/ 
FAST-1.03
River stage zero No dependents
/ gbfcut

NAME

gbfcut - search features from GenBank files and print corresponding sequences

SYNOPSIS

gbfcut [OPTIONS]... [GENBANK-FILE]...

DESCRIPTION

gbfcut takes GenBank-sequence input and outputs subsequences that correspond to features annotated on all input sequences in Multi-Fasta format. Both simple and more complex split features are supported. Optionally, gbfcut may be directed to only output sequences corresponding to features with one or more qualifiers, the values of match specific perl regular expressions (regexes). Alternatively, features may be filtered by regular expression matching against particular keys. By default all features are printed.

Options specific to gbfcut: -q, --qualifier=<string> search features for qualifer values by regular expressions -i, --insensitive case-insensitive pattern matching for qualifier regex matching -k, --key=<string> restrict search to features whose keys match regex <string>. -j, --join=<string> use <string> to join feature annotations in descriptions -c, --context=<int> include <int> positions of sequence context for each sequence output

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 --moltype=<[dna|rna|protein]> specify input sequence type

INPUT AND OUTPUT

gbfcut 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

-q <qualifier>[=^]<perl-regex>, --qualifier [qualifier][=^]<perl-regex>

Filter only features that have a specified qualifier and for each qualifier, at least one value that either matches (=) or no value that matches (^) their corresponding perl-regexes. Examples of qualifiers: 'product', 'note', 'gene', 'db_xref'. Multiple qualifier options are allowed; features will be printed for which all qualifier expressions are true.

-i, --case-insensitive

Enable case-insensitive matching of qualifiers.

-k <string>, --key=<string>

Filter only features with keys that match perl-regex <string>. Matching is done case-insensitively. Examples of key-matching regexes (called "primary-tags" in BioPerl): 'CDS', 'RNA', 'CDS|RNA' 'UTR' This regex is always matched case-insensitively.

-c <int>, --context=<int>

Include <int> positions of sequence context for each sequence record extracted.

-j <string>, --join=<string>

Use <string> as delimiter to concatenate annotation data in output sequence record descriptions.

-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).

EXAMPLES

Output the 5' and 3' UTR sequences:

    gbfcut -p UTR t/data/AF194338.1.gb

Output all sequences under the feature "exon" and add location labels:

    gbfcut -lp exon t/data/AF194338.1.gb

Output all feature sequences with an "organism" tag set to "Stylonychia lemnae":

    gbfcut -q organism="Stylonychia lemnae" t/data/AF194338.1.gb

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..