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Michael T. Wolfinger > Bio-ViennaNGS > fasta_subgrep.pl

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NAME ^

fasta_subgrep.pl - Extract subsequence from a (multi) Fasta file

SYNOPSIS ^

fasta_subgrep.pl [--fa FILE] [-s INT] [-e INT] [-id STRING] [--strand +/-]

DESCRIPTION ^

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.

OPTIONS ^

-f|--fa

Input file in Fasta format (mandatory)

-s|--start

Start of the sequence interval to extract

-e|--end

End of the sequence interval to extract

--id

Fasta ID of the sequence to extract from. This is only required for multi Fasta input files.

--strand

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.

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR ^

Michael T. Wolfinger <michael@wolfinger.eu>

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