.argv[1:])
pileup2bed()
### close the logfile
o.close()