bio::searchio::gmap_f9(3pm) [debian man page]
Bio::SearchIO::gmap_f9(3pm) User Contributed Perl Documentation Bio::SearchIO::gmap_f9(3pm) NAME
Bio::SearchIO::gmap_f9 - Event generator for parsing gmap reports (Z format) SYNOPSIS
# Do not use this object directly - it is used as part of the # Bio::SearchIO system. use Bio::SearchIO; my $searchio = Bio::SearchIO->new(-format => 'gmap', -file => 't/data/her2.gmapz'); while( my $result = $searchio->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { # ... } } } DESCRIPTION
This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a GMAP "compressed" report (from gmap run with -Z flag) Read the Bio::SearchIO for more information about how to use this. REVERSE STRAND AND BIOPERL COORDINATES I believe that I'm doing the correct thing when reporting hits on the negative strand of the genome. In particular, I've compared the "exons" this code generates with the set returned by ncbi's megablast web service. NCBI's hsp's are ordered differently and have a different genomic location (off by ~18,000,000 bases, padding?) but the starts, ends, and lengths were similar and my strand handling matches theirs. E.g. CDNA GENOME start end strand start end strand blast 1913 2989 1 86236731 86237808 -1 1 475 1 86260509 86260983 -1 1510 1727 1 86240259 86240476 -1 841 989 1 86243034 86243182 -1 1381 1514 1 86240630 86240763 -1 989 1122 1 86242457 86242590 -1 599 729 1 86247470 86247600 -1 473 608 1 86259972 86260107 -1 1255 1382 1 86240837 86240964 -1 730 842 1 86244040 86244152 -1 1813 1921 1 86238123 86238231 -1 1725 1814 1 86239747 86239836 -1 1167 1256 1 86241294 86241383 -1 1120 1188 1 86242319 86242387 -1 gmap 1 475 1 104330509 104330983 -1 476 600 1 104329980 104330104 -1 601 729 1 104317470 104317598 -1 730 841 1 104314041 104314152 -1 842 989 1 104313034 104313181 -1 990 1121 1 104312458 104312589 -1 1122 1187 1 104312320 104312385 -1 1188 1256 1 104311294 104311362 -1 1257 1382 1 104310837 104310962 -1 1383 1511 1 104310633 104310761 -1 1512 1726 1 104310260 104310474 -1 1727 1814 1 104309747 104309834 -1 1815 1917 1 104308127 104308229 -1 1918 2989 1 104306731 104307802 -1 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 the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - George Hartzell Email hartzell@alerce.com CONTRIBUTORS
Additional contributors names and emails here APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore (_). next_result Title : next_result Usage : $result = stream->next_result Function: Reads the next ResultI object from the stream and returns it. Returns : A Bio::Search::Result::ResultI object Args : n/a perl v5.14.2 2012-03-02 Bio::SearchIO::gmap_f9(3pm)
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Bio::SearchIO::hmmer_pull(3pm) User Contributed Perl Documentation Bio::SearchIO::hmmer_pull(3pm) NAME
Bio::SearchIO::hmmer_pull - A parser for HMMER output SYNOPSIS
# do not use this class directly it is available through Bio::SearchIO use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer_pull', -file => 't/data/hmmpfam.bigout'); while (my $result = $in->next_result) { # this is a Bio::Search::Result::HmmpfamResult object print $result->query_name(), " for HMM ", $result->hmm_name(), " "; while (my $hit = $result->next_hit) { print $hit->name(), " "; while (my $hsp = $hit->next_hsp) { print "length is ", $hsp->length(), " "; } } } DESCRIPTION
This object implements a pull-parser for HMMER output. It is fast since it only does work on request (hence 'pull'). 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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Sendu Bala Email bix@sendu.me.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::SearchIO::hmmer_pull->new(); Function: Builds a new Bio::SearchIO::hmmer_pull object Returns : Bio::SearchIO::hmmer_pull Args : -fh/-file => HMMER output filename -format => 'hmmer_pull' -evalue => float or scientific notation number to be used as an evalue cutoff for hits -score => integer or scientific notation number to be used as a score value cutoff for hits -hsps => integer minimum number of hsps (domains) a hit must have -piped_behaviour => 'temp_file'|'memory'|'sequential_read' -piped_behaviour defines what the parser should do if the input is an unseekable filehandle (eg. piped input), see Bio::PullParserI::chunk for details. Default is 'sequential_read'. next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed. Returns : integer Args : none rewind Title : rewind Usage : $searchio->rewind; Function: Allow one to reset the Result iterator to the beginning, so that next_result() will subsequently return the first result and so on. NB: result objects are not cached, so you will get new result objects each time you rewind. Also, note that result_count() counts the number of times you have called next_result(), so will not be able tell you how many results there were in the file if you use rewind(). Returns : n/a Args : none perl v5.14.2 2012-03-02 Bio::SearchIO::hmmer_pull(3pm)