--- name: "Bio::Tools::GuessSeqFormat" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tools::GuessSeqFormat" --- # Bio::Tools::GuessSeqFormat(3pm) Module for determining the sequence format of the contents of a file, a string, or through a filehandle. ## 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; # 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. ``` 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: ``` https://github.com/bioperl/bioperl-live/issues ``` ## AUTHOR Andreas Kähäri, andreas.kahari@ebi.ac.uk ## CONTRIBUTORS Heikki Lehväslaiho, 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.