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)
Check Out this Related Man Page
BP_PAIRWISE_KAKS(1p) User Contributed Perl Documentation BP_PAIRWISE_KAKS(1p)NAME
pairwise_kaks - script to calculate pairwise Ka,Ks for a set of sequences
SYNOPSIS
pairwise_kaks.PLS -i t/data/worm_fam_2785.cdna [-f fasta/genbank/embl...] [-msa tcoffee/clustal] [-kaks yn00/codeml]
DESCRIPTION
This script will take as input a dataset of cDNA sequences verify
that they contain no stop codons, align them in protein space,
project the alignment back into cDNA and estimate the Ka
(non-synonymous) and Ks (synonymous) substitutions based on the ML
method of Yang with the PAML package.
Requires:
* bioperl-run package
* PAML program codeml or yn00
* Multiple sequence alignment programs Clustalw OR T-Coffee
Often there are specific specific parameters you want to run when you
a computing Ka/Ks ratios so consider this script a starting point and
do not rely it on for every situation.
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_PAIRWISE_KAKS(1p)
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