.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "Bio::Tools::Sim4::Results 3pm" .TH Bio::Tools::Sim4::Results 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Tools::Sim4::Results \- Results of one Sim4 run .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 8 \& # to preset the order of EST and genomic file as given on the sim4 \& # command line: \& my $sim4 = Bio::Tools::Sim4::Results\->new(\-file => \*(Aqresult.sim4\*(Aq, \& \-estfirst => 1); \& # to let the order be determined automatically (by length comparison): \& $sim4 = Bio::Tools::Sim4::Results\->new( \-file => \*(Aqsim4.results\*(Aq ); \& # filehandle: \& $sim4 = Bio::Tools::Sim4::Results\->new( \-fh => \e*INPUT ); \& \& # parse the results \& while(my $exonset = $sim4\->next_exonset()) { \& # $exonset is\-a Bio::SeqFeature::Generic with Bio::Tools::Sim4::Exons \& # as sub features \& print "Delimited on sequence ", $exonset\->seq_id(), \& "from ", $exonset\->start(), " to ", $exonset\->end(), "\en"; \& foreach my $exon ( $exonset\->sub_SeqFeature() ) { \& # $exon is\-a Bio::SeqFeature::FeaturePair \& print "Exon from ", $exon\->start, " to ", $exon\->end, \& " on strand ", $exon\->strand(), "\en"; \& # you can get out what it matched using the est_hit attribute \& my $homol = $exon\->est_hit(); \& print "Matched to sequence ", $homol\->seq_id, \& " at ", $homol\->start," to ", $homol\->end, "\en"; \& } \& } \& \& # essential if you gave a filename at initialization (otherwise the file \& # stays open) \& $sim4\->close(); .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" The sim4 module provides a parser and results object for sim4 output. The sim4 results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the \*(L"normal\*(R" seqfeature manner. .PP The sim4 Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The \&\f(CW$esthit\fR = \f(CW$exon\fR\->\fBest_hit()\fR is the alignment as a feature on the matching object (normally, an \s-1EST\s0), in which the start/end points are where the hit lies. .PP To make this module work sensibly you need to run .PP .Vb 3 \& sim4 genomic.fasta est.database.fasta \&or \& sim4 est.fasta genomic.database.fasta .Ve .PP To get the sequence identifiers recorded for the first sequence, too, use A=4 as output option for sim4. .PP One fiddle here is that there are only two real possibilities to the matching criteria: either one sequence needs reversing or not. Because of this, it is impossible to tell whether the match is in the forward or reverse strand of the genomic \s-1DNA.\s0 We solve this here by assuming that the genomic \s-1DNA\s0 is always forward. As a consequence, the strand attribute of the matching \s-1EST\s0 is unknown, and the strand attribute of the genomic \s-1DNA\s0 (i.e., the Exon object) will reflect the direction of the hit. .PP See the documentation of \fBparse_next_alignment()\fR for abilities of the parser to deal with the different output format options of sim4. .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- Ewan Birney, Hilmar Lapp" .IX Header "AUTHOR - Ewan Birney, Hilmar Lapp" Ewan Birney Hilmar Lapp or . .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "analysis_method" .IX Subsection "analysis_method" .Vb 5 \& Usage : $sim4\->analysis_method(); \& Purpose : Inherited method. Overridden to ensure that the name matches \& /sim4/i. \& Returns : String \& Argument : n/a .Ve .SS "parse_next_alignment" .IX Subsection "parse_next_alignment" .Vb 9 \& Title : parse_next_alignment \& Usage : @exons = $sim4_result\->parse_next_alignment; \& foreach $exon (@exons) { \& # do something \& } \& Function: Parses the next alignment of the Sim4 result file and returns the \& found exons as an array of Bio::Tools::Sim4::Exon objects. Call \& this method repeatedly until an empty array is returned to get the \& results for all alignments. \& \& The $exon\->seq_id() attribute will be set to the identifier of the \& respective sequence for both sequences if A=4 was used in the sim4 \& run, and otherwise for the second sequence only. If the output does \& not contain the identifier, the filename stripped of path and \& extension is used instead. In addition, the full filename \& will be recorded for both features ($exon inherits off \& Bio::SeqFeature::SimilarityPair) as tag \*(Aqfilename\*(Aq. The length \& is accessible via the seqlength() attribute of $exon\->query() and \& $exon\->est_hit(). \& \& Note that this method is capable of dealing with outputs generated \& with format 0,1,3, and 4 (via the A=n option to sim4). It \& automatically determines which of the two sequences has been \& reversed, and adjusts the coordinates for that sequence. It will \& also detect whether the EST sequence(s) were given as first or as \& second file to sim4, unless this has been specified at creation \& time of the object. \& \& Example : \& Returns : An array of Bio::Tools::Sim4::Exon objects \& Args : .Ve .SS "next_exonset" .IX Subsection "next_exonset" .Vb 12 \& Title : next_exonset \& Usage : $exonset = $sim4_result\->parse_next_exonset; \& print "Exons start at ", $exonset\->start(), \& "and end at ", $exonset\->end(), "\en"; \& foreach $exon ($exonset\->sub_SeqFeature()) { \& # do something \& } \& Function: Parses the next alignment of the Sim4 result file and returns the \& set of exons as a container of features. The container is itself \& a Bio::SeqFeature::Generic object, with the Bio::Tools::Sim4::Exon \& objects as sub features. Start, end, and strand of the container \& will represent the total region covered by the exons of this set. \& \& See the documentation of parse_next_alignment() for further \& reference about parsing and how the information is stored. \& \& Example : \& Returns : An Bio::SeqFeature::Generic object holding Bio::Tools::Sim4::Exon \& objects as sub features. \& Args : .Ve .SS "next_feature" .IX Subsection "next_feature" .Vb 7 \& Title : next_feature \& Usage : while($exonset = $sim4\->next_feature()) { \& # do something \& } \& Function: Does the same as L. See there for documentation of \& the functionality. Call this method repeatedly until FALSE is \& returned. \& \& The returned object is actually a SeqFeatureI implementing object. \& This method is required for classes implementing the \& SeqAnalysisParserI interface, and is merely an alias for \& next_exonset() at present. \& \& Example : \& Returns : A Bio::SeqFeature::Generic object. \& Args : .Ve