[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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