Mercurial > repos > bgruening > repeat_masker
changeset 3:bdfc22c1c3e3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker commit 8dacb4321122d92df0983e0794cf23572be03224
| author | iuc |
|---|---|
| date | Wed, 02 May 2018 20:18:11 -0400 |
| parents | 5673e72241aa |
| children | 04f5c3d7448e |
| files | RepeatMasker.xml readme.rst repeatmasker.xml test-data/repeats.fasta test-data/small.fasta test-data/small.fasta.align test-data/small.fasta.cat test-data/small.fasta.gff test-data/small.fasta.log test-data/small.fasta.masked test-data/small.fasta.poly test-data/small.fasta.stats |
| diffstat | 12 files changed, 1099 insertions(+), 370 deletions(-) [+] |
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--- a/RepeatMasker.xml Tue Sep 17 03:23:49 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,307 +0,0 @@ -<tool id="repeatmasker_wrapper" name="RepeatMasker" version="0.1.2"> - <description>Masks different kind of repeats</description> - <requirements> - <requirement type="binary">RepeatMasker</requirement> - </requirements> - <command> -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces - -## create temp directory -#import tempfile, os -#set $dirname = os.path.abspath( tempfile.mkdtemp() ) -#set $input_filename = os.path.split( str($query) )[-1] -#set $output_basename = os.path.join( $dirname, $input_filename ) - - -RepeatMasker --parallel 8 - -$nolow -$noint -$norna - -#if str($species)!="all": - $species -#end if - - --dir $dirname - -#if $adv_opts.adv_opts_selector=="advanced": - - #if str($adv_opts.gc)!="0": - -gc $adv_opts.gc - #end if - - $adv_opts.gccalc - - #set $output_files_list = str($adv_opts.output_files).split(',') - #if "gff" in $output_files_list: - -gff - #end if - #if "html" in $output_files_list: - -html - #end if - - $adv_opts.slow_search - $adv_opts.quick_search - $adv_opts.rush_search - $adv_opts.only_alus - $adv_opts.is_only - -#else: - ## Set defaults - -gff - -## End of advanced options: -#end if - -$query - -2>&1; - -## Copy the output files to galaxy -## AgR: if there are no repeats, the output files may not exist. -## This causes the job to fail, so touch files to ensure they exist. -#if $adv_opts.adv_opts_selector=="advanced": - - #if "summary" in $output_files_list: - ## Write out the summary file (default) - #set $summary_file = $output_basename + '.tbl' - touch $summary_file; - cp $summary_file $output_summary; - #end if - - #if "gff" in $output_files_list: - ## Write out the gff file (default) - #set $gff_file = $output_basename + '.out.gff' - touch $gff_file; - cp $gff_file $output_gff; - #end if - - #if "html" in $output_files_list: - ## Write out the html file - #set $html_file = $output_basename + '.out.html' - touch $html_file; - cp $html_file $output_html; - #end if - -#else: - - ## Write out the summary file (default) - #set $summary_file = $output_basename + '.tbl' - touch $summary_file; - cp $summary_file $output_summary; - - ## Write out the gff file (default) - #set $gff_file = $output_basename + '.out.gff' - touch $gff_file; - cp $gff_file $output_gff; - - -## End of advanced options: -#end if - -## Write out mask sequence file -#set $mask_sequence_file = $output_basename + '.masked' -touch $mask_sequence_file; -cp $mask_sequence_file $output_mask; - -## Write out standard file (default) -## The default '.out' file from RepeatMasker has a 3-line header and spaces rather -## than tabs. Remove the header and replace the whitespaces with tab -#set $standard_file = $output_basename + '.out' -tail -n +4 $standard_file | tr -s ' ' '\t' > $output_std; - -## Delete all temporary files -rm $dirname -r - - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - - <param name="nolow" type="boolean" label="No low complexity DNA" truevalue="-nolow" falsevalue="" checked="false" help="Does not mask low_complexity DNA or simple repeats."/> - <param name="noint" type="boolean" label="No interspersed repeats" truevalue="-noint" falsevalue="" checked="false" help="Only masks low complex/simple repeats (no interspersed repeats)."/> - - <param name="norna" type="boolean" label="No small RNA genes" truevalue="-norna" falsevalue="" checked="false" help="Does not mask small RNA (pseudo) genes."/> - - <!-- - Specify the species or clade of the input sequence. The species name - must be a valid NCBI Taxonomy Database species name and be contained - in the RepeatMasker repeat database. The following collection is not complete. - --> - <param name="species" type="select" label="Species" help="The list is not complete, if you need other species contact your administrator."> - <option value="-species anopheles">anopheles</option> - <option value="-species arabidopsis">arabidopsis</option> - <option value="-species artiodactyl">artiodactyl</option> - <option value="-species aspergillus">aspergillus</option> - <option value="-species carnivore">carnivore</option> - <option value="-species cat">cat</option> - <option value="-species chicken">chicken</option> - <option value="-species 'ciona intestinalis'">ciona intestinalis</option> - <option value="-species 'ciona savignyi'">ciona savignyi</option> - <option value="-species cow">cow</option> - <option value="-species danio">danio</option> - <option value="-species diatoaea">diatoaea</option> - <option value="-species dog">dog</option> - <option value="-species drosophila">drosophila</option> - <option value="-species elegans">elegans</option> - <option value="-species fugu">fugu</option> - <option value="-species fungi" selected="true">fungi</option> - <option value="-species human">human</option> - <option value="-species maize">maize</option> - <option value="-species mammal">mammal</option> - <option value="-species mouse">mouse</option> - <option value="-species pig">pig</option> - <option value="-species rat">rat</option> - <option value="-species rice">rice</option> - <option value="-species rodentia">rodentia</option> - <option value="-species ruminantia">ruminantia</option> - <option value="-species wheat">wheat</option> - </param> - - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="is_only" type="boolean" label="Mask only E coli insertion elements" truevalue="-is_only" falsevalue="" checked="false" help="Only clips E coli insertion elements out of fasta and .qual files."