Bio::Tools::GuessSeqFormat - Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
# 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;
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.
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")
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
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.
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/
Andreas Kähäri, andreas.kahari@ebi.ac.uk
Heikki Lehväslaiho, heikki-at-bioperl-dot-org
Methods available to Bio::Tools::GuessSeqFormat objects are described below. Methods with names beginning with an underscore are considered to be internal.
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.
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.
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.
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.
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.
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.
From bioperl test data, and from "http://www.isrec.isb-sib.ch/DEA/module8/B_Stevenson/Practicals/transcriptome_recon/transcriptome_recon.html".
From various blast results.
From "http://www.ebi.ac.uk/help/formats.html".
From "http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3.3".
From bioperl test data.
From bioperl testdata.
From bioperl, Bio::SeqIO::gcg.
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)
From "http://paup.csit.fsu.edu/nfiles.html".
From bioperl test data. More detail from "http://www.umdnj.edu/rcompweb/PA/Notes/GenbankFF.htm" (TODO: dead link)
From the ensembl broswer (AlignView data export).
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).
From "http://www.ebi.ac.uk/help/formats.html". The ".,()" spotted in bioperl test data.
From "http://www.ebi.ac.uk/help/formats.html". Initial space allowed on first line (spotted in ensembl AlignView exported data).
From "http://prodom.prabi.fr/prodom/current/documentation/data.php".
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.
From "http://ca.expasy.org/sprot/userman.html#entrystruc".
Contributed by Heikki.
1 POD Error
The following errors were encountered while parsing the POD:
Non-ASCII character seen before =encoding in 'Kähäri,'. Assuming CP1252
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.