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129_splitIPR.py
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129_splitIPR.py
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#-----------------------------------------------------------+
# |
# 129_splitIPR.py - Script to split IPRscan output |
# |
#-----------------------------------------------------------+
# |
# 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, out
### 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, out
ifile = ''
try:
opts, args = getopt.getopt(argv,"hi:o:",["ifile=","out="])
except getopt.GetoptError:
help()
for opt, arg in opts:
if opt == '-h':
help()
elif opt in ("-i", "--ifile"):
ifile = arg
elif opt in ("-o", "--out"):
out = arg
logfile(ifile)
def IPRstring():
string1 = '<EBIInterProScanResults > \n' + \
'<Header> \n' + \
' <program name="InterProScan" version="4.8" citation="PMID:11590104"/> \n' + \
' <parameters> \n' + \
' <sequences total="1"/> \n' + \
' <databases total="13"> \n' + \
' <database number="1" name="PRODOM" type="sequences"/> \n' + \
' <database number="2" name="PRINTS" type="matrix"/> \n' + \
' <database number="3" name="PIR" type="model"/> \n' + \
' <database number="4" name="PFAM" type="model"/> \n' + \
' <database number="5" name="SMART" type="model"/> \n' + \
' <database number="6" name="TIGRFAMs" type="model"/> \n' + \
' <database number="7" name="PROFILE" type="strings"/> \n' + \
' <database number="8" name="PROSITE" type="strings"/> \n' + \
' <database number="9" name="SUPERFAMILY" type="model"/> \n' + \
' <database number="10" name="GENE3D" type="model"/> \n' + \
' <database number="11" name="PANTHER" type="model"/> \n' + \
' <database number="12" name="SIGNALP" type="model"/> \n' + \
' <database number="13" name="TMHMM" type="model"/> \n' + \
' </databases> \n' + \
' </parameters> \n' + \
'</Header>\n'
string2 = '</EBIInterProScanResults> \n'
return string1, string2
def readIn(string1, string2):
print_flag = False
i = 0
for line in open(ifile,'r'):
line = line.strip()
if len(line) > 0 and not line.startswith('#'):
if line.startswith('<protein id='):
i += 1
g_id = line.split('"')[1]
if i%100 == 0:
print g_id
print 'Processing ProteinID: ', g_id, '{:7,.0f}'.format(i)
print_flag = True
o = open(out+'/'+g_id +'.xml','w')
o.write(string1)
o.write('<interpro_matches>'+'\n')
elif line.startswith('</protein>'):
print_flag = False
o.write(line+'\n')
o.write('</interpro_matches>'+'\n')
o.write(string2)
if print_flag == True:
o.write(line + '\n')
if __name__ == "__main__":
options(sys.argv[1:])
string1, string2 = IPRstring()
readIn(string1, string2)
### close the logfile
o.close()