7c934496e3650521dc129b65658326d542cbd20b hiram Tue May 17 12:52:51 2022 -0700 trying out new rmsk format bigBed joined display no redmine diff --git src/hg/utils/automation/asmHubRmskJoinAlign.pl src/hg/utils/automation/asmHubRmskJoinAlign.pl new file mode 100755 index 0000000..1dfc735 --- /dev/null +++ src/hg/utils/automation/asmHubRmskJoinAlign.pl @@ -0,0 +1,571 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use FindBin qw($Bin); +use lib "$Bin"; +use AsmHub; +use File::Basename; + +my $argc = scalar(@ARGV); + +if ($argc != 2) { + printf STDERR "usage: asmHubRmskJoinAlign.pl asmId buildDir > asmId.repeatMasker.html\n"; + printf STDERR "where asmId is the assembly identifier,\n"; + printf STDERR "expecting to find buildDir/html/asmId.names.tab naming file for this assembly,\n"; + printf STDERR "and buildDir/trackData/repeatMasker/asmId.rmsk.class.profile counts of rmsk categories.\n"; + exit 255; +} + +my $asmId = shift; +my $buildDir = shift; +my $namesFile = "$buildDir/html/$asmId.names.tab"; +my $rmskClassProfile = "$buildDir/trackData/repeatMasker/$asmId.rmsk.class.profile.txt"; +my $rmskVersion = "$buildDir/$asmId.repeatMasker.version.txt"; + +my $errOut = 0; +if ( ! -s $rmskClassProfile ) { + printf STDERR "ERROR: can not find rmsk class profile file:\n\t'%s'\n", $rmskClassProfile; + $errOut = 255; +} + +if ( ! -s $namesFile ) { + printf STDERR "ERROR: can not find rmsk class profile file:\n\t'%s'\n", $rmskClassProfile; + $errOut = 255; +} + +if ($errOut) { + exit $errOut; +} + +my $em = "<em>"; +my $noEm = "</em>"; +my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`; +chomp $assemblyDate; +my $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`; +chomp $ncbiAssemblyId; +my $organism = `grep -v "^#" $namesFile | cut -f5`; +chomp $organism; + +print <<_EOF_ +<h2>Description</h2> +<p> +This track shows the Repeat Masker annotations on the $assemblyDate $em${organism}$noEm/$asmId genome assembly. +</p> + +<p> +This track was created by using Arian Smit's +<a href="http://www.repeatmasker.org/" target="_blank">RepeatMasker</a> +program, which screens DNA sequences +for interspersed repeats and low complexity DNA sequences. The program +outputs a detailed annotation of the repeats that are present in the +query sequence (represented by this track), as well as a modified version +of the query sequence in which all the annotated repeats have been masked +(generally available on the +<a href="http://hgdownload.soe.ucsc.edu/downloads.html" +target=_blank>Downloads</a> page). RepeatMasker uses the +<a href="http://www.girinst.org/repbase/update/index.html" +target=_blank>Repbase Update</a> library of repeats from the +<a href="http://www.girinst.org/" target=_blank>Genetic +Information Research Institute</a> (GIRI). +Repbase Update is described in Jurka (2000) in the References section below.</p> +_EOF_ +; + +if ( -s "$rmskVersion" ) { + +print <<_EOF_ +<h2>RepeatMasker and libraries version</h2> +<p> +<pre> +_EOF_ +; +print `cat $rmskVersion`; +print <<_EOF_ +</pre> +</p> +_EOF_ +; + +} + +print <<_EOF_ +<h2>Display Conventions and Configuration</h2> +<h4>Context Sensitive Zooming</h4> +<p> +This track employs a technique which chooses the appropriate visual representation for the data based on the +zoom scale, and or the number of annotations currently in view. The track will automatically switch from the +most detailed visualization ('Full' mode) to the denser view ('Pack' mode) when the window size is greater +than 45kb of sequence. It will further switch to the even denser single line view ('Dense' mode) if more than +500 annotations are present in the current view. +</p> +<h4>Dense Mode Visualization</h4> +<p> +In dense display mode, a single line is displayed denoting the coverage of repeats using a series +of colored boxes. The boxes are colored based on the classification of the repeat (see below for legend). +<br> +<br> +<!-- t2tRepeatMasker-dense-mode.png --> +<img height="31" width="1070" src="/images/rmskDense.jpg"> +</p> +<h4>Pack Mode Visualization</h4> +<p> +In pack mode, repeats are represented as sets of joined features. These are color coded as above based on the +class of the repeat, and the further details such as orientation (denoted by chevrons) and a family label are provided. +This family label may be optionally turned off in the track configuration. +<br> +<br> +<!