/> - <param name="slow_search" type="boolean" label="Slow search" truevalue="-s" falsevalue="" checked="false" help="0-5% more sensitive, 2-3 times slower than default."/> - <param name="quick_search" type="boolean" label="Quick search" truevalue="-q" falsevalue="" checked="false" help="5-10% less sensitive, 2-5 times faster than default."/> - <param name="rush_search" type="boolean" label="Rush search" truevalue="-qq" falsevalue="" checked="false" help="about 10% less sensitive, 4->10 times faster than default."/> - <param name="only_alus" type="boolean" label="Only Alus" truevalue="-alu" falsevalue="" checked="false" help="Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)."/> - <param name="gccalc" type="boolean" label="Use GC depended matrices, automaticly" truevalue="-gccalc" falsevalue="" checked="true" help="RepeatMasker calculates the GC content even for batch files/small seqs"/> - - <param name="output_files" type="select" multiple="true" label="Additional output files"> - <option selected="true" value="summary">Summary file</option> - <option value="gff">GFF file</option> - <option value="html">HTML file</option> - <option value="mask">Mask FastA file</option> - </param> - - <param name="gc" type="integer" value="0" label="Use GC depended matrices" help="Use matrices calculated for 'number' percentage background GC level"> - <validator type="in_range" min="0" /> - <validator type="in_range" max="100" /> - </param> - - </when> - </conditional> - - </inputs> - <outputs> - <data name="output_std" format="tabular" label="${tool.name} on ${on_string}: Standard" /> - <data name="output_mask" format="fasta" label="${tool.name} on ${on_string}: Mask sequence"> - <filter> - (adv_opts['adv_opts_selector'] == 'advanced' and 'mask' in adv_opts['output_files']) - </filter> - </data> - <data name="output_summary" format="txt" label="${tool.name} on ${on_string}: Summary"> - <filter>( - (adv_opts['adv_opts_selector'] == 'advanced' and 'summary' in adv_opts['output_files']) - or - (adv_opts['adv_opts_selector'] == 'basic') - ) - </filter> - </data> - <data name="output_html" format="html" label="${tool.name} on ${on_string}: HTML"> - <filter>(adv_opts['adv_opts_selector'] == 'advanced' and 'html' in adv_opts['output_files'])</filter> - </data> - <data name="output_gff" format="gff" label="${tool.name} on ${on_string}: GFF"> - <filter> - (adv_opts['adv_opts_selector'] == 'advanced' and 'gff' in adv_opts['output_files']) - </filter> - </data> - </outputs> - <help> - -.. class:: warningmark - -**What it does** - -RepeatMasker is a program that screens DNA sequences for *interspersed repeats* -and *low complexity* DNA sequences. The output of the program is a detailed -annotation of the repeats that are present in the query sequence as well as a -modified version of the query sequence in which all the annotated repeats have -been masked (default: replaced by Ns). - ------ - -**How to read the results** - - - -The annotation file contains the cross_match output lines. It lists all best matches -(above a set minimum score) between the query sequence and any of the sequences in -the repeat database or with low complexity DNA. The term "best matches" reflects -that a match is not shown if its domain is over 80% contained within the domain -of a higher scoring match, where the "domain" of a match is the region in -the query sequence that is defined by the alignment start and stop. These domains -have been masked in the returned masked sequence file. In the output, matches are -ordered by query name, and for each query by position of the start of the alignment. - -Example: - -======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= == -SW score perc div. perc del. perc ins. query seq. q-pos begin q-pos end (left) w complement matching repeat repeat class/family repeat-pos begin repeat-pos end (left) ID -======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= == - 1306 15.6 6.2 0.0 HSU08988 6563 6781 \(22462) C MER7A DNA/MER2_type 336 103 \(0) 1 - 12204 10.0 2.4 1.8 HSU08988 6782 7714 \(21529) C TIGGER1 DNA/MER2_type 2418 1493 \(0) 2 - 279 3.0 0.0 0.0 HSU08988 7719 7751 \(21492) + (TTTTA)n Simple_repeat 1 33 \(0) 3 - 1765 13.4 6.5 1.8 HSU08988 7752 8022 \(21221) C AluSx SINE/Alu 289 1 \(23) 4 - 12204 10.0 2.4 1.8 HSU08988 8023 8694 \(20549) C TIGGER1 DNA/MER2_type 1493 827 \(925) 5 - 1984 11.1 0.3 0.7 HSU08988 8695 9000 \(20243) C AluSg SINE/Alu 305 1 \(5) 6 - 12204 10.0 2.4 1.8 HSU08988 9001 9695 \(19548) C TIGGER1 DNA/MER2_type 827 2 \(1591) 7 - 711 21.2 1.4 0.0 HSU08988 9696 9816 \(19427) C MER7A DNA/MER2_type 122 2 \(224) 8 -======== ========= ========= ========= ========== =========== ========= ========= ============ =============== =================== ================ ============== ======= == - -This is a sequence in which a Tigger1 DNA transposon has integrated into a MER7 DNA transposon copy. -Subsequently two Alus integrated in the Tigger1 sequence. The simple repeat is derived from the -poly A of the Alu element. The first line is interpreted like this: - -:Table description: - -1. **1306** = Smith-Waterman score of the