++ed by:
MOCNII

1 PAUSE user
1 non-PAUSE user.

Michael T. Wolfinger
and 1 contributors

NAME

bed2nt2aa.pl - Get nucleotde and amino acid sequences from BED intervals

SYNOPSIS

bed2nt2aa.pl [--bed FILE] [--fa FILE] [--aa] [options]

DESCRIPTION

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.

OPTIONS

--bed

Input file in BED6 format (mandatory)

--fa

Input file in Fasta format (mandatory)

-a|--aa

Translate nucleotide into amino acid sequences, providing all three possible frames

-s|--stdout

Write output to STDOUT instead of an output file 'sequence.fa'

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Michael T. Wolfinger <michael@wolfinger.eu>