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Bio::Tools::GuessSeqFoUser(Contributed Perl DocumBio::Tools::GuessSeqFormat(3)

NAME
       Bio::Tools::GuessSeqFormat - Module for determining the sequence format
       of the contents of a file, a string, or through a filehandle.

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;
	   # If the filehandle is seekable (STDIN isn't), it will be
	   # returned to its original position.

	   # 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 which is
       seekable, 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")

       ·   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")

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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

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

       bioperl-l@bioperl.org

       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:

	 http://bugzilla.open-bio.org/

AUTHOR
       Andreas Kaehaeri, andreas.kahari@ebi.ac.uk

CONTRIBUTORS
       Heikki Lehvaeslaiho, heikki-at-bioperl-dot-org

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, 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 and if that
	   filehandle is searchable, 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_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_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 precense 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.

perl v5.14.1			  2011-07-22	 Bio::Tools::GuessSeqFormat(3)
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