/ 
Bio-CUA-1.04
River stage zero No dependents
/ tabulate_codons.pl

NAME

tabulate_codons.pl - a program to output codons in a sequence file as a table

VERSION

VERSION: 0.01

SYNOPSIS

This progran reads fasta-formated sequences and output codon counts in the sequence as a table.

# count the codons of all sequences in longest_cds.dmel_5_57.fa
tabulate_codons.pl -s longest_cds.dmel_5_57.fa -o codon_counts.tsv

# the same as above, but output counts for each sequence
tabulate_codons.pl -s longest_cds.dmel_5_57.fa -o codon_counts_each.tsv --each

# you can also count for a subset of sequences, like
tabulate_codons.pl -s longest_cds.dmel_5_57.fa -o \
codon_counts_sub.tsv --id-file subset_ids.tsv

# subset_ids.tsv contains sequence IDs, one ID per line

OPTIONS

Mandatory options:

-s/--seq-file

the file containing fasta-formated sequences.

Auxiliary options:

-i/--id-file

a file containing sequence IDs. This option is used to filter the sequences in the file by option "-s", so that only sequences listed in this id-file are parsed. Note, the IDs should match those in the sequence file by "-s", one ID per line. In default, all the sequences in the input file are analyzed.

-e/--each

a switch option. If provided, codons are counted for each sequence. Default is summing up all the codons in all the sequences.

-o/--out-file

the file to store the result. Default is standard output.

-h/--help

show this help message. For more detailed information, run 'perldoc tabulate_codons.pl'

AUTHOR

Zhenguo Zhang, <zhangz.sci at gmail.com>

BUGS

Please report any bugs or feature requests to bug-bio-cua at rt.cpan.org or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-CUA. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this class with the perldoc command.

perldoc Bio::CUA

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2015 Zhenguo Zhang.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.