def init_args(args):
global new_state, behaviour
i = 0
while i < len(args):
if args[i] in ['-i', '--input']:
f = fasta.read_from(args[i + 1])
i += 1
new_state['SEQUENCE'] = f[0].sequence
elif args[i] in ['-f', '--fast']:
behaviour["fast"] = True
elif args[i] in ['-o', '--output']:
i += 1
behaviour["output"] = open(args[i], 'w')
elif args[i] in ['-h', '--help']:
print "Query Primer3"
print "by Damien Leroux <*****@*****.**>"
print
print "Usage: %s [-f,--fast] [-o,--output filename]",
print "[configuration_key=value...]" % args[0]
print "Configuration keys:"
for (k, v) in filter(lambda x: ' ' not in x, state.items()):
if v:
print ' ', k.lower(), '(default %s)' % v
else:
print ' ', k.lower()
sys.exit(0)
else:
key, value = args[i].split("=")
key = key.upper()
if ' ' not in key and key in state:
new_state[key] = value
else:
print "I don't know nothing about a '%s', I do mean it." % key
sys.exit(1)
i += 1
def main(argv):
lines = files.read_lines(argv[0])
tree = lines[0]
strings = fasta.read_from(lines[1:])
z, L = phylogeny.small_parsimony(tree, strings)
print z
print '\n'.join('>%s\n%s' % (key, value) for key, value in L.iteritems())
def extract(filename):
global fcount, ftotal
fcount += 1
#print "\r%i/%i" % (fcount, ftotal),
print "%i/%i" % (fcount, ftotal),
exti = filename.rfind('.')
ext = filename[exti:]
path, query = os.path.split(filename[:exti])
fhits = fasta.read_from(filename)
print filename, exti, ext, path, query
if query in fhits:
fquery = fasta.Fasta()
fquery.add_seq(fhits[query])
fhits.remove(query)
fhits.save_to(os.path.join(path, query + '-hits' + ext))
fquery.save_to(os.path.join(path, query + '-query' + ext))
def main(argv):
lines = files.read_lines(argv[0])
tree = lines[0]
strings = fasta.read_from(lines[1:])
output = []
for r in phylogeny.reverse_substitutions(tree, strings):
path = r[0]
position = r[1]
original = strings[path[0].name][position]
substituted = strings[path[1].name][position]
reverted = strings[path[-1].name][position]
output.append('%s %s %s %s->%s->%s' %
(path[1].name, path[-1].name, position + 1, original,
substituted, reverted))
print '\n'.join(output)
#!/usr/bin/env python
from query_primer3 import query_primer3
import fasta
import sys
import re
import os
executable = True
if len(sys.argv) < 2:
print "Usage: %s multi_fasta PRIMER3_ARG=VALUE..."
mfas = fasta.read_from(sys.argv[1])
primer3args = sys.argv[2:]
bad_chr = re.compile("[^a-zA-Z0-9_-]")
basedir, basename = os.path.split(sys.argv[1])
for i, s in enumerate(mfas):
out = os.path.join(basedir, bad_chr.sub('_', s.header) + '.primer3')
print '[%i/%i]' % (1 + i, len(mfas)), "Querying", s.header
query_primer3(['SEQUENCE=' + s.sequence, '-o', out] + primer3args)