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Top Forums Shell Programming and Scripting Please suggest alternative to grep Post 302652699 by binlib on Thursday 7th of June 2012 02:23:18 PM
Old 06-07-2012
Assuming both files are sorted, maybe you can use "join".
If all the 300 million numbers of file1 start with 372846 (if not, then multiple passes maybe), then you can treat them as integers (minus the prefix). This way you can store them as bitmaps and do look up of the numbers (check prefix first separately) from file2. The first chapter of Jon Bentley's book "programming pearl" talked exactly about this problem.
 

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BP_DBSPLIT(1p)						User Contributed Perl Documentation					    BP_DBSPLIT(1p)

NAME
dbsplit - script to split an input set of database(s) into smaller pieces SYNOPSIS
dbsplit.PLS --size 50 [-i inputfile] [-if inputformat] [-of outputformat] [--prefix outputprefix] [ < file1 file 2 OR file1 file2] DESCRIPTION
This script will take as input a list of filenames or a single file or from STDIN a sequence database and split the database into separate files of X numbers of sequences. You specify X with the "--size/-s" parameter. The input and output sequence format is any that is supported by bioperl (fasta,embl,genbank,gcg, swissprot, etc). You can specify the input data either as a single file with -i filename, or as a single file as an argument like % dbsplit file1 file2 or as a list of sequence data with % cat file1 file2 file3 | dbsplit You'll want to use the "--prefix" to specify what the output prefix will be. FEEDBACK
Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
Jason Stajich, jason-at-bioperl-dot-org perl v5.14.2 2012-03-02 BP_DBSPLIT(1p)
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