NAME

fassub -- regex-based substitutions on sequence records

SYNOPSIS

fassub [OPTION]... [PERL-REGEX] [SUBSTITUTION] [MULTIFASTA-FILE]...

DESCRIPTION

fassub takes multifasta format sequence or alignment data as input, and faciliates text substitutions on sequence identifiers (by default), sequences or descriptions using the Perl s/// substitution operator. fassub takes two mandatory arguments corresponding to the two arguments of s///; the first a Perl regex matching a set of strings to be substituted and the second, replacement text, possibly including special characters that require backslash quoting or capture buffer expressions. The first regex argument may require quoting to protect special characters from interpretation by the shell. By default, only the left-most match is substituted, use --global/-g to substitute all matches. Use single quotes on arguments at the shell to deploy numbered match variables like "$1" in your substitutions, which will back-reference capture groups in your regex.

Options specific to fassub: -s, --sequence substitute on sequences -d, --description substitute on descriptions -i, --insensitive match text case-insensitively -g, --global substitute all matches in the data

Options general to FAST: -h, --help print a brief help message --man print full documentation --version print version -l, --log create/append to logfile -L, --logname=<string> use logfile name <string> -C, --comment=<string> save comment <string> to log --format=<format> use alternative format for input -q, --fastq use fastq format as input and output

INPUT AND OUTPUT

fassub is part of FAST, the FAST Analysis of Sequences Toolbox, based on Bioperl. Most core FAST utilities expect input and return output in multifasta format. Input can occur in one or more files or on STDIN. Output occurs to STDOUT. The FAST utility fasconvert can reformat other formats to and from multifasta.

OPTIONS

-s, --sequence

Substitute on the sequences. By default substitution occurs on identifiers.

-d, --description

Substitute on the descriptions. By default substitution occurs on identifiers.

-i, --insensitive

Substitute case-insensitively.

-g, --global

Substitute all matches in the data. By default only the first match on each line will be subsituted.

-h, --help

Print a brief help message and exit.

--man

Print the manual page and exit.

--version

Print version information and exit.

-l, --log

Creates, or appends to, a generic FAST logfile in the current working directory. The logfile records date/time of execution, full command with options and arguments, and an optional comment.

-L [string], --logname=[string]

Use [string] as the name of the logfile. Default is "FAST.log.txt".

-C [string], --comment=[string]

Include comment [string] in logfile. No comment is saved by default.

--format=[format]

Use alternative format for input. See man page for "fasconvert" for allowed formats. This is for convenience; the FAST tools are designed to exchange data in Fasta format, and "fasta" is the default format for this tool.

-m [dna|rna|protein], --moltype=[dna|rna|protein]

Specify the type of sequence on input (should not be needed in most cases, but sometimes Bioperl cannot guess and complains when processing data).

-q --fastq

Use fastq format as input and output.

EXAMPLES

Reverse genus and species in t/data/P450.fas:

fassub -d '\[(\w+) (\w+)\]' '[$2 $1]' t/data/P450.fas

SEE ALSO

man perlre

perldoc perlre

Documentation on perl regular expressions.

man FAST

perldoc FAST

Introduction and cookbook for FAST

The FAST Home Page"

CITING

If you use FAST, please cite Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..