[Biopython] Fasta.index_file: functionality removed?
Cedar McKay
cmckay at u.washington.edu
Wed Jun 17 13:37:03 EDT 2009
Hello, I depend on functionality provided by Fasta.index_file to index
a large file (5 million sequences), too large to put in memory, and
access it in a dictionary-like way. Newer versions of Biopython have
removed (or hopefully moved) this functionality. I attempted to figure
out what happened to the functionality by searching the mailing list,
to no avail. Also Biopython's ViewCVS page is down, so I can't pursue
that route. So if someone would please suggest an alternative way to
do the same thing in newer biopython versions, I'd appreciate it. I
tried SeqIO.to_dict, but it seems to load the whole 5 million
sequences (or just the index?) into memory rather than make an index
file. I become memory bound rather quickly this way, and then my
script grinds to a halt.
As a side issue, how can I tell what version of biopython I'm using in
old versions before "Bio.__version__" was introduced?
thanks,
Cedar
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