match, usually complexity adjusted - The SW scores are not always directly comparable. Sometimes - the complexity adjustment has been turned off, and a variety of - scoring-matrices are used. - -#. **15.6** = % substitutions in matching region compared to the consensus -#. **6.2** = % of bases opposite a gap in the query sequence (deleted bp) -#. **0.0** = % of bases opposite a gap in the repeat consensus (inserted bp) -#. **HSU08988** = name of query sequence -#. **6563** = starting position of match in query sequence -#. **7714** = ending position of match in query sequence -#. **(22462)** = no. of bases in query sequence past the ending position of match -#. **C** = match is with the Complement of the consensus sequence in the database -#. **MER7A** = name of the matching interspersed repeat -#. **DNA/MER2_type** = the class of the repeat, in this case a DNA transposon fossil of the MER2 group (see below for list and references) -#. **2418** = starting position of match in database sequence (using top-strand numbering) -#. **1465** = ending position of match in database sequence -#. **(0)** = no. of bases in (complement of) the repeat consensus sequence prior to beginning of the match (so 0 means that the match extended all the way to the end of the repeat consensus sequence) -#. **1** = Identifier - -An asterisk (\*) in the final column (no example shown) indicates that there is -a higher-scoring match whose domain partly (<80%) includes the domain of this match. - -Note that the SW score and divergence numbers for the three Tigger1 lines are identical. -This is because the information is derived from a single alignment (the Alus were deleted -from the query before the alignment with the Tigger element was performed). -The program makes educated guesses about many fragments if they are derived from -the same element (e.g. it knows that the MER7A fragments represent one insert). -In a next version I can identify each element with a unique ID, if interest exists -(this could help to represent repeats cleaner in graphic displays). - - -------- - -**References** - -Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0. - -http://www.repeatmasker.org/ - - </help> -</tool>
--- a/readme.rst Tue Sep 17 03:23:49 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -=============================== -Galaxy wrapper for RepeatMasker -=============================== - -This wrapper is copyright 2013 by Björn Grüning. - -This is a wrapper for the command line tool of RepeatMasker from the Institute for Systems Biology. -http://www.repeatmasker.org/ - - -Smit, AFA, Hubley, R & Green, P. RepeatMasker Open-3.0. -1996-2010 <http://www.repeatmasker.org>. - - -Additional Information: -Using RepeatMasker to identify repetitive elements in genomic sequences. -http://www.ncbi.nlm.nih.gov/pubmed/19274634 - -============ -Installation -============ - -To install RepeatMasker, please use the following instructions: - -http://www.repeatmasker.org/RMDownload.html - -To install the wrapper copy the file RepeatMasker.xml in the galaxy tools -folder and modify the tools_conf.xml file to make the tool available to Galaxy. -Add a line like the following: - -Add the tool definition to your tool_conf.xml file under Galaxy root. - <tool file="RepeatMasker/RepeatMasker.xml" /> - -======= -History -======= - -- v1.1: Initial public release -- v0.1.1: patch from Simon Guest, to create empty files if no repeat is found -- v0.1.2: remove trailing semicolon, redirect all output to stdout - -=============================== -Wrapper Licence (MIT/BSD style) -=============================== - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repeatmasker.xml Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,230 @@ +<tool id="repeatmasker_wrapper" name="RepeatMasker" version="4.0.7" profile="17.01"> + <description>RepeatMasker</description> + + <requirements> + <requirement type="package" version="4.0.7">repeatmasker</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ + RM_LIB_PATH=\$(dirname \$(which RepeatMasker))/../share/RepeatMasker/Libraries && + mkdir lib && + export REPEATMASKER_LIB_DIR=\$(pwd)/lib && + for file in \$(ls \$RM_LIB_PATH) ; do ln -s \$RM_LIB_PATH/\$file lib/\$file ; done && + #if $repeat_source.source_type == "repbase": + cp '${repeat_source.repbase_file}' lib/RMRBSeqs.embl && + #end if + ln -s '${input_fasta}' rm_input.fasta && + RepeatMasker -dir \$(pwd) + #if $repeat_source.source_type == "library": + -lib '${repeat_source.repeat_lib}' + -cutoff '${repeat_source.cutoff}' + #else if $repeat_source.source_type == "repbase": + #if $repeat_source.species_source.species_from_list == 'yes': + $repeat_source.species_source.species_list + #else + -species '${repeat_source.species_source.species_name}' + #end if + #end if + -parallel \${GALAXY_SLOTS:-1} + '${gff}' + '${ignore_n_stretches}' + '${advanced.is_only}' + '${advanced.is_clip}' + '${advanced.no_is}' + '${advanced.rodspec}' + '${advanced.primspec}' + '${advanced.nolow}' + '${advanced.noint}' + '${advanced.norna}' + '${advanced.alu}' + '${advanced.div}' + '${advanced.search_speed}' + '${advanced.frag}' + '${advanced.maxsize}' + #if $advanced.gc is not None: + '${advanced.gc}' + #end if + '${advanced.gccalc}' + '${advanced.nocut}' + '${advanced.keep_alignments}' + '${advanced.invert_alignments}' + '${advanced.xout}' + '${advanced.xsmall}' + '${advanced.poly}' + rm_input.fasta && + #if $advanced.is_only != '-is_only': + mv rm_input.fasta.masked '${output_masked_genome}' && + sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g ; 1,2c SW score\t% div.\t% del.\t% ins.