From: martinahansen Date: Mon, 16 Nov 2009 07:39:44 +0000 (+0000) Subject: misc changes X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=a4aed65b5dac7de589e08050958213260d58626d;p=biopieces.git misc changes git-svn-id: http://biopieces.googlecode.com/svn/trunk@760 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq index 44d09ae..8ccd201 100755 --- a/bp_bin/bowtie_seq +++ b/bp_bin/bowtie_seq @@ -153,21 +153,9 @@ sub bowtie2biopiece my ( $record, $s_id, $s_len, $hits ); - # S_ID: contig00005 length=75232 numreads=13115 - - if ( $entry->[ 2 ] =~ /^(.+) length=(\d+)\s+numreads=(\d+)$/ ) - { - $record->{ 'S_ID' } = $1; - # $record->{ 'S_LEN' } = $2; - $record->{ 'HITS' } = $3; - } - else - { - Maasha::Common::error( qq(BAD S_ID: "$entry->[ 2 ]") ); - } - $record->{ 'Q_ID' } = $entry->[ 0 ]; $record->{ 'STRAND' } = $entry->[ 1 ]; + $record->{ 'S_ID' } = $entry->[ 2 ]; $record->{ 'S_BEG' } = $entry->[ 3 ]; $record->{ 'SEQ' } = $entry->[ 4 ]; $record->{ 'SCORES' } = $entry->[ 5 ]; @@ -179,6 +167,7 @@ sub bowtie2biopiece $record->{ 'SCORES' } =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) ); + $record->{ 'HITS' } = '.'; $record->{ 'REC_TYPE' } = "BOWTIE"; return wantarray ? %{ $record } : $record; diff --git a/www/cgi-bin/index.cgi b/www/cgi-bin/index.cgi index 1b327bc..01a0011 100755 --- a/www/cgi-bin/index.cgi +++ b/www/cgi-bin/index.cgi @@ -218,7 +218,7 @@ sub sec_browse map { push @img, Maasha::XHTML::area( href => "www.dmi.dk", shape => "rect", coords => "$_->{ x1 }, $_->{ y1 }, $_->{ x2 }, $_->{ y2 }", title => "$_->{ title }" ) } @{ $features }; - push @img, Maasha::XHTML::map_beg(); + push @img, Maasha::XHTML::map_end(); push @html, Maasha::XHTML::p( txt => join( "\n", @img ) ); @@ -230,11 +230,18 @@ sub sec_browse sub nav_list_clade { - my ( $list_clade ); + my ( @dirs, $dir, @list_clade ); - $list_clade = [ qw( Eukaryote Bacillus Fish ) ]; + @dirs = Maasha::Filesys::ls_dirs( "Data" ); - return wantarray ? @{ $list_clade } : $list_clade; + foreach $dir ( @dirs ) + { + next if $dir eq "Data/." or $dir eq "Data/.."; + + push @list_clade, ( split "/", $dir )[ -1 ]; + } + + return wantarray ? @list_clade : \@list_clade; } diff --git a/www/cgi-bin/kiss.css b/www/cgi-bin/kiss.css new file mode 100644 index 0000000..af21647 --- /dev/null +++ b/www/cgi-bin/kiss.css @@ -0,0 +1,318 @@ +/* CSS test /* + +/* Martin A. Hansen, July 2005 /* +/* email: mail@maasha.dk */ + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUGGESTED READING <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +/* +/* +/* http://www.w3.org/TR/CSS21/ +/* http://www.w3.org/TR/CSS21/propidx.html +/* http://www.w3schools.com/css/css_reference.asp +/* http://htmldog.com/guides/cssbeginner/ +/* http://htmldog.com/guides/cssintermediate/ +/* http://htmldog.com/guides/cssadvanced/ +/* +/* +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> UNITS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +/* +/* +/* Unit Description +/* % a percentage of something +/* in inch +/* cm centimeter +/* mm millimeter +/* em one em is equal to the font size of the current element +/* ex one ex is the x-height of a font, the x-height is usually about half the font-size +/* pt point (1 pt is the same as 1/72 inch) +/* pc pica (1 pc is the same as 12 points) +/* px pixels (a dot on the computer screen) +/* +/* +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> COLORS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +/* +/* +/* Examples (all give the same result): +/* red +/* rgb(255,0,0) +/* rgb(100%,0%,0%) +/* #ff0000 +/* #f00 +/* +/* There are 16 valid predefined colour names: +/* aqua +/* black +/* blue +/* fuchsia +/* gray +/* green +/* lime +/* maroon, +/* navy +/* olive +/* purple +/* red, +/* silver +/* teal +/* white +/* yellow +/* +/* transparent is also valid +/* +/* +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PROPERTIES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +/* +/* +/* background-attachment +/* background-color +/* background-image +/* background-position +/* background-repeat +/* background +/* border-collapse +/* border-color +/* border-spacing +/* border-style +/* border-top border-right border-bottom border-left +/* border-top-color border-right-color