Bio::Tools::GuessSeqFormat(3) Module for determining the sequence

SYNOPSIS


# To guess the format of a flat file, given a filename:
my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $filename );
my $format = $guesser->guess;
# To guess the format from an already open filehandle:
my $guesser = Bio::Tools::GuessSeqFormat->new( -fh => $filehandle );
my $format = $guesser->guess;
# The filehandle will be returned to its original position. Note that this
# filehandle can be STDIN.
# To guess the format of one or several lines of text (with
# embedded newlines):
my $guesser = Bio::Tools::GuessSeqFormat->new( -text => $linesoftext );
my $format = $guesser->guess;
# To create a Bio::Tools::GuessSeqFormat object and set the
# filename, filehandle, or line to parse afterwards:
my $guesser = Bio::Tools::GuessSeqFormat->new();
$guesser->file($filename);
$guesser->fh($filehandle);
$guesser->text($linesoftext);
# To guess in one go, given e.g. a filename:
my $format = Bio::Tools::GuessSeqFormat->new( -file => $filename )->guess;

DESCRIPTION

Bio::Tools::GuessSeqFormat tries to guess the format (``swiss'', ``pir'', ``fasta'' etc.) of the sequence or MSA in a file, in a scalar, or through a filehandle.

The guess() method of a Bio::Tools::GuessSeqFormat object will examine the data, line by line, until it finds a line to which only one format can be assigned. If no conclusive guess can be made, undef is returned.

If the Bio::Tools::GuessSeqFormat object is given a filehandle, e.g. STDIN, it will be restored to its original position on return from the guess() method.

Formats

Tests are currently implemented for the following formats:
  • ACeDB (``ace'')
  • Blast (``blast'')
  • ClustalW (``clustalw'')
  • Codata (``codata'')
  • EMBL (``embl'')
  • FastA sequence (``fasta'')
  • FastQ sequence (``fastq'')
  • FastXY/FastA alignment (``fastxy'')
  • Game XML (``game'')
  • GCG (``gcg'')
  • GCG Blast (``gcgblast'')
  • GCG FastA (``gcgfasta'')
  • GDE (``gde'')
  • Genbank (``genbank'')
  • Genscan (``genscan'')
  • GFF (``gff'')
  • HMMER (``hmmer'')
  • PAUP/NEXUS (``nexus'')
  • Phrap assembly file (``phrap'')
  • NBRF/PIR (``pir'')
  • Mase (``mase'')
  • Mega (``mega'')
  • GCG/MSF (``msf'')
  • Pfam (``pfam'')
  • Phylip (``phylip'')
  • Prodom (``prodom'')
  • Raw (``raw'')
  • RSF (``rsf'')
  • Selex (``selex'')
  • Stockholm (``stockholm'')
  • Swissprot (``swiss'')
  • Tab (``tab'')
  • Variant Call Format (``vcf'')

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: 

  https://github.com/bioperl/bioperl-live/issues

AUTHOR

Andreas Ka.ha.ri, [email protected]

CONTRIBUTORS

Heikki Lehva.slaiho, heikki-at-bioperl-dot-org Mark A. Jensen, maj-at-fortinbras-dot-us

METHODS

Methods available to Bio::Tools::GuessSeqFormat objects are described below. Methods with names beginning with an underscore are considered to be internal.

new

 Title      : new
 Usage      : $guesser = Bio::Tools::GuessSeqFormat->new( ... );
 Function   : Creates a new object.
 Example    : See SYNOPSIS.
 Returns    : A new object.
 Arguments  : -file The filename of the file whose format is to
                    be guessed, e.g. STDIN, or
              -fh   An already opened filehandle from which a text
                    stream may be read, or
              -text A scalar containing one or several lines of
                    text with embedded newlines.
    If more than one of the above arguments are given, they
    are tested in the order -text, -file, -fh, and the first
    available argument will be used.

file

 Title      : file
 Usage      : $guesser->file($filename);
              $filename = $guesser->file;
 Function   : Gets or sets the current filename associated with
              an object.
 Returns    : The new filename.
 Arguments  : The filename of the file whose format is to be
              guessed.
    A call to this method will clear the current filehandle and
    the current lines of text associated with the object.

