.\" 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++. 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::gmap_f9 3pm" .TH Bio::SearchIO::gmap_f9 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::SearchIO::gmap_f9 \- Event generator for parsing gmap reports (Z format) .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& # 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 => \*(Aqgmap\*(Aq, \& \-file => \*(Aqt/data/her2.gmapz\*(Aq); \& while( my $result = $searchio\->next_result ) { \& while( my $hit = $result\->next_hit ) { \& while( my $hsp = $hit\->next_hsp ) { \& # ... \& } \& } \& } .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a \s-1GMAP\s0 \*(L"compressed\*(R" report (from gmap run with \-Z flag) Read the Bio::SearchIO for more information about how to use this. .SS "\s-1REVERSE STRAND AND BIOPERL COORDINATES\s0" .IX Subsection "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 \&\*(L"exons\*(R" this code generates with the set returned by ncbi's megablast web service. \s-1NCBI\s0'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. .PP .Vb 2 \& CDNA GENOME \& start end strand start end strand .Ve .PP 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 .PP 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 .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 the Bioperl mailing list. 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 "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHOR \- George Hartzell" .IX Header "AUTHOR - George Hartzell" Email hartzell@alerce.com .SH "CONTRIBUTORS" .IX Header "CONTRIBUTORS" Additional contributors names and emails here .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore (_). .SS "next_result" .IX Subsection "next_result" .Vb 5 \& 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 .Ve