action='store_true',
help='Input from stdin')
parser.add_option('-o',
'--stdout',
dest='stdout',
action='store_true',
help='Output to stdout')
options, args = parser.parse_args()
if len(args) == 0:
parser.print_help()
sys.exit()
if options.stdin:
f = FastaFile(sys.stdin)
else:
f = FastaFile(args[0])
if options.stdout:
w = FastaFile(sys.stdout, 'w')
else:
w = FastaFile(args[1], 'w')
accList = []
for h, s in f:
acc = h.split()[0]
if not acc in accList:
w.write(h, s)
accList.append(acc)
w.close()
f.close()
#!/usr/bin/env python
"""
exciseRepeats.py
Author: Tony Papenfuss
Date: Fri Mar 21 13:25:51 EST 2008
"""
import os, sys, re
from mungo.fasta import FastaFile
iFilename = sys.argv[1]
oFilename = iFilename + '.excised'
# Cleaned & now masked reads
fi = FastaFile(iFilename)
fo = FastaFile(oFilename, 'w')
for h,s in fi:
s = s.replace('N', '')
fo.write(h,s)
fi.close()
fo.close()
from mungo.fasta import FastaFile
from optparse import OptionParser
usage = "%prog <Input file1> <Output file>"
parser = OptionParser(usage=usage, version="%prog - Version 1")
parser.add_option('-i', '--stdin', dest='stdin', action='store_true', help='Input from stdin')
parser.add_option('-o', '--stdout', dest='stdout', action='store_true', help='Output to stdout')
options, args = parser.parse_args()
if len(args)==0:
parser.print_help()
sys.exit()
if options.stdin:
f = FastaFile(sys.stdin)
else:
f = FastaFile(args[0])
if options.stdout:
w = FastaFile(sys.stdout, 'w')
else:
w = FastaFile(args[1], 'w')
accList= []
for h,s in f:
acc = h.split()[0]
if not acc in accList:
w.write(h,s)
accList.append(acc)
w.close()
f.close()
fasta_block_split.py <iFilenames> <oFilename>
Author: Tony Papenfuss
Date: Fri Mar 30 12:58:58 EST 2007
"""
import os, sys
from mungo.fasta import FastaFile
from optparse import OptionParser
usage = "%prog [-b <block_size>] <input_file1> [<input_file2> ...] <output_file>"
parser = OptionParser(usage=usage, version="%prog - Version 1")
parser.add_option("-b", "--blocksize", action="store", type="int",
dest="blocksize", default="10000000")
options, args = parser.parse_args()
if len(args)==0:
parser.print_help()
sys.exit()
iFilenames = args[:-1]
oFilename = args[-1]
writer = FastaFile(oFilename, 'w', blockSize=10000000)
for iFilename in iFilenames:
for h,s in FastaFile(iFilename):
writer.write(h,s)
writer.close()
#!/usr/bin/env python
"""
fasta_truncate.py
Author: Tony Papenfuss
Date: July 2013
"""
import sys
import argparse
from mungo.fasta import FastaFile
usage = "%prog <length> <Input file> <Output file>"
parser = argparse.ArgumentParser(description='Truncate fasta files')
parser.add_argument('length', type=int, help='Truncate to length')
parser.add_argument('input_filename', type=str, help='Input filename')
parser.add_argument('output_filename', type=str, help='Output filename')
args = parser.parse_args()
w = FastaFile(args.output_filename, 'w')
for h,s in FastaFile(args.input_filename):
w.write(h, s[0:args.length])
w.close()
#!/usr/bin/env python
"""
fasta_truncate.py
Author: Tony Papenfuss
Date: July 2013
"""
import sys
import argparse
from mungo.fasta import FastaFile
usage = "%prog <length> <Input file> <Output file>"
parser = argparse.ArgumentParser(description='Truncate fasta files')
parser.add_argument('length', type=int, help='Truncate to length')
parser.add_argument('input_filename', type=str, help='Input filename')
parser.add_argument('output_filename', type=str, help='Output filename')
args = parser.parse_args()
w = FastaFile(args.output_filename, 'w')
for h, s in FastaFile(args.input_filename):
w.write(h, s[0:args.length])
w.close()
#!/usr/bin/env python
"""
exciseRepeats.py
Author: Tony Papenfuss
Date: Fri Mar 21 13:25:51 EST 2008
"""
import os, sys, re
from mungo.fasta import FastaFile
iFilename = sys.argv[1]
oFilename = iFilename + ".excised"
# Cleaned & now masked reads
fi = FastaFile(iFilename)
fo = FastaFile(oFilename, "w")
for h, s in fi:
s = s.replace("N", "")
fo.write(h, s)
fi.close()
fo.close()
"""
fastaRename.py <iFilename> <oFilename>
Author: Tony Papenfuss
Date: Fri Mar 7 14:17:14 EST 2008
"""
import sys
from mungo.fasta import FastaFile
iFilename = sys.argv[1]
oFilename = sys.argv[2]
def getSpp(line):
token = line.split('[')[-1].split(']')[0]
return token
writer= FastaFile(oFilename, 'w')
for h,s in FastaFile(iFilename):
tokens = h.split()
name = tokens[0]
spp = getSpp(h)
sppParts = spp.split()
h2 = "%s%s_%s" % (sppParts[0][0:5], sppParts[1][0:2].title(), name)
writer.write(h2, s)
writer.close()
