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>
  --extend <integer>
  --zero
  --cat
  --pad <integer>
  --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 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. If Bam support is available, the fasta file can be indexed with samtools, allowing for a faster fasta experience. Alternatively, the name of a Bio::DB::SeqFeature::Store annotation database that contains genomic sequence may be provided. The database name may be obtained from the input file metadata. Required only if collecting sequence from genomic coordinates.

--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.

--extend <integer>

Optionally provide the number of extra base pairs to extend the start and stop positions. This will then include the given number of base pairs of flanking sequence from the database. This only applies when sequence is obtained from the database.

--zero

Input file is in interbase or 0-based coordinates. This should be automatically detected for most known file formats, e.g. BED.

--cat

Optionally indicate that all of the sequences should be concatenated into a single Fasta sequence. The default is to write a multi-fasta file with separate sequences.

--pad <integer>

When concatenating sequences into a single Fasta sequence, optionally indicate the number of 'N' bases to insert between the individual sequences. The default is zero.

--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 (BED file, for example) and generate either a multi-sequence fasta file containing the sequences of each feature defined in the input file, or optionally a single concatenated fasta file. If concatenating, the individual sequences may be padded with the given number of 'N' bases.

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.

Alternatively, 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 Artistic License 2.0.