Bio::ToolBox - data2fasta

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data2fasta.pl

A program to retrieve sequences from a list of features

SYNOPSIS

data2fasta.pl [–options…] <filename>

File Options:
-i --in <filename>                input file: txt, gff, bed, ucsc, vcf, etc
-o --out <filename>               output file name

Database:
-d --db <name|fasta>              annotation database with sequence or fasta

Feature selection:
-f --feature <text>               feature when parsing gff3, gtf, or ucsc input
-u --subfeature [exon|cds|        collect over subfeatures 
      5p_utr|3p_utr] 

Column indices:
-n --name --id <index>            name or ID column
-s --seq <index>                  column with sequence
-c --chr <index>                  chromosome column
-b --begin --start <index>        start coordinate column
-e --end --stop <index>           stop coordinate column
-t --strand <index>               strand column
-x --extend <integer>             extend coordinates in both directions
--desc <index>                    description column

Fasta output options:
--cat                             concatenate all sequences into one
--pad <integer>                   pad concatenated sequences with Ns

General options:
-z --gz                           compress output fasta file
-v --version                      print version and exit
-h --help                         show extended documentation

OPTIONS

The command line flags and descriptions:

File options

• –in <filename>

  Specify the input data file. The file may be a tab-delimited text file with coordinate columns for fetching genomic sequence. Alternatively it may be an annotation file such as GFF3, GTF, refFlat, genePred, etc, in which case sequence may be selected from certain features and subfeatures, for example mRNA and CDS. Note that no collapsing of redundant or overlapping subfeatures is performed; see get_features.pl. Finally, text files with sequence in a column, for example oligo sequences, may be used, skipping the need for database sequence retrieval. The file may be compressed with gzip.

• –out <filename>

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

Database

• –db <name

  fasta>

  Provide the name of an uncompressed Fasta file (multi-fasta is ok) or directory containing multiple fasta files representing the genomic sequence. If Bam file support is available, then the fasta will be indexed and searched with a fasta index .fai file. If not, then the fasta can by indexed by the older Bio::DB::Fasta adapter, which also supports a directory of multiple fasta files. If the index is not present, then the parent directory must be writeable. Alternatively, the name of a Bio::DB::SeqFeature::Store annotation database that contains genomic sequence may also be provided. The database name may be obtained from the input file metadata. Required only if collecting sequence from genomic coordinates.

Feature selection

• –feature <text>

  When parsing a gene annotation file such as a GFF3, GTF, or UCSC format file, provide a feature type to select features if desired.

• –subfeature [exon

  cds

  5p_utr

  3p_utr]

  When collecting from subfeatures, indicate the subfeature type from list available. No merging of overlapping or redundant subfeatures is performed here. See get_features.pl.

Column indices

• –name –id <column_index>

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

• –seq <column_index>

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

• –chr <column_index>

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

• –start <column_index>

• –begin <column_index>

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

• –stop <column_index>

• –end <column_index>

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

• –strand <column_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.

• –desc <column_index>

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

Fasta output options

• –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.

General options

• –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. Multiple database adapters are supported for indexing genomic fastas, including the Bio::DB::HTS package, the Bio::DB::Sam package, or the BioPerl Bio::DB::Fasta adapter. Annotation databases such as Bio::DB::SeqFeature::Store are also supported.
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.