bed2nt2aa.pl - Get nucleotde and amino acid sequences from BED intervals
bed2nt2aa.pl [--bed FILE] [--fa FILE] [--aa] [options]
Extract sequence intervals from Fasta files, provided as BED6 records. Optionally translate nucleotide into amino acid sequences. Output is written to a 'sequence.fa' output file. This can be overriden with the -s switch, which triggers STDOUT output.
-s
Input file in BED6 format (mandatory)
Input file in Fasta format (mandatory)
Translate nucleotide into amino acid sequences, providing all three possible frames
Write output to STDOUT instead of an output file 'sequence.fa'
Print short help
Prints the manual page and exits
Michael T. Wolfinger <michael@wolfinger.eu>
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ViennaNGS
CPAN shell
perl -MCPAN -e shell install Bio::ViennaNGS
For more information on module installation, please visit the detailed CPAN module installation guide.