[BioPython] Large GenBank files: impossible to handle?

[Hans Meier]

 Dear friends,
 
 I tried to handle a .gbk file of 4,7MB in size
 with a "700MHz, Pentium III, 256 MB RAM"-box.
 
 Parsing with "RecordParser" and indexing with "index_file"
 crushed the machine in both cases, I had to reboot
 (what happens not so often with Debian).
 My final goal is to access the .gbk file somehow like a database.
 The alternative would be to use .fna,.faa and .fnn files 
 and write my own methods. Or stuff all the data in a SQL-database.
 But I still hope that Biopython could help.
 
 Before I spend more time on this, I'd like to ask you:
 
 With the Biopython tools, is it possible to handle
 .gbk files of about 5MB in a reasonable time with 
 a low- to middle-class desktop computer? If so, how?
 
 
 All the best and a Happy New Year, Harald
 
 
 
 
 
 

		
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