.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35) .\" .\" 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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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::AlignIO::stockholm \- stockholm sequence input/output stream .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 1 \& # Do not use this module directly. Use it via the L class. \& \& use Bio::AlignIO; \& use strict; \& \& my $in = Bio::AlignIO\->new(\-format => \*(Aqstockholm\*(Aq, \& \-file => \*(Aqt/data/testaln.stockholm\*(Aq); \& while( my $aln = $in\->next_aln ) { \& \& } .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This object can transform Bio::Align::AlignI objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a \fIwrite_aln()\fR method for (almost) complete stockholm format output. .PP Stockholm alignment records normally contain additional sequence-based and alignment-based annotation .PP .Vb 3 \& GF Lines (alignment feature/annotation): \& #=GF \& Placed above the alignment \& \& GC Lines (Alignment consensus) \& #=GC \& Placed below the alignment \& \& GS Lines (Sequence annotations) \& #=GS \& \& GR Lines (Sequence meta data) \& #=GR .Ve .PP Currently, sequence annotations (those designated with \s-1GS\s0 tags) are parsed only for accession numbers and descriptions. It is intended that full parsing will be added at some point in the near future along with a builder option for optionally parsing alignment annotation and meta data. .PP The following methods/tags are currently used for storing and writing the alignment annotation data. .PP .Vb 7 \& Tag SimpleAlign \& Method \& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- \& AC accession \& ID id \& DE description \& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- \& \& Tag Bio::Annotation TagName Parameters \& Class \& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- \& AU SimpleValue record_authors value \& SE SimpleValue seed_source value \& GA SimpleValue gathering_threshold value \& NC SimpleValue noise_cutoff value \& TC SimpleValue trusted_cutoff value \& TP SimpleValue entry_type value \& SQ SimpleValue num_sequences value \& PI SimpleValue previous_ids value \& DC Comment database_comment comment \& CC Comment alignment_comment comment \& DR Target dblink database \& primary_id \& comment \& AM SimpleValue build_method value \& NE SimpleValue pfam_family_accession value \& NL SimpleValue sequence_start_stop value \& SS SimpleValue sec_structure_source value \& BM SimpleValue build_model value \& RN Reference reference * \& RC Reference reference comment \& RM Reference reference pubmed \& RT Reference reference title \& RA Reference reference authors \& RL Reference reference location \& \-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- \& * RN is generated based on the number of Bio::Annotation::Reference objects .Ve .SS "Custom annotation" .IX Subsection "Custom annotation" Some users may want to add custom annotation beyond those mapped above. Currently there are two methods to do so; however, the methods used for adding such annotation may change in the future, particularly if alignment Writer classes are introduced. In particular, do not rely on changing the global variables \f(CW@WRITEORDER\fR or \f(CW%WRITEMAP\fR as these may be made private at some point. .PP 1) Use (and abuse) the 'custom' tag. The tagname for the object can differ from the tagname used to store the object in the AnnotationCollection. .PP .Vb 10 \& # AnnotationCollection from the SimpleAlign object \& my $coll = $aln\->annotation; \& my $factory = Bio::Annotation::AnnotationFactory\->new(\-type => \& Bio::Annotation::SimpleValue\*(Aq); \& my $rfann = $factory\->create_object(\-value => $str, \& \-tagname => \*(Aqmytag\*(Aq); \& $coll\->add_Annotation(\*(Aqcustom\*(Aq, $rfann); \& $rfann = $factory\->create_object(\-value => \*(Aqfoo\*(Aq, \& \-tagname => \*(Aqbar\*(Aq); \& $coll\->add_Annotation(\*(Aqcustom\*(Aq, $rfann); .Ve .PP \&\s-1OUTPUT:\s0 .PP .Vb 1 \& # STOCKHOLM 1.0 \& \& #=GF ID myID12345 \& #=GF mytag katnayygqelggvnhdyddlakfyfgaglealdffnnkeaaakiinwvaEDTTRGKIQDLV?? \& #=GF mytag TPtd~????LDPETQALLV???????????????????????NAIYFKGRWE?????????