more efficient snippet about metamos HOT 4 CLOSED

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

from metamos.

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.

from metamos.