Comments (4)
hi Daniel,
I just made a similar change to the metagenemark parser, thanks for
sending! I'll get this added in, but definitely would be happy to add you
in as a collaborator/developer so you can directly commit any future
changes/improvements. just send me your github id/login and I'll get you
added.
and please keep me posted on how your metAMOS run goes.
best,
Todd
On Tue, Apr 24, 2012 at 2:16 PM, dbrami <
[email protected]
wrote:
Hi Todd,
I made some changes to the FragGeneScan portion of the findorfs.py that
have yielded efficiency improvements by orders of magnitude.
I am not quite sure how to submit the code to the github so I will post
here and leave it to your discretion to incorporate it (old code commented
out for comparison).
I am still trying to get the pipeline to complete end-to-end on actual
data set...I will keep you posted.Cheers!
for seq in seqs:
hdr,gene = seq.split("\n",1)
#hdr = hdr.split("\n")[0]
hdr = hdr.rstrip("\n")
#gene_ids.append(hdr)
#split the header in two
orfkey = ''.join(hdr.split('')[:6])
orfval = ''.join(hdr.split('')[7:])
orfhdrs[orfkey]=orfval#for key in gene_ids:
# genecnt = 1
# gkey = ""
# if not is_scaff:
# for ckey in cvg_dict.keys():
# if ckey in key:
# gkey = ckey# if gkey != "": # cvgg.write("%s\t%s\n"%(key,cvg_dict[gkey])) # else: # cvgg.write("%s\t%s\n"%(key,1.0))
for key in orfhdrs.keys():
if key in cvg_dict:
cvgg.write("%s\t%s\n"%((key + orfhdrs[key]),cvg_dict[key]))
else:
cvgg.write("%s\t%s\n"%((key + orfhdrs[key]),str(1.0)))
cvgg.close()
Reply to this email directly or view it on GitHub:
#49
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Fantastic! Thanks Todd ;)
from metamos.
I will make another very slight chang and add the "if not is_scaff" above our loop in th fraggenescan portion
from metamos.
I added in the more efficient code snippet, tested and committed, closing issue.
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Related Issues (20)
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