~?? \& #=GF mytag ??HEF?A?EMDTKPY??DFQH?TNen?????GRI??????V???KVAM??MF?????????N?? \& #=GF mytag ???DD?VFGYAEL????DE???????L??D??????A??TALELAY?????????????????? \& #=GF mytag ?????????????KG??????Sa???TSMLILLP???????????????D?????????????? \& #=GF mytag ???????????EGTr?????AGLGKLLQ??QL????????SREef??DLNK??L???AH????R \& #=GF mytag ????????????L????????????????????????????????????????R?????????R \& #=GF mytag ??QQ???????V???????AVRLPKFSFefefdlkeplknlgmhqafdpnsdvfklmdqavlvi \& #=GF mytag gdlqhayafkvd???????????????????????????????????????????????????? \& #=GF mytag ???????????????????????????????????????????????????????????????? \& #=GF mytag ???????????????????????????????????????????????????????????????? \& #=GF mytag ???????????????????????????????????????????????????????????????? \& #=GF mytag ?????????????INVDEAG?TEAAAATAAKFVPLSLppkt??????????????????PIEFV \& #=GF mytag ADRPFAFAIR??????E?PAT?G????SILFIGHVEDPTP?msv? \& #=GF bar foo \& ... .Ve .PP 2) Modify the global \f(CW@WRITEORDER\fR and \f(CW%WRITEMAP\fR. .PP .Vb 2 \& # AnnotationCollection from the SimpleAlign object \& my $coll = $aln\->annotation; \& \& # add to WRITEORDER \& my @order = @Bio::AlignIO::stockholm::WRITEORDER; \& push @order, \*(Aqmy_stuff\*(Aq; \& @Bio::AlignIO::stockholm::WRITEORDER = @order; \& \& # make sure new tag maps to something \& $Bio::AlignIO::stockholm::WRITEMAP{my_stuff} = \*(AqHobbit/SimpleValue\*(Aq; \& \& my $rfann = $factory\->create_object(\-value => \*(AqFrodo\*(Aq, \& \-tagname => \*(AqHobbit\*(Aq); \& $coll\->add_Annotation(\*(Aqmy_stuff\*(Aq, $rfann); \& $rfann = $factory\->create_object(\-value => \*(AqBilbo\*(Aq, \& \-tagname => \*(AqHobbit\*(Aq); \& $coll\->add_Annotation(\*(Aqmy_stuff\*(Aq, $rfann); .Ve .PP \&\s-1OUTPUT:\s0 .PP .Vb 1 \& # STOCKHOLM 1.0 \& \& #=GF ID myID12345 \& #=GF Hobbit Frodo \& #=GF Hobbit Bilbo \& .... .Ve .SH "FEEDBACK" .IX Header "FEEDBACK" .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 "AUTHORS \- Chris Fields, Peter Schattner" .IX Header "AUTHORS - Chris Fields, Peter Schattner" Email: cjfields-at-uiuc-dot-edu, schattner@alum.mit.edu .SH "CONTRIBUTORS" .IX Header "CONTRIBUTORS" Andreas Kahari, ak\-at\-ebi.ac.uk Jason Stajich, jason\-at\-bioperl.org .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 12 \& Title : new \& Usage : my $alignio = Bio::AlignIO\->new(\-format => \*(Aqstockholm\*(Aq \& \-file => \*(Aq>file\*(Aq); \& Function: Initialize a new L reader or writer \& Returns : L object \& Args : \-line_length : length of the line for the alignment block \& \-alphabet : symbol alphabet to set the sequences to. If not set, \& the parser will try to guess based on the alignment \& accession (if present), defaulting to \*(Aqdna\*(Aq. \& \-spaces : (optional, def = 1) boolean to add a space in between \& the "# STOCKHOLM 1.0" header and the annotation and \& the annotation and the alignment. .Ve .SS "next_aln" .IX Subsection "next_aln" .Vb 5 \& Title : next_aln \& Usage : $aln = $stream\->next_aln() \& Function: returns the next alignment in the stream. \& Returns : L object \& Args : NONE .Ve .SS "write_aln" .IX Subsection "write_aln" .Vb 5 \& Title : write_aln \& Usage : $stream\->write_aln(@aln) \& Function: writes the $aln object into the stream in stockholm format \& Returns : 1 for success and 0 for error \& Args : L object .Ve .SS "line_length" .IX Subsection "line_length" .Vb 5 \& Title : line_length \& Usage : $obj\->line_length($newval) \& Function: Set the alignment output line length \& Returns : value of line_length \& Args : newvalue (optional) .Ve .SS "spaces" .IX Subsection "spaces" .Vb 6 \& Title : spaces \& Usage : $obj\->spaces(1) \& Function: Set the \*(Aqspaces\*(Aq flag, which prints extra newlines between the \& header and the annotation and the annotation and the alignment \& Returns : sequence data type \& Args : newvalue (optional) .Ve .SS "alignhandler" .IX Subsection "alignhandler" .Vb 5 \& Title : alignhandler \& Usage : $stream\->alignhandler($handler) \& Function: Get/Set the Bio::HandlerBaseI object \& Returns : Bio::HandlerBaseI \& Args : Bio::HandlerBaseI .Ve