NAME

gbfalncut - cut sites from alignments by regex-matching on features in an annotated GenBank file

SYNOPSIS

gbfalncut [OPTIONS] ALIGNMENT-FILE GENBANK-FILE PERL-REGEX

DESCRIPTION

gbfalncut extracts sites from alignments that correspond to one or more features annotated on a sequence in a GenBank file. The alignment must contain exactly one sequence with the same identifier as the sequence in the GenBank file. By default all features in the GenBank file are searched for a qualifier "/note" whose value matches the perl regex given as the third argument. By default all features are searched, but the search may be restricted to features with a specific key. Optionally, regex matching may occur directly on feature keys (the labels for features at the left side of the feature table), allowing matching to features without qualifiers.

Both simple and split features (specified with a "join" operator) are supported. Reverse-strand features (specified with a "complement" operator) are not reverse-complemented; check fasrc for that.

Options specific to gbfalncut: -i, --insensitive case-insensitive pattern matching -v, --negate cut sites that don't belong to a feature -q, --qualifier=<string> match on values of qualifier <string> default qualifier is "note" (as in /note="intron") -k, --key regex match directly on feature keys --verbose produce verbose 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

gbfalncut 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

-i, --insensitive

Match data case-insensitively.

-n, --negate

Output sites that fall outside the features matched by the regular expression argument.

-q=<string>, --qualifier=<string>

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

-v, --verbose

-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

Print alignment of 5'UTRs

gbfalncut -K --verbose t/data/AF194338.1.gb 5.UTR t/data/ArdellEtAl03_ncbi_popset_32329588.fas

Print alignment of coding regions (CDS), remove sequences, degap and translate them

gbfalncut -K t/data/ArdellEtAl03_ncbi_popset_32329588.fas t/data/AF194338.1.gb CDS | fasgrep -v "(AF194|3496)" | fastr -snD "-" | fasxl -t 6

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. (2014). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..