def run_sp_acc_update(inf,outf,updateaccs_f):
updateaccs_f.seek(0)
update_dict = my_gb.make_update_dict(updateaccs_f)
line = inf.readline()
while line:
tmp = string.split(line)
key = tmp[len(tmp)-1]
if update_dict.has_key(key):
value = update_dict[key]
line = tmp[0] + '\t' + tmp[1] + '\t' + value + '\n'
else:
sys.stderr.write("%s: no update_acc found\n" % key)
outf.write(line)
line = inf.readline()
def run_embl_pr2est(inf,outf,embl_pr2est_f):
embl_pr2est_f.seek(0)
embl_pr2est_dict = my_gb.make_update_dict(embl_pr2est_f)
line = inf.readline()
while line:
tmp = string.split(line)
key = tmp[len(tmp)-1]
if embl_pr2est_dict.has_key(key):
value = embl_pr2est_dict[key]
line = line[0:len(line)-1] + '\t' + value + '\n'
else:
sys.stderr.write("%s: EST not found\n" % key)
outf.write(line)
line = inf.readline()
def run_fasta_title_update(inf,outf,sdgnames_f):
from Bio import Fasta
parser = Fasta.RecordParser()
fasta_iterator = Fasta.Iterator(inf,parser)
sdgnames_f.seek(0)
sdgnames_dict = my_gb.make_update_dict(sdgnames_f)
while 1:
record = fasta_iterator.next()
if record is None:
break
if sdgnames_dict.has_key(record.title):
value = sdgnames_dict[record.title]
else:
value = record.title
outf.write('>%s\n%s\n' % (value,record.sequence))