-- t2tRepeatMasker-pack-mode.png --> +<img height="94" width="1092" src="/images/rmskPack.jpg"> +<br> +<br> +The pack display mode may also be configured to resemble the original UCSC repeat track. In this visualization +repeat features are grouped by classes (see below), and displayed on seperate track lines. The repeat ranges are +denoted as grayscale boxes, reflecting both the size of the repeat and +the amount of base mismatch, base deletion, and base insertion associated with a repeat element. +The higher the combined number of these, the lighter the shading. +<br> +<br> +<!-- t2tRepeatMasker-orig-pack-mode.png --> +<img height="116" width="1216" src="/images/rmskClassicPack.jpg"> +</p> +<h4>Full Mode Visualization</h4> +<p> +In the most detailed visualization repeats are displayed as chevron boxes, indicating the size and orientation of +the repeat. The interior grayscale shading represents the divergence of the repeat (see above) while the outline color +represents the class of the repeat. Dotted lines above the repeat and extending left or right +indicate the length of unaligned repeat model sequence and provide context for where a repeat fragment originates in its +consensus or pHMM model. If the length of the unaligned sequence +is large, an iterruption line and bp size is indicated instead of drawing the extension to scale. +<br> +<br> +<!-- t2tRepeatMasker-full-mode.png --> +<img height="90" width="1098" src="/images/rmskFull.jpg"> +</p> +<p> +For example, the following repeat is a SINE element in the forward orientation with average +divergence. Only the 5' proximal fragment of the consensus sequence is aligned to the genome. +The 3' unaligned length (384bp) is not drawn to scale and is instead displayed using a set of +interruption lines along with the length of the unaligned sequence. +</p> + +<svg width="640.0000000000001" height="150" xmlns="http://www.w3.org/2000/svg" xmlns:svg="http://www.w3.org/2000/svg"> + <!-- Created with SVG-edit - http://svg-edit.googlecode.com/ --> + <g> + <title>Layer 1</title> + <path id="svg_4" d="m231.1875,66l132,0l0.5,13.5l0.5,14.5l-133,0l0,-14l0,-14z" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" stroke-width="5" stroke="#f90404" fill="#999999"/> + <line stroke="#000000" id="svg_7" y2="49.79012" x2="458.68436" y1="49.79012" x1="366.35802" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="2,2" stroke-width="2" fill="none"/> + <line stroke="#000000" id="svg_8" y2="57.79012" x2="455.35802" y1="41.79012" x1="462.35802" stroke-linecap="null" 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In the example below, a LINE element is found as two fragments. The solid +connection lines indicate that there are no unaligned consensus bases between the two fragments. +Also note these fragments form the 3' extremity of the repeat, as there is no unaligned consensus +sequence following the last fragment. +</p> + +<svg width="640" height="150" xmlns="http://www.w3.org/2000/svg" xmlns:svg="http://www.w3.org/2000/svg"> +<!-- Created with SVG-edit - http://svg-edit.googlecode.com/ --> +<g> +<title>Layer 1</title> +<path fill="#D8D8D8" stroke="#FF7F0E" stroke-width="5" stroke-dasharray="null" stroke-linejoin="null" stroke-linecap="null" d="m130.1582,51.8418l132,0l0.5,15l0.5,13l-133,0l0.25,-13l-0.25,-15z" id="svg_5"/> +<path fill="#D8D8D8" stroke="#FF7F0E" stroke-width="5" stroke-dasharray="null" stroke-linejoin="null" stroke-linecap="null" d="m397,50l132,0l0.5,15l0.5,13l-133,0l0.25,-12l-0.25,-16z" id="svg_16"/> +<line fill="none" stroke-width="2" stroke-linejoin="null" stroke-linecap="null" x1="263" y1="49" x2="328" y2="35" id="svg_17" 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stroke="#fffcfc" y2="60.46094" x2="511.3516" y1="49.71094" x1="500.82035" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> +<line id="svg_54" stroke="#fcf7f7" y2="60.74219" x2="510.88283" y1="72.11719" x1="501.38283" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> +<line id="svg_55" stroke="#fffcfc" y2="60.48437" x2="520.26566" y1="49.73437" x1="509.7344" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> +<line