tabulate_codons.pl - a program to output codons in a sequence file as a table
VERSION: 0.01
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
the file containing fasta-formated sequences.
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.
a switch option. If provided, codons are counted for each sequence. Default is summing up all the codons in all the sequences.
the file to store the result. Default is standard output.
show this help message. For more detailed information, run 'perldoc tabulate_codons.pl'
Zhenguo Zhang, <zhangz.sci at gmail.com>
<zhangz.sci at gmail.com>
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.
bug-bio-cua at rt.cpan.org
You can find documentation for this class with the perldoc command.
perldoc Bio::CUA
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Bio-CUA
CPAN Ratings
http://cpanratings.perl.org/d/Bio-CUA
Search CPAN
http://search.cpan.org/dist/Bio-CUA/
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/.
To install Bio::CUA, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::CUA
CPAN shell
perl -MCPAN -e shell install Bio::CUA
For more information on module installation, please visit the detailed CPAN module installation guide.