NAME

FASTX::ScriptHelper - Shared routines for binaries using FASTX::Reader and FASTX::PE.

VERSION

version 1.12.0

NAME

FASTX::ScriptHelper - Shared routines for binaries using FASTX::Reader and FASTX::PE.

VERSION

version 1.11.0

new()

Initialize a new FASTX::ScriptHelper object. Notable parameters:

verbose

logfile

fu_printfasta

arguments: sequenceName, sequenceComment, sequence

Prints a sequence in FASTA format.

fu_printfastq

arguments: sequenceName, sequenceComment, sequence, Quality

Prints a sequence in FASTQ format.

rc

arguments: sequence

Returns the reverse complementary of a sequence

is_seq

arguments: sequence

Returns true if the sequence only contains DNA-IUPAC chars

split_string

arguments: sequence

Returns a string with newlines at a width specified by 'linesize'

verbose

arguments: message

Prints to STDERR (and log) a message, only if verbose is set

writelog

arguments: message, []

Writes a message to the log file and STDERR, regardless of --verbose

download

arguments: url, destination

Download a remote file

run

arguments: command, [%options]

Execute a command. Options are: * candie BOOL, to tolerate non zero exit * logall BOOL, save to log STDOUT and STDERR

cpu_count

Returns the number of detected cores, default 1

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2019 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2019 by Andrea Telatin.

This is free software, licensed under:

The MIT (X11) License

cpanm FASTX::Reader

perl -MCPAN -e shell
install FASTX::Reader