NAME

data2fasta.pl

A script to retrieve sequences from a list of features

SYNOPSIS

data2fasta.pl [--options...] <filename>

Options:
--in <filename>
--db <name|file|directory>
--id <index>
--seq <index>
--desc <index>
--chr <index>
--start <index>
--stop <index>
--strand <index>
--out <filename> 
--gz
--version
--help

OPTIONS

The command line flags and descriptions:

--in <filename>

Specify the input data file. The file should be a tab-delimited text file with columns representing the sequence id or name, sequence, description, chromosome, start, stop, and/or strand information. The file may be compressed with gzip.

--db <name|file|directory>

Provide the name of a Bio::DB::SeqFeature::Store database from which to collect the genomic sequence. A relational database name, SQLite file, or GFF3 file with sequence may be provided. Alternatively, provide the name of an uncompressed Fasta file (multi-fasta is ok) or directory containing multiple fasta files representing the genomic sequence. The directory must be writeable for a small index file to be written. The database name may be obtained from the input file metadata. Required.

--id <index>

Optionally specify the index for the name or ID column. It may be automatically determined from the column header.

--seq <index>

Optionally specify the index for the sequence column. It may be automatically determined from the column header.

--desc <index>

Optionally specify the index of the description column. It may be automatically determined from the column header.

--chr <index>

Optionally specify the index for the chromosome column. It may be automatically determined from the column header.

--start <index>

Optionally specify the index for the start position column. It may be automatically determined from the column header.

--stop <index>

Optionally specify the index for the stop position column. It may be automatically determined from the column header.

--strand <index>

Optionally specify the index for the strand column. It may be automatically determined from the column header.

--out <filename>

Specify the output filename. By default it uses the input file basename.

--gz

Specify whether (or not) the output file should be compressed with gzip.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

This program will take a tab-delimited text file (tim data formated file, for example) and generate a multi-sequence fasta file containing the sequences of each feature defined in the input file. This program has two modes.

If the name and sequence is already present in the file, it will generate the fasta file directly from the file content.

If only genomic position information (chromosome, start, stop, and optionally strand) is present in the file, then the sequence will be retrieved from a database, either a Bio::DB::SeqFeature::Store database, a genomic sequence multi-fasta, or a directory of multiple fasta files. If strand information is provided, then the sequence reverse complement is returned for reverse strand coordinates.

AUTHOR

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0.