fh

 Title      : fh
 Usage      : $guesser->fh($filehandle);
              $filehandle = $guesser->fh;
 Function   : Gets or sets the current filehandle associated with
              an object.
 Returns    : The new filehandle.
 Arguments  : An already opened filehandle from which a text
              stream may be read.
    A call to this method will clear the current filename and
    the current lines of text associated with the object.

text

 Title      : text
 Usage      : $guesser->text($linesoftext);
              $linesofext = $guesser->text;
 Function   : Gets or sets the current text associated with an
              object.
 Returns    : The new lines of texts.
 Arguments  : A scalar containing one or several lines of text,
              including embedded newlines.
    A call to this method will clear the current filename and
    the current filehandle associated with the object.

guess

 Title      : guess
 Usage      : $format = $guesser->guess;
              @format = $guesser->guess; # if given a line of text
 Function   : Guesses the format of the data accociated with the
              object.
 Returns    : A format string such as "swiss" or "pir".  If a
              format can not be found, undef is returned.
 Arguments  : None.
    If the object is associated with a filehandle, the position
    of the filehandle will be returned to its original position
    before the method returns.

HELPER SUBROUTINES

All helper subroutines will, given a line of text and the line number of the same line, return 1 if the line possibly is from a file of the type that they perform a test of.

A zero return value does not mean that the line is not part of a certain type of file, just that the test did not find any characteristics of that type of file in the line.

_possibly_ace

From bioperl test data, and from ``http://www.isrec.isb-sib.ch/DEA/module8/B_Stevenson/Practicals/transcriptome_recon/transcriptome_recon.html''.

_possibly_blast

 From various blast results.

_possibly_bowtie

Contributed by kortsch.

_possibly_clustalw

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_codata

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_embl

From ``http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3.3''.

_possibly_fasta

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_fastq

From bioperl test data.

_possibly_fastxy

From bioperl test data.

_possibly_game

From bioperl testdata.

_possibly_gcg

From bioperl, Bio::SeqIO::gcg.

_possibly_gcgblast

From bioperl testdata.

_possibly_gcgfasta

From bioperl testdata.

_possibly_gde

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_genbank

From ``http://www.ebi.ac.uk/help/formats.html''. Format of [apparantly optional] file header from ``http://www.umdnj.edu/rcompweb/PA/Notes/GenbankFF.htm''. (TODO: dead link)

_possibly_genscan

From bioperl test data.

_possibly_gff

From bioperl test data.

_possibly_hmmer

From bioperl test data.

_possibly_nexus

From ``http://paup.csit.fsu.edu/nfiles.html''.

_possibly_mase

From bioperl test data. More detail from ``http://www.umdnj.edu/rcompweb/PA/Notes/GenbankFF.htm'' (TODO: dead link)

_possibly_mega

From the ensembl broswer (AlignView data export).

_possibly_msf

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_phrap

From ``http://biodata.ccgb.umn.edu/docs/contigimage.html''. (TODO: dead link) From ``http://genetics.gene.cwru.edu/gene508/Lec6.htm''. (TODO: dead link) From bioperl test data (``*.ace.1'' files).

_possibly_pir

From ``http://www.ebi.ac.uk/help/formats.html''. The ``.,()'' spotted in bioperl test data.

_possibly_pfam

From bioperl test data.

_possibly_phylip

From ``http://www.ebi.ac.uk/help/formats.html''. Initial space allowed on first line (spotted in ensembl AlignView exported data).

_possibly_prodom

From ``http://prodom.prabi.fr/prodom/current/documentation/data.php''.

_possibly_raw

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_rsf

From ``http://www.ebi.ac.uk/help/formats.html''.

_possibly_selex

From ``http://www.ebc.ee/WWW/hmmer2-html/node27.html''.

Assuming presence of Selex file header. Data exported by Bioperl on Pfam and Selex formats are identical, but Pfam file only holds one alignment.

_possibly_stockholm

From bioperl test data.

_possibly_swiss

From ``http://ca.expasy.org/sprot/userman.html#entrystruc''.

_possibly_tab

Contributed by Heikki.

_possibly_vcf

From ``http://www.1000genomes.org/wiki/analysis/vcf4.0''.

Assumptions made about sanity - format and date lines are line 1 and 2 respectively. This is not specified in the format document.

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