.\" Automatically generated by Pod::Man 4.11 (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++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. 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::SearchIO::Writer::HitTableWriter 3pm" .TH Bio::SearchIO::Writer::HitTableWriter 3pm "2020-10-28" "perl v5.30.3" "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::SearchIO::Writer::HitTableWriter \- Tab\-delimited data for Bio::Search::Hit::HitI objects .SH "SYNOPSIS" .IX Header "SYNOPSIS" .SS "Example 1: Using the default columns" .IX Subsection "Example 1: Using the default columns" .Vb 2 \& use Bio::SearchIO; \& use Bio::SearchIO::Writer::HitTableWriter; \& \& my $in = Bio::SearchIO\->new(); \& \& my $writer = Bio::SearchIO::Writer::HitTableWriter\->new(); \& \& my $out = Bio::SearchIO\->new( \-writer => $writer ); \& \& while ( my $result = $in\->next_result() ) { \& $out\->write_result($result, ($in\->report_count \- 1 ? 0 : 1) ); \& } .Ve .SS "Example 2: Specifying a subset of columns" .IX Subsection "Example 2: Specifying a subset of columns" .Vb 2 \& use Bio::SearchIO; \& use Bio::SearchIO::Writer::HitTableWriter; \& \& my $in = Bio::SearchIO\->new(); \& \& my $writer = Bio::SearchIO::Writer::HitTableWriter\->new( \& \-columns => [qw( \& query_name \& query_length \& hit_name \& hit_length \& frac_identical_query \& expect \& )] ); \& \& my $out = Bio::SearchIO\->new( \-writer => $writer, \& \-file => ">searchio.out" ); \& \& while ( my $result = $in\->next_result() ) { \& $out\->write_result($result, ($in\->report_count \- 1 ? 0 : 1) ); \& } .Ve .SS "Custom Labels" .IX Subsection "Custom Labels" You can also specify different column labels if you don't want to use the defaults. Do this by specifying a \f(CW\*(C`\-labels\*(C'\fR hash reference parameter when creating the HitTableWriter object. The keys of the hash should be the column number (left-most column = 1) for the label(s) you want to specify. Here's an example: .PP .Vb 7 \& my $writer = Bio::SearchIO::Writer::HitTableWriter\->new( \& \-columns => [qw( query_name \& query_length \& hit_name \& hit_length )], \& \-labels => { 1 => \*(AqQUERY_GI\*(Aq, \& 3 => \*(AqHIT_IDENTIFIER\*(Aq } ); .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" Bio::SearchIO::Writer::HitTableWriter outputs summary data for each Hit within a search result. Output is in tab-delimited format, one row per Hit. .PP The reason why this is considered summary data is that if a hit contains multiple HSPs, the HSPs will be tiled and the data represents a summary across all HSPs. See below for which columns are affected. See the docs in Bio::Search::Hit::BlastHit for more details on \s-1HSP\s0 tiling. .SS "Available Columns" .IX Subsection "Available Columns" Here are the columns that can be specified in the \f(CW\*(C`\-columns\*(C'\fR parameter when creating a HitTableWriter object. If a \f(CW\*(C`\-columns\*(C'\fR parameter is not specified, this list, in this order, will be used as the default. .PP .Vb 10 \& query_name # Sequence identifier of the query. \& query_length # Full length of the query sequence \& hit_name # Sequence identifier of the hit \& hit_length # Full length of the hit sequence \& round # Round number for hit (PSI\-BLAST) \& expect # Expect value for the alignment \& score # Score for the alignment (e.g., BLAST score) \& bits # Bit score for the alignment \& num_hsps # Number of HSPs (not the "N" value) \& frac_identical_query* # fraction of identical substitutions in query \& frac_identical_hit* # fraction of identical substitutions in hit \& frac_conserved_query* # fraction of conserved substitutions in query \& frac_conserved_hit* # fraction of conserved substitutions in hit \& frac_aligned_query* # fraction of the query sequence that is aligned \& frac_aligned_hit* # fraction of the hit sequence that is aligned \& length_aln_query* # Length of the aligned portion of the query sequence \& length_aln_hit* # Length of the aligned portion of the hit sequence \& gaps_query* # Number of gap characters in the aligned query sequence \& gaps_hit* # Number of gap characters in the aligned hit sequence \& gaps_total* # Number of gap characters in the aligned query and hit sequences \& start_query* # Starting coordinate of the aligned portion of the query sequence \& end_query* # Ending coordinate of the aligned portion of the query sequence \& start_hit* # Starting coordinate of the aligned portion of the hit sequence \& end_hit* # Ending coordinate of the aligned portion of the hit sequence \& strand_query # Strand of the aligned query sequence \& strand_hit # Strand of the aligned hit sequence \& frame # Frame of the alignment (0,1,2) \& ambiguous_aln # Ambiguous alignment indicator (\*(Aqqs\*(Aq, \*(Aqq\*(Aq, \*(Aqs\*(Aq) \& hit_description # Full description of the hit sequence \& query_description # Full description of the query sequence \& rank # The rank order of the hit \& num_hits # Number of hits for the query finding this hit .Ve .PP Items marked with a \f(CW\*(C`*\*(C'\fR report data summed across all HSPs after tiling them to avoid counting data from overlapping regions multiple times. .PP For more details about these columns, see the documentation for the corresponding method in Bio::Search::Result::BlastHit. .SH "TODO" .IX Header "TODO" Figure out the best way to incorporate algorithm-specific score columns. The best route is probably to have algorithm-specific subclasses (e.g., BlastHitTableWriter, FastaHitTableWriter). .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" .IX Header "AUTHOR" Steve Chervitz .PP See the \s-1FEEDBACK\s0 section for where to send bug reports and comments. .SH "COPYRIGHT" .IX Header "COPYRIGHT" Copyright (c) 2001, 2002 Steve Chervitz. All Rights Reserved. .PP This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. .SH "DISCLAIMER" .IX Header "DISCLAIMER" This software is provided \*(L"as is\*(R" without warranty of any kind. .SH "SEE ALSO" .IX Header "SEE ALSO" Bio::SearchIO::Writer::HitTableWriter, Bio::SearchIO::Writer::ResultTableWriter .SH "METHODS" .IX Header "METHODS" .SS "\fBto_string()\fP" .IX Subsection "to_string()" Note: this method is not intended for direct use. The \&\fBSearchIO::write_result()\fR method calls it automatically if the writer is hooked up to a SearchIO object as illustrated in the \s-1SYNOPSIS\s0 section . .PP .Vb 11 \& Title : to_string() \& : \& Usage : print $writer\->to_string( $result_obj, [$include_labels] ); \& : \& Argument : $result_obj = A Bio::Search::Result::BlastResult object \& : $include_labels = boolean, if true column labels are included (default: false) \& : \& Returns : String containing tab\-delimited set of data for each hit \& : in a BlastResult object. Some data is summed across multiple HSPs. \& : \& Throws : n/a .Ve .SS "end_report" .IX Subsection "end_report" .Vb 8 \& Title : end_report \& Usage : $self\->end_report() \& Function: The method to call when ending a report, this is \& mostly for cleanup for formats which require you to \& have something at the end of the document. Nothing for \& a text message. \& Returns : string \& Args : none .Ve .SS "filter" .IX Subsection "filter" .Vb 6 \& Title : filter \& Usage : $writer\->filter(\*(Aqhsp\*(Aq, \e&hsp_filter); \& Function: Filter out either at HSP,Hit,or Result level \& Returns : none \& Args : string => data type, \& CODE reference .Ve