\tquery sequence\tpos in query: begin\tend\t(left)\trepeat\tclass/family\tpos in repeat: begin\tend\t(left)\tID' rm_input.fasta.out >'${output_log}' && + mv rm_input.fasta.tbl '${output_table}' && + #if $gff == '-gff': + mv rm_input.fasta.out.gff '${output_gff}' && + #end if + #if $advanced.keep_alignments == '-ali': + mv rm_input.fasta.align '${output_alignment}' && + #end if + #if $advanced.poly == '-poly': + sed -r 's/^ *// ; s/ *$//; s/\+ //; s/ +/\t/g' rm_input.fasta.polyout >'${output_polymorphic}' && + #end if + #end if + mv rm_input.fasta.cat '${output_repeat_catalog}' + ]]> + </command> + + <inputs> + <param name="input_fasta" type="data" format="fasta" label="Genomic DNA" /> + <conditional name="repeat_source"> + <param label="Repeat library source" name="source_type" type="select"> + <option selected="true" value="repbase">RepBase</option> + <option value="library">Custom library of repeats</option> + </param> + <when value="repbase"> + <param name="repbase_file" type="data" format="embl" label="RepBase (RMRBSeqs.embl) file" /> + <conditional name="species_source"> + <param label="Select species name from a list?" name="species_from_list" type="select"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="species_list" type="select" label="Species"> + <option value="-species anopheles" selected="true">anopheles</option> + <option value="-species arabidopsis">arabidopsis</option> + <option value="-species artiodactyl">artiodactyl</option> + <option value="-species aspergillus">aspergillus</option> + <option value="-species carnivore">carnivore</option> + <option value="-species cat">cat</option> + <option value="-species chicken">chicken</option> + <option value="-species 'ciona intestinalis'">ciona intestinalis</option> + <option value="-species 'ciona savignyi'">ciona savignyi</option> + <option value="-species cow">cow</option> + <option value="-species danio">danio</option> + <option value="-species diatoaea">diatomea</option> + <option value="-species dog">dog</option> + <option value="-species drosophila">drosophila</option> + <option value="-species elegans">elegans</option> + <option value="-species fugu">fugu</option> + <option value="-species fungi" selected="true">fungi</option> + <option value="-species human">human</option> + <option value="-species maize">maize</option> + <option value="-species mammal">mammal</option> + <option value="-species mouse">mouse</option> + <option value="-species pig">pig</option> + <option value="-species rat">rat</option> + <option value="-species rice">rice</option> + <option value="-species rodentia">rodentia</option> + <option value="-species ruminantia">ruminantia</option> + <option value="-species wheat">wheat</option> + </param> + </when> + <when value="no"> + <param name="species_name" type="text" value="homo sapiens" label="Repeat source species" help="Source species (or clade name) used to select repeats from RepBase" /> + </when> + </conditional> + </when> + <when value="library"> + <param name="repeat_lib" type="data" format="fasta" label="Custom library of repeats" /> + <param name="cutoff" type="integer" argument="-cutoff" value="225" label="Cutoff score for masking repeats" /> + </when> + </conditional> + <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" /> + <param name="ignore_n_stretches" type="boolean" argument="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" /> + <section name="advanced" title="Advanced options" expanded="false"> + <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" /> + <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" /> + <param argument="-no_is" type="boolean" truevalue="-no_is" falsevalue="" checked="false" label="Skip bacterial insertion element check" /> + <param argument="-rodspec" type="boolean" truevalue="-rodspec" falsevalue="" checked="false" label="Only check for rodent specific repeats" help="If this option is select a check for rodent specific repeats is done instead of a full RepeatMasker run" /> + <param argument="-primspec" type="boolean" truevalue="-primspec" falsevalue="" checked="false" label="Only check for primate specific repeats" help="If this option is select a check for primate specific repeats is done instead of a full RepeatMasker run" /> + <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="false" label="No low complexity masking" help="Skip masking of simple tandem repeats and low complexity regions." /> + <param argument="-noint" type="boolean" truevalue="-noint" falsevalue="" checked="false" label="No interspersed repeat masking" help="Only mask simple repeats, skip masking of interspersed repeats." /> + <param argument="-norna" type="boolean" truevalue="-norna" falsevalue="" checked="false" label="No repeat-like-RNA masking" help="Skip masking of small pol III transcribed RNA (these are masked by default because they resemble SINEs)" /> + <param argument="-alu" type="boolean" truevalue="-alu" falsevalue="" checked="false" label="Limit masking to (primate) Alu repeats" /> + <param argument="-div" type="boolean" truevalue="-div" falsevalue="" checked="false" label="Limit masking to less diverged (younger) repeats" /> + <param type="select" name="search_speed" label="Search speed vs sensitiviy trade-off"> + <option value="">Default</option> + <option value="-q">Quick (5-10% less sensitive, 3-4 times speedup)</option> + <option value="-qq">Rush (10% less sensitive)</option> + <option value="-s">Slow (0-5% more sensitive, 2.5 times slowdown)</option> + </param> + <param type="integer" argument="-frag" value="40000" label="Maximum contiguous sequence searched" help="Maximum length of sequencing that is search without fragmenting" /> + <param type="integer" argument="-maxsize" value="4000000" label="Maximum length for IS or repeat clipped