fasta_subgrep.pl - Extract subsequence from a (multi) Fasta file
fasta_subgrep.pl [--fa FILE] [-s INT] [-e INT] [-id STRING] [--strand +/-]
Extract a subsequence from a (multi) Fasta file. Interval coordinates are passed as start and end coordinates via the -s and -e options, respectively. Output is written to STDOUT.
Input file in Fasta format (mandatory)
Start of the sequence interval to extract
End of the sequence interval to extract
Fasta ID of the sequence to extract from. This is only required for multi Fasta input files.
Specify the strand to extract sequence data from. Allowed arguments are + amd -. In the latter case, retrieve reverse complement of the sequence interval from start to end.
Print short help
Prints the manual page and exits
Michael T. Wolfinger <firstname.lastname@example.org>
To install Bio::ViennaNGS, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.