id="svg_56" stroke="#fcf7f7" y2="60.76562" x2="519.79689" y1="72.14062" x1="510.29689" stroke-linecap="null" stroke-linejoin="null" stroke-dasharray="null" fill="none"/> +</g> +</svg> + +<p> +The following table lists the repeat class colors: +</p> + +<table> + <thead> + <tr> + <th style="border-bottom: 2px solid #6678B1;">Color</th> + <th style="border-bottom: 2px solid #6678B1;">Repeat Class</th> + </tr> + </thead> + <tr> + <th bgcolor="#1F77B4"></th> + <th align="left">SINE - Short Interspersed Nuclear Element</th> + </tr> + <tr> + <th bgcolor="#FF7F0E"></th> + <th align="left">LINE - Long Interspersed Nuclear Element</th> + </tr> + <tr> + <th bgcolor="#2CA02C"></th> + <th align="left">LTR - Long Terminal Repeat</th> + </tr> + <tr> + <th bgcolor="#D62728"></th> + <th align="left">DNA - DNA Transposon</th> + </tr> + <tr> + <th bgcolor="#9467BD"></th> + <th align="left">Simple - Single Nucleotide Stretches and Tandem Repeats</th> + </tr> + <tr> + + <tr> + <th bgcolor="#8C564B"></th> + <th align="left">Low_complexity - Low Complexity DNA</th> + </tr> + <tr> + <th bgcolor="#E377C2"></th> + <th align="left">Satellite - Satellite Repeats</th> + </tr> + <tr> + <th bgcolor="#7F7F7F"></th> + <th align="left">RNA - RNA Repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)</th> + </tr> + <tr> + <th bgcolor="#BCBD22"></th> + <th align="left">Other - Other Repeats (including class RC - Rolling Circle)</th> + </tr> + <tr> + <th bgcolor="#17BECF"></th> + <th align="left">Unknown - Unknown Classification</th> + </tr> +</table> +</p> + +<p> +A "?" at the end of the "Family" or "Class" (for example, DNA?) +signifies that the curator was unsure of the classification. At some point in the future, +either the "?" will be removed or the classification will be changed.</p> + +<h2>Methods</h2> + +<p> +The RepeatMasker (<a href="www.repeatmasker.org">www.repeatmasker.org</a>) tool was used to generate the datasets found on this track hub. +</p> + +<h2>Class profiles</h2> +<p> +<ul> +_EOF_ + ; + +open (FH, "grep classBed $rmskClassProfile | sed -e 's/^ *//; s#$asmId.rmsk.##; s#classBed/##; s#.bed##;'|sort -rn|") or die "can not grep $rmskClassProfile"; +while (my $line = <FH>) { + chomp $line; + my ($count, $class) = split('\s+', $line); + printf "<li>%s - %s</li>\n", &AsmHub::commify($count), $class; +} +close (FH); +printf "</ul>\n</p>\n<h2>Detail class profiles</h2>\n<p>\n<ul>\n"; +open (FH, "grep rmskClass $rmskClassProfile | sed -e 's/^ *//; s#rmskClass/##; s#.tab##;'|sort -rn|") or die "can not grep $rmskClassProfile"; +while (my $line = <FH>) { + chomp $line; + my ($count, $class) = split('\s+', $line); + printf "<li>%s - %s</li>\n", &AsmHub::commify($count), $class; +} +close (FH); + +print <<_EOF_ +</ul> +</p> +<h2>Credits</h2> + +<p> +Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and +repeat libraries used to generate this track. +</p> + +<h2>References</h2> + +<p> +Smit AFA, Hubley R, Green P. ${em}RepeatMasker Open-3.0${noEm}. +<a href="http://www.repeatmasker.org" target="_blank"> +http://www.repeatmasker.org</a>. 1996-2010. +</p> + +<p> +Repbase Update is described in: +</p> + +<p> +Jurka J. +<a href="http://www.sciencedirect.com/science/article/pii/S016895250002093X" target="_blank"> +Repbase Update: a database and an electronic journal of repetitive elements</a>. +${em}Trends Genet${noEm}. 2000 Sep;16(9):418-420. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10973072" target="_blank">10973072</a> +</p> + +<p> +For a discussion of repeats in mammalian genomes, see: +</p> + +<p> +Smit AF. +<a href="http://www.sciencedirect.com/science/article/pii/S0959437X99000313" target="_blank"> +Interspersed repeats and other mementos of transposable elements in mammalian genomes</a>. +${em}Curr Opin Genet Dev${noEm}. 1999 Dec;9(6):657-63. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10607616" target="_blank">10607616</a> +</p> + +<p> +Smit AF. +<a href="http://www.sciencedirect.com/science/article/pii/S0959437X9680030X" target="_blank"> +The origin of interspersed repeats in the human genome</a>. +${em}Curr Opin Genet Dev${noEm}. 1996 Dec;6(6):743-8. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8994846" target="_blank">8994846</a> +</p> +_EOF_ + ;