border-bottom-color border-left-color +/* border-top-style border-right-style border-bottom-style border-left-style +/* border-top-width border-right-width border-bottom-width border-left-width +/* border-width +/* border +/* bottom +/* caption-side +/* clear +/* clip +/* color +/* content +/* counter-increment +/* counter-reset +/* cursor +/* direction +/* display +/* empty-cells +/* float +/* font-family +/* font-size +/* font-style +/* font-variant +/* font-weight +/* font +/* height +/* left +/* letter-spacing +/* line-height +/* list-style-image +/* list-style-position +/* list-style-type +/* list-style +/* margin-right margin-left +/* margin-top margin-bottom +/* margin +/* max-height +/* max-width +/* min-height +/* min-width +/* orphans +/* outline-color +/* outline-style +/* outline-width +/* outline +/* overflow +/* padding-top padding-right padding-bottom padding-left +/* padding +/* page-break-after +/* page-break-before +/* page-break-inside +/* position +/* quotes +/* right +/* table-layout +/* text-align +/* text-decoration +/* text-indent +/* text-transform +/* top +/* unicode-bidi +/* vertical-align +/* visibility +/* white-space +/* widows +/* width +/* word-spacing +/* z-index +/* +/* +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTORS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +/* +/* +/* Name Values +/* ---- ------ +/* ascent +/* baseline +/* bbox , , , +/* cap-height +/* centerline +/* definition-src +/* descent +/* font-family [ | ] [, [ | ]] +/* font-size all | [, ] +/* font-stretch all | [ normal | ultra-condensed | extra-condensed | condensed | semi-condensed | semi-expanded | expanded | extra-expanded | ultra-expanded ] [, [ normal | +/* ultra-condensed | extra-condensed | condensed | semi-condensed | semi-expanded | expanded | extra-expanded | ultra-expanded] ] +/* font-style all | [ normal | italic | oblique ] [, [normal | italic | oblique] ] +/* font-variant [normal | small-caps] [,[normal | small-caps]] +/* font-weight all | [normal | bold | 100 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900] [, [normal | bold | 100 | 200 | 300 | 400 | 500 | 600 | 700 | 800 | 900]] +/* mathline +/* panose-1 []{10} +/* slope +/* src [ [format( [, ]*)] | ] [, [format( [, ]*)] | ] +/* stemh +/* stemv +/* topline +/* unicode-range [, ] +/* units-per-em +/* widths [ ]? [ ]+ [,[ ]? ]+] +/* x-height +/* +/* +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PROPERTY & VALUE EXAMPLES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +/* +/* +/* color: yellow; +/* background-color: blue; +/* font-family: "Times New Roman", arial, helvetica, serif; +/* font-size: 0.8em; +/* text-decoration: none; +/* font-style: italic; +/* text-transform: uppercase; +/* letter-spacing: 0.5em; +/* word-spacing: 2em; +/* line-height: 1.5em; +/* text-align: center; +/* margin: 1em; +/* padding: 3em; +/* border-style: dashed; +/* border-width: 3px; +/* border-left-width: 10px; +/* border-right-width: 10px; +/* border-color: red; +/* +/* +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DIV <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */ + +div.navigate { + +} + +div.browse { + text-align: center; +} + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GENERIC CLASSES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */ + + +.bold { + font-weight: bold; +} + + +.italic { + font-style: italic; +} + + +.oblique { + font-style: oblique; +} + + +.align_right { + text-align: right; +} + + +.align_center { + text-align: center; +} + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> HEADINGS AND PARAGRAPH <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */ + + +h1.right { + text-align: right +} + +h1.center { + text-align: center +} + +h2.right { + text-align: right +} + +h2.center { + text-align: center +} + +h3.right { + text-align: right +} + +h3.center { + text-align: center +} + +h4.right { + text-align: right +} + +h4.center { + text-align: center +} + +h5.right { + text-align: right +} + +h5.center { + text-align: center +} + +h6.right { + text-align: right +} + +h6.center { + text-align: center +} + +p.right { + text-align: right +} + +p.center { + text-align: center +} + + +/* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< */