[Biopython] suggestion for a little change in the ACE cookbook
Fungazid
fungazid at yahoo.com
Sun Jul 5 22:57:08 UTC 2009
Hi,
About the cookbook here
http://biopython.org/wiki/ACE_contig_to_alignment
instead of:
def cut_ends(read, start, end):
return (start-1) * '-' + read[start-1:end] + (end +1) * '-'
I think it is better to write:
def cut_ends(self,read, start, end):
return (start-1) * 'x' + read[start-1:end-1] + (len(read)-end) * 'x'
The 2 changes are:
1) correcting the coordinates of the clipped 5' region
2) adding 'x' instead of '-' to separate the clipped region from the gaps
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