sequences" /> + <param type="integer" argument="-gc" optional="True" label="Select matrices for this GC%" help="Valid values are a percentage or -1 to choose the default" /> + <param type="boolean" argument="-gccalc" truevalue="-gcccalc" falsevalue="" checked="false" label="Calculate GC % for all sequences" help="By default RepeatMasker skips calculating GC % for small sequences" /> + <param type="boolean" argument="-nocut" truevalue="-nocut" falsevalue="" checked="false" label="Skips cutting of repeats" /> + <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" /> + <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" /> + <param name="invert_alignments" type="boolean" argument="-inv" truevalue="-inv" falsevalue="" checked="false" label="Invert alignments in alignment file" help="Show alignments in the orientation of the repeat sequence, not the query sequence" /> + <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Output repetitive regions as lowercase, non-repetitive regions as uppercase" /> + <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" /> + </section> + </inputs> + <outputs> + <data name="output_masked_genome" format="fasta" label="RepeatMasker masked sequence on ${on_string}"> + <filter>not advanced['is_only']</filter> + </data> + <data name="output_log" format="tabular" label="RepeatMasker output log on ${on_string}"> + <filter>not advanced['is_only']</filter> + </data> + <data name="output_table" format="txt" label="RepeatMasker repeat statistics on ${on_string}"> + <filter>not advanced['is_only']</filter> + </data> + <data name="output_repeat_catalog" format="txt" label="RepeatMasker repeat catalogue on ${on_string}" /> + <data name="output_alignment" format="txt" label="RepeatMasker alignment on ${on_string}"> + <filter>not advanced['is_only'] and advanced['keep_alignments']</filter> + </data> + <data name="output_polymorphic" format="tabular" label="RepeatMasker possible polymorphic repeats on ${on_string}"> + <filter>not advanced['is_only'] and advanced['poly']</filter> + </data> + <data name="output_gff" format="gff" label="RepeatMasker repeat annotation on ${on_string}"> + <filter>not advanced['is_only'] and gff is True</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="4"> + <param name="input_fasta" value="small.fasta" ftype="fasta" /> + <param name="source_type" value="library" /> + <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> + <output name="output_masked_genome" file="small.fasta.masked" /> + <output name="output_table" file="small.fasta.stats" lines_diff="2" /> + <output name="output_repeat_catalog" file="small.fasta.cat" /> + <output name="output_log" file="small.fasta.log" /> + </test> + <test expect_num_outputs="7"> + <param name="input_fasta" value="small.fasta" ftype="fasta" /> + <param name="source_type" value="library" /> + <param name="gff" value="-gff" /> + <!-- <param name="show" value="yes" /> --> + <param name="keep_alignments" value="-ali" /> + <param name="poly" value="-poly" /> + <param name="repeat_lib" value="repeats.fasta" ftype="fasta" /> + <output name="output_masked_genome" file="small.fasta.masked" /> + <output name="output_table" file="small.fasta.stats" lines_diff="4" /> + <output name="output_repeat_catalog" file="small.fasta.cat" /> + <output name="output_log" file="small.fasta.log" /> + <output name="output_alignment" file="small.fasta.align" /> + <output name="output_polymorphic" file="small.fasta.poly" /> + <output name="output_gff" file="small.fasta.gff" lines_diff="4" /> + </test> + </tests> + <help><![CDATA[ +RepeatMasker is a program that screens DNA for interspersed repeats and low +complexity DNA sequences. The database of repeats to screen for can be +provided as a FASTA file or downloaded from RepBase_. If the RepBase option is +chosen the RepBaseRepeatMaskerEdition file should be downloaded and +unpacked, and the enclosed EMBL format file ('RMRBSeqs.embl') should +be uploaded to Galaxy for use with this tool. + +Further documentation is available on the RepeatMasker homepage_. + +.. _RepBase: http://www.girinst.org/repbase/ +.. _homepage: http://www.repeatmasker.org/webrepeatmaskerhelp.html + ]]> + </help> + <citations> + <citation type="bibtex"> + @misc{RepeatMasker, + title = {RepeatMasker Open-4.0}, + howpublished = {\url{http://www.repeatmasker.org}}, + author = {Smit, AFA and Hubley, R and Green, P.}, + year = {2013-2015}} + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/repeats.fasta Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,64 @@ +>Asian_seabass_ONSAT_SB_Concensus_Lenght_170_bp +CGAAAAATTTAATAATTTAGGGGTCTTGAGCATGGGCGTGGTAAAATGCCCTCGGTAGCG +CCACCTACATTTTTAAACGGAACAGCCCCTCAAGCCCGTTGCGCCTAAAAATCTGAAAAT +CTGCACACATATGTAACATCCCATGACGCACCAAAAAGTCTCTTGGAGCCA +>Asian_seabass_MOSAT_SB_T_34a_satellite_DNA +TTTGTGACATCACTACATAGTTTGTTGAAAACGTAC +>Asian_seabass_MOSAT_SB_T_34b_satellite_DNA +TTTGTGACATCACACATAGTTGTGGGTCAGTAC +>Sat_38 +AAAAAATGTCATAGTATAGTATGGCGTCAAAAAACATG +>Asian_seabass_Sat_217_Consensus_Length_217_bp +AGTAAACAAGCATTATGGTTGAAACCATAATTTCCTGTCGGGAGAGCCTTTCCCTCTTTT +GTGCACTGTATGCAATCCCAGAGTGTGAATAAGCGCTTTTCCAGCGTTTTGAGGCTTATT +CAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGACAAAGACAAACTAAGAACTCA +GCCACACGGACATGAAAGTTGTTTTACTTACAATATT +>Asian_seabass_Sat_217_Consensus_Length_427_bp +CCAGCGTTTTGAGGCTTATTCAGCTCAGAATGGCTTAATACTGCACTATCTGACCAGGAC +AAGACAAACTAAGAACTCAACACACTGACATGAAAGTTTCTATATTTCTATTAAAATAAA +CAAACATTATGGTTGAAACCATAATTTCATTTCGGGAGAGCCTTTCCCTCTTTGTGGCAC +TGTATGTAATCTGAAGTGTGAATAACGCTTTTCCCGCGTTTGAGGCTTATTCAGCTCAGA +ATGGCTTAATACTGCACTATCTGACCAGGACAAGACAAACTAAGAACTCAGCCACACGGA +CATGAAAGTTGTTTACTTTACAATATTAGTAAACAAGCATTATGGTTGAAACCATAATTT +CCTGTCGGGAAGAGCTTCCCTCTTTTTGTGCACTGTATGCAATCCCAGAGTGTGAATAAG +CGCTTTT +>Asian_seabass_Sat_LM_Consensus_Length_453_bp +CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG +TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC +ATGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAG +AAATCATGAGTGGCTCTTATTGAAGTGATCAGAGTTGGACTCCATTAAGAAAATGGCTTT +CAATGTAGTCAGTTGCTTTGTCACTTAAAACTGCCCCAACAAGTAGCACTTACTGCAATT +TGGTAGTCAAAGTCAATGCTCAAGTTAAGGGTAATAGTAGTGACATAATAGAAAAATCTC +TAAATATATTTGCTGGCAGCTTTAATATACAGAATGAGTGCCATGATGAATTCTTGATAC +AGAACAGGGACTTCCAAAATCAGCCAACACTAA +>Asian_seabass_Sat_LM_Consensus_Length_218_bp +CCCAACAAAATAGCACTTACTGCTTTCCAAATTCAAGTCTGTGCCTGTGTTAGGGTAATG +TTGGTGATAAATTGATGTACTTAGCTTATCCTGTGAAAATGGTGTAAAATGGCAGTCTCC +TGTTTGTTGAAGAAACTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAGA +AATCATGAGTGGCTCTTATTGAAGTGATCAGAGTTGG +>Asian_seabass_Sat_LM Consensus_Length_150_bp +CTCACAACCAAGACAACCCCAAAGAGAAGCACTTATGAAGACAGAAATCATGAGTGGCTC +TTATTGAAGTGATCAGAGTTGGACTCCATTAAGAAAATGGCTTTCAATGTAGTCAGTTGC +TTTGTCACTTAAAACTGCCCCAACAAGTAGCA +>Asian_seabass_Sat_Unk_Consensus_Length_341_bp +GTTTGGGTAAAAATATTGTCTATTTACGAGCTATCCTCTATATATTTTTGATCTGATTAA +TAAATACCTCTAGCCCACAAACTGTGGTATTTTGCTATGTGGCAGTTCACCCGAAAGTCC +AGTAGCATTTATCGCATTTTCTAAAGATAGTCAGTGCCTGAAAGTTTGAGGCAGATAAAC +AAATTGTTCAAGTAAGAACTATATCTTTCTTATGATTTTACCGCAATCATACAGGTTGTT +TCTTGTGGTCTGCTGGGCATTGTATCCCTTTGTTGTATGGATTTTTCCTTTCTTTAATGA +TCTCCTCCCTGGAGTTTGTAATCCCTGTTTGTAGTGGAATT +>Asian_seabass_Sat_Unk_Consensus_Length_789_bp +CAAAAAAATGGAAAAAAAAAAAGTGGCTCATTTGAAGTGAATCAGAGTTGGGTAACATTG +TCCTTAATTACAGCTATGCTTATATACTTGATCTGATAATAATACTCTAGCCACAATCTG +TGGGTATTCTGCTATTTGCAGTCCACCCAAAGTCATAGCATTTAATCCATTCTAGGAAGA +TACGTCAGTGCTGAGTTGAGCCAATAACACCAAATTGTCATAAGAACTATTATTTTCTTT +ATGATTTTTACGCATCAGTACAGGTGTTTTCTTGTGGTTTCTGCTGCATGTATCCCTGTT +GTAAGTGGATTCTCCTTTGCTTATGATCTCCTCCGCTGCGTTGTATCCTGTTTGTAGTGG +ATTTCCTTGCACTGATTCTGCCCGCTCTTAATACTGAATGAACGCCCTCCCACCAGTAGT +ACTGCCACCTTTGTTTTTTCACAAAGTGTTCAATGGCCTTGATAATGACTTGGTAACTAC +ATCACCACTTTTTTGTACGTAATCAACAGACAATCACCCATTAAATTCATGCGGCCATTA +GGCAGCTTGATGAGCTGGACATTTGACCTCCCCAATGAATCTTTGCTGATGGGAAACTTA +TTGCCACCATAAAGTGAACCAGCATTGCTATGTCCATGCTGTAATTTGAAAACCCAATAC +AAAGAAGCCCTGCATATATACCTCCCAAATTGGCTTCTGAGACCCGGGCGTAATCACTGC +ATGGCCATAGATAAACATTGAAATCTTCTGTTGCAGTCAGTTTGCTTTTTGTCAACTTTA +AAAACTGCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,238 @@ +>scaffold_1 +TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATCCAATATATTC +CTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGACATCCTCAGTGATTGAAGTGA +CAAAAAGTGGAGCGCACGCAGTGGTCATTACCCTCCAATGGTACTTCTAATTAAGGAAAG +ATTTTTTGCATTCACTGAGCAAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGG +GTCCATTAAACAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT +AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGCCCCAAATTGT +CTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATAATTGTGTTTCTCTCTAGATG +TGCGGTGTCCATCAAGACACTGGATGTCACGTGGTCACTCCTGTGAAGAGCGAACTGTGT +GGAACCCGAAGTACTGTGTGGTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGG +TGGTGAGAGCAGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC +TCTCATCTGCTCGTGTGTGTGTGTGTGTGTGTCCTTGTCAATGTCATTACACAATTTATG +TTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACATCTACTTTCTGTCACCTGATA +CCTCATACTTTACACTCTAATCCCTTTTTCCTTTCTAACTGCTGCTGTGTTAAGCTGTCA +TATTAATATACTAAATAATGATAATATTAATTCTAATAATGATAGTGAATGGAGATTCAC +AATGAAGAAACACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT +TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCAAGGCTGAGTC +TGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGGATTATGCTAGTTTGTGTGAG +ATTAGAGGTCCTGTTGTTACGAGCAAATCAGCAGTCAGCAGGGTAATCTAAATTACATTG +TTCTGTCGGCAATATCCTCTCCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCC +CCACAGTAGTGCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT +ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTGTGATTGTTGG +TGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGATCTCCTGGGATTTTCACACAC +GGCATTCTCTAGAGTTTACTCAGAACGGTGTGGAAAGCAAAAAAACATCCCGCGAGCTGC +AATCCTGCGGATGGAAACACCTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGAT +CAATCTGACAGAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA +AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTACAGCAGCAGAT +GAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACATCTCAGACTGCACAGGACACC +AAAACAAAAACACATCCTGTTTTCTACTGGTGGTAGAGTCACAATTTGGCAATAAGATAA +ATCCATGGACCCAACTTGCCTTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATG +TTTTCTTTACACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG +TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGATACCTGCGGC +AATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTATTATAGAGAGTAATTTCACTG +TCCATGTCTTTTTTGATCATAAAGCAGGTCTAGGTGCTGTATACAACACTGTATTGAAAT +GCTGAAGCAGGTCTAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCCAATATATC +AATCTATCTGTCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT +GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCACCACAGCATTT +ACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGTTACCTGTTATTGGCCTGGCT +CTATGGCATGCAGAAAACAGTCAGCCAATCAGAGGACAGACTCAGAGACAGACACAAAGT +GCCCTGTTCTTGTTAGAGCAGAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGA +TGGTTTTTTGGTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA +AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGTTTCGTAGTTC +TAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTAAAGCGGCTACATGTAGAATT +TGACCCACTTTGGTGCCCACATATGGTAACTAAAACACTACAGACAGTATGCACTCCAAC +CCTATATAATTTATGTCCTTCAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGAT +TAATACCTAGAATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG +AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAACCTGGTCATT +CCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCTCCTGCTGTGGGTGCCAATAG +CTCATGCAAGTTGGTGTCTTTCAACTAAGGCCACTATGTGAGGACCATCAGCAGCAAATT +AAATTAGAAGTGCCTTGGAGTTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGA +CAGAACAGTGCCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT +GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAAGGCATAGTTA +CTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGCTGGAACTTGGAACATGTAGC +CTAAGTTTCCCTTTGTCTGCAATTACTGAGGTATGCCATGTTGAAATAGAACAATAATTG +CAGGGAGGAATTATTCCAATCGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTT +CACAGCAACAAAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT +CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAAGCGATGATAC +AGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACATGGTTTAAACAAGCTCAGTT +AAATGGATCAGAGCATCAACTGCTGTGAACAAGCAATCACACGGTCAAGGTCAAACATTT +ACACTTCTGAGAGATCTGGAGAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTA +ACTGATTACGCCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA +TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCATGCAGCCTAAT +TTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATGTTTTAGGCAGTTTTAGGCAC +TAAAGGTGAACTGAGGATGCAGTCCCACGATTAATTTTTATTCATCAGTTAACCTCATGT +GAAGTGTAGTAAACAGAAAAAACCTAAATCAGATCAGTATTTCTTATGACCCCCCTCCCC +TACCACCCATCTTTAAAACAGCTCCAGTTCTCCTCAATCCCCCTGTACTTAGGTAGTTTT +TTTCTAGCGTCTTGGAGAAGTTGCCTCAGTTCTTCTGTGGATTTTAGGCTGTCTCTGTGT +CTTCTGTCTCCTCATGTATTCTCAGACTGACTCCATGATGTTGAGATCAGGGCTCTGTGG +TGGGGGGGTCAGACCATCTGTTGCGGGACTCCTTGTTCTTCTTGTCTCTGAGGATAGTTC +TTTATGATGCTGACTGTGTGATTGGACTCATTGTCCTGCTGCAGAATTAATCTGGGACTG +ATCAGACATCTCCCTGATTGTACTGACAAAGGATAAGAGCAAAAACCTGTAGACTGCCTA +AAACTTCTGCACAGTACTGCACAATACTGTATGTATGTGTGATAATACTCAGAAGTGATA +TAGAGTGGTTCAGGAGAAGCCTTAACTTACTTGTTCTTCTTTTCCCTATGATGCAATTTC +TCTCCAAGCAAACAGTACATAATGAAATATGTCTAAGAAAACACTAGCTGTTTGTCTTTT +TGAAACACATTTAATAATTCAGATTTAGCCACAAATTAAAAATGAGCTTATACTTTGAAC +TTGCCCATTGGTTTTGATGTATGAAGCTGACAGATTTAGTCCACTGCATACTGCACTTTT +TTGGATAGTGAAATAAATTAATTTATTATGCAGCATTTAAGCATATTGCTGTTATCTAGA +ATTTTATATATTAATAGGTATATATTATATTAACTCTTCATTTGCTTAAATTTGGCCTGT +ATATTCCTCCATTTTATACAACCTTTAGAAAACACTGGAGTGAACAAAAATGTGAGGTTC +AAAAGTGAGAGGAAAGAAAAATCAGTGTGTGCAGCAAGACTGTAAGAGTCCCTGAACAAA +AGTGTTGATTTATTGTTGGCTGTGAAAGTTTTTGCTGCAGGGGTTTTTGTAAACAGTGAC +TCTTCTTTATGTCTTTGTTTCTATCTTTTTGTGTTTTCTTTTTTCATCTTATTCTATTTT +TCTCTCTCTCTCTTCGGTCAGTTTCTCTTCTTCTCCTCCTCATACTCATGCTTCTCTTTT +ACTCTAATGGAAAACATAGAATTGAGGTGCAGTATCACTGAGAACAGCCAATGCTGATAC +TGTCATTTGTTATAGGATGTTTACTTAAGAAATGATTGTGGCCTTATTTGCCAAAGACGA +TTAGGCCCTGAGCCATTTGTACAGCCAATGTGACACCTCCGTAACCATAAGAAAAATTAT +GCTTCCACAAACAGAAAGAGAGACAAATACAGACAGTGAAAGCAAAACTATGAGAGAAGG +GATAGCCATCTCAGCATTCAGCCAGTGTGTCACATGTCCAGAGGGCTGCAATATGAAGCC +AATAAACTGAGAGAAAGGTGTGATTCCAGAGGGCTTTCCGGACTTTAAACTTTTCTCATT +TTCACCTTCAGCTCGTTGTGAAGCCTTCAATTGTTCCTTGGTCACATGAAGCCCCCTGTG +TGTAAAATTGACATTCAGCTTATTACTCTCATCTACATCTCTAAAGTTGCACATGACTGC +CAGTAGAGGGTGCTCATGATTTGAGACAAGTAACTTTTCTGTGCTTGTGTCAACAGTTAA +AAATTCCCTATGGATACTTGAAAGAAATGCACCAGTGTTTAAATTTAGACTCAGTCCAAG +TAGGCTTTGCCATTTGCTTTACTGTTGTAATCAAATCAGTGCTCACAGTACATCAGTGGC +AAAAGCAATTAGCTTAATTGAGTTAGTAGGGAGTGAAAAGATAGATCACTATTTCCTGGC +AGCGATATATTTTTCTCAGTTAACCTTCTCACAGAAAATTAGTTAGATGAGTTTCTTATC +TCATTAGAACCATTGTTGTTTATTATTTAAACCTGACCTTTATCCAGAGAATGTTTTTCA +CAGTAAGCATGTGTTTCACTCCAGCTCATACAGACACACCTTGTGGCCAGTCAGGGAATG +TGCATTAAAACTAATGTTCTCTCTGGTAGAGCCATTCTGCCTATTCTGTTATTCACCAAA +ACTTTCCTGCCCAGATTTTTCCATCTAGTCAGGGGACTTTTTCCTCAGCTGAACTGTCAG +TAGCCAGCTGCTCTGACCTTTACTCACCTCAGAGATTACTCATTCAAGTTATTTTACCAA +TGATGGAATAAAGTGAATACACACATCGTGACTTCATCATACTTTCCCTCCTTTACCGTA +CTTTCCTAACATCAGTTAGCAAATTATACACTTAAATATGCTAAAATAGAGATTTGTTTC +AAATTGAAGAGCAACACAGGACACATTTGCTTACACAAGTGACTCTATCTTATTTTTTAA +GTGGCTGTCATCCTCAATATCATCAATATTTTAGGCATGTGAATGTAGGTAATGAGTATT +ACTAATTAATAATTGGATGAGTTTATGAATTCATCATTAAATAAGATTATTATGATAAAG +CTACACATTATACTGCAATTCCGGGCCAACACTATTGTTTCGCCCTTACAGTACAGGACT +GTACATATCACTGTCACTACAAATTGTTTCAGTGAGGCTCAGATTACAGCTCATCTTGCT +TAGTCATTACGGCTCAGACCACCAGACAATGTCTTTACGTCAGAGAAAGTCTGAGTGAGA +GCTGTCCTTAAAACCAAGTCCCATGAGGCAAGTAAAGAGGTGACTCGCTGAGAGGATCAG +GGAGAGGGACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAAGAC +AGAGAGGGTGCTGCATTGAGTCGAGAGGTGTGAGGATGTTCGATAAGCCATTATCACTCT +GCTCGGAGGACGTCAGGCCCTATCCTTTTTTCTTTGAGTCACCACTTTCTCACCACAGCC +ATCCTTCTTCCTTTGTCTGTTTAATCTTTTGCAGCCAAACATTTGGTATGCAAACTATAG +GAAGATATGGTCTGACACCGACTGATGTGATGCTAATGCCTTCTCTGTTTTATCCAATGA +CTCCTCATTTATCAGGACCAATCCAGCTATTGTGTGCTATTGGCCCAACACAGCATTAAA +CATGGTGACCAGAATAGCCACAGCAAAATAAATAACGGGCCTCTGTGACTATTGTATGTG +CATTTCTTACAGCTGTCATTTTTCTTTTCTGTTAGCTTTCATTCTACTGTGCGTGCTCTC +TATCTGCCTACGTTGTATCTGTGCCTTTTGTTAAATTCATTCAGCCTTTTATCTGTCTTG +AATTTCTTTCTCTGTGTCCTCCTTTCCCTCTCTGTCTCAGCAGATCCGTCCCTTGTTTTT +GCAGGAGAAGCGCTCTGCGTCATGCAAGGTCCATCTTCTGCGACGCACCATCAGCGTTCC +AGTGGAAACACAGTTTCCAGAACTCCATAGCCAGCTGTCCACTGAGAGCGGTGAGTAGCC +TGAGGACATGCCTCTGCTGTGATTAGCATGCATCATTATTTCCATACACACACTGGAAAT +CTTTTAATCGTTTTTCTTGACACAATTTAATTAATTTAAATAATTAATAACATTGAAATC +AACTGTTAAACACTTGTTCAACATGGTTGTGGACAAAATCATCATAATGACTGTGGAGAC +TAAGGAGAAACAATGCTTTGTTAAAATCTTTGCTCTGGTTTTGGCTTTTTCTATATTCTA +TTTGTGTGTGCAGTGCTGCTAAACATCATCTTAGTCAGAGTCAAACTTGAGCACTCATGC +AGATGCTTGTTCTATTCAGTGGTCAAATGGGCAGTGTAGCTTAGGAGAAGCACTTCTTTC +CGCTCCTCAGTGACATAACCAGTCACACACTCACACAGGCAAGTGAGCCTTTTAAAATTG +CTGATACTATTTTTTTCTACTTCATATCCACTAGATGGAGAGCTTGGTGCTTTGTAGCAC +TCCAGTGTACTTGGAATGTTTCATCATAACCACTAAGGCAGACATTGATAAAGGCTTCGG +TCTCTTTCAAACTGCAGGTGTCATGTTGCACTCTCCCTATTGCTTTTATGAAAATGTAGT +GCCGGTAATATAACACAGTTACTCTCTGCATATATCACTATGTACACTTACTTCTATGGA +AAAGATGGAGCGCCACAGTGAAAACTGTTTTGAGTCTGTGAGGGGAAAACACAGCATCAG +TCACAGTGAAACACTAGGTGGCACTCAGGTTTGACATTCAAGCATTTGTATCCCACAGTT +ACTGTTGCTGGGTTGTTGGCTGGCATGCAACTTAATATGATCTATCTTTAAATCAGTGTG +TGCAGTGGTTATTTAGTTTAAGTGCTTTTTAATGATGTCACAACATTATTTTGTCTACAC +CCTGCATACAGCACAGTATATTAAATTTAGGTTTTATTAAGTTAAGTAATGTTCTGAGGT +GGCATTGCCCTCAGGTATATATCCCTCAGGCAGTGTTACTGGACAGCATATAGATTGTAA +TGTTGTGTAAGCAGTGTTGTGTAAGCTTTTTTAACCAAAATGCTCTCATGTTTCTTTGTT +ACCACAGTGGTTTTAGTGATGTTTTGTGCTGTGAACAGAATCATGATTTCTGCAGACACT +CCACATCTGTTTAAACAGTGATTTTCACATCTGTCTGTAACTGAGTCAGTCAGTTTGTGG +TTGGATTGATGTGTAGTGGGATCTACAGATCATCAACCCTCGGGGAAGCCATTTAGTTCT +GTGTTAAATAAAAATACAACTTTTGAGCACTGTTTTTTCATATTTTTCTTCATCCCTTAG +TTGATATTAAAGGTGCTATATGTAGATTTTTGCTATCACTACATAGCCAATGTTAGGATT +AAGAACCCCAGCAACCCGAATGTTAACTCGTACTTTGCTTCTATTTCTATTACATATTTT +CTTCTATGGAAGTTAGGATGTTAACCAGCTAACCCCAGGTCATCTCATAATACCACTTGG +CAATAGTCAGTCACTGTTGCATTCAGTCTGCCCCTCCAGCATGAAAGGATGAAGAAGTAC +CGCTACCCAGAAGGCGTAGTCTAACCCCTTGTCTTGTAAACACAGCAATGGCTGAAGCTC +TTGGTAAGTAAACAGCTGTTAATGTCAGTGTTGGCTACATAGCTAAAACTTACACATAGC +ACCGTTAAAAAAATAAATGGTAAGTTTTTGTCCTTTTAGTTAAAGCATGTAAATGTCAGT +TAAAACAATTTAGAAAATTTCTCATTCAAATAGTCATTTTATTTTGTGTGCTATAAATAC +CTTCAGTTTTTTTTCTTGTACTTTATTTTAAACTCTTGTCTTTCTCTTATGCCCCTTATC +TACCAGGAGAGGTCACACTCTTGTTGATAGCATGATAAGGAAATGAGCAGAGATGTCCTT +ATTTCTCCTCAAAGTTATTCCCTGCATAGCACATATTTGACTTTAAAAATACAAAGACTA +CAGGTGCTAAATCACACACACAACACCCAAAAGAATAGAGGACTTTTAAATATGTGCATC +CCATTTTCTAATCTATATTCACCACTGATACAAGTGATGACACGGTGATGAGAAAATAAC +GTAACATACATTATTATACAAGATTGGTATGATTGCTGTAGGTTGGTTTTGTTTATCTGA +GAAGGGACAGAGGCTAAAAGAATAAACAAAGTCTGCCAGCTACTTCACTAATTACAGAGT +ACCCCTGCAACTCTGCCAATGACATTCTGAAACTTTTCCATGACTATTATGTAAGATAAT +TTTTGAATCACTGATTCAGATTTCCATAGCCAAGATACACTATTCTGCATGTTGGCTAGA +ATACATTACAATACATTAATATATTACTGTAGTGGTTATTATGTCAGCCATTTAAACATA +ATTTCATACTTTCAGCTGTTCGCAGGGCAAACTTTTTATTTTTGTCACCTGAATCCAGTT +GCATTTGGATTTGAATTCAGTGGTGACTGCCAATGAAAAATAACTCACAGGGGCACTTAG +AGATCTGAGGCGGCATTGACTGAACATCGAAGGGCTACTATTACAGAAATGCAAGTGGAA +AAAGAATCTGATATGATACTTGCCAGTATGAAAAGCATAATTAGGACTTTAAATGCATGT +TTTAAATGTTTTTGTGAACCATAATTTCAGTGTAAAAGTTCCAGTTATATTTTAAAAGGA +ACTCCAAATATCCAGTGGTAGCATCAAGGTAACCTGAGATAAGTGAAAAGTAATTCTAAA +TTAATCAGTATGTTGAAATATCAGACATTTGTGTGCATTATTGTTAGTGTGACCATGGTG +GGATACTTCAAACACACTTGTTCATTGGCAAAATAATTGTCACATGAATTAACACAAGTG +ACACTTTCAGTATCATACTGACAGAATGTTTGTTGTTAACTTTATCCCTGAAAACAAACA +CTAATACATGTTCTTGTCGCCCCTTCAGTGCCTAACCTTTAAAATTGTGCTTGTGAGTGT +GTGTATGTGAGCGCACCTGTATGGTTTTCAAATAATGTTCCACATCACAACACTACAAAC +ACTCACATGGTCTATGTTTTACTAAATTATTCATTGGCGTAGGCCCCACCTGCTCTTGTC +CTTGTGTGACACAGGCTCTAAATAAGCAGCATGATGAATAAAAATGACACTGAGATGAAT +AGGAATCCACAGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG +AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAACATGCCAGAGA +CAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTTAATTTTACTGAGGTGAAAGT +TTTTTTTTTTTTTCTGGATAAAGCTTTGGAAAAGTTCTCAACTGTTGCTTCTTTAAAGAT +GCTGGGGCATATTCTGCCCTATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAA +GCTGTAACATTTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT +ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTATCTTAATATT +CCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCATCTCTCTCCTCATAGTTTTT +CATTACAATTAGCTCTCATTAGATAGAATTGTATTTGTTGTCTTTGTGCCAGTCACTCCA +GTCTATTTTGCCAGCACACAACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACA +GTTTTAATGATGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG +GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCATTTGGCCACAA +AATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGTACAGGTTGCATATGAGCTGG +TAGGAAAGATATAGAATCATTATCAGCTGATAATCTAACAGTAGCAGTCAGTGTAGATGC +TGTGCTAACGCAAAGTTGTGAAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCT +GCCAAGCTTAAGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC +GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTTTTCAAGCAAA +AATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAGATTAAATATCTTTTGGGTTT +TGGCACAGGCTGGACAAAAAAACCTCTGAGACGCTGTGATAAGAATTTATTTTCACATTT +TTTTTACTTTTCAGGGACTACACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCC +CAAATGTTAACTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT +TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTGGTCAGGTTTT +TGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGGGAAGTTCCTAAATTCTTCTG +GCATGTTAATGTTTTCCAAACTGATGTTACCAAGTCCTCGTTATGATGAGAAAAAAATAT +GCTGAGAGTGAAATTGATCAAAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCA +TCTTTCTCCCTCTCTCTCCACCGCAACGTGGAAACTGCTCCTCTCTCTCTCTCCCTCTCC +CTCTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCCCTCCCA +TTCTGTGCTCCGGTATACTCGCTCTCTCACTCTCTCCCTCTCTCCCCACTCTCCAGAGAG +GGGTTCAGTCAGACAGATGTAACACAGCAGTAGAAGCCTGAGCTGAGCTGGCAGGCTGCG +GAGGCCAGACCAGAGCCAGCAGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCA +GCGGCAGCACAGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT +TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCATCACCCTGTG +AATTTAACATGGACCCTGACACCAGCACCCATCCAGAGACACAACATGGTGAGTGAGATT +TGAAGGAGGAAAAGATTAGAAACAATGAGAGTGATACTGTGGGAAAAGTTGAGGAGCGTG +TTAGTGAACAAGGGAGTCAGGTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGG +CTCTCCATTTGGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC +AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCAATGTGATGAA +ATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTCTTGTCATTACTTTAACAGGG +TTGTAAAGTTTTTTTTGCTTTTTTGTAGCTAAGAAAGTTGAGAATTGTTTTGTCTGAACT +CTCTCTGGGATTTGTCTTGTCGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAG +GAAGCTCTCCTCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT +TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATATTTGTATGCTG +TGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACAGAGGGGCACCAAAGAATGAA +AGTGGGAGACAGAGGGAACGAGAAGGGGAGAGACCGAGAGAGAAGGACTTATGTACACAA +ATAAATCCAGGGGGATCTAGACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTT +CCCCCTCATTTTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA +CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGAAAAGACGATG +TTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTGCTGATGAAGAATