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Top Forums Shell Programming and Scripting Need help splitting huge single record file Post 302578858 by Corona688 on Friday 2nd of December 2011 03:07:00 PM
Old 12-02-2011
Those commands are trying to load the entire line into memory at once, which won't work on a 64 32-bit system since there's a 4GB limit on per-process memory and sufficient clutter in the way that you probably can't get an entire 2.5G in one chunk.

How big are the individual records? You can tell awk to use things other than \n as a record separator, changing its definition of lines:

Code:
$  awk -v RS='\\*end\\*' '1' < data
RANDOMDATA
RANDOMDATA
RANDOMDATA
RANDOMDATA
$

Use nawk or gawk if you have it.

Last edited by Corona688; 12-02-2011 at 04:39 PM..
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Bio::SeqIO::tab(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::tab(3pm)

NAME
Bio::SeqIO::tab - nearly raw sequence file input/output stream. Reads/writes id" "sequence" " SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTION
This object can transform Bio::Seq objects to and from tabbed flat file databases. It is very useful when doing large scale stuff using the Unix command line utilities (grep, sort, awk, sed, split, you name it). Imagine that you have a format converter 'seqconvert' along the following lines: my $in = Bio::SeqIO->newFh(-fh => *STDIN , '-format' => $from); my $out = Bio::SeqIO->newFh(-fh=> *STDOUT, '-format' => $to); print $out $_ while <$in>; then you can very easily filter sequence files for duplicates as: $ seqconvert < foo.fa -from fasta -to tab | sort -u | seqconvert -from tab -to fasta > foo-unique.fa Or grep [-v] for certain sequences with: $ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' | seqconvert -from tab -to fasta > foo-without-controls.fa Or chop up a huge file with sequences into smaller chunks with: $ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk- $ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done # (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10 # sequences) 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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHORS
Philip Lijnzaad, p.lijnzaad@med.uu.nl APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object perl v5.14.2 2012-03-02 Bio::SeqIO::tab(3pm)
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