fastaexplod1

Usage

Overview

fastaexplod reads a FastA file from standard input and writes the contained sequences to a set of files. It writes one sequence per output file. The file names used are fasta_<id>.fasta where id is a git digit running decimal number. The prefix (fasta_ by default) can be set using the -p switch. The .fasta suffix is omitted if the data only switch is given (see below). The program writes a two column table to the standard output channel. The first column contains an output file name and the second the respective sequence id written to this file.

The following options can be given

-p<prefix>: file name prefix. The files will be called <prefix>000000<suffix>, <prefix>000000<suffix><suffix>, etc. where <suffix> is .fasta unless the data only flag is set

-d/--dataonly: write only the base data but no header/prolog line. This sets the file name suffix to the empty string.

-s/--singleline: write a single line of base data instead of breaking the base data into multiple lines

-L/--longname: do not shorten read names by clipping of everything starting from first white space

-l<num>: set the length of the base data lines (80 by default).

-v/--version: print the version number and quit

-h/--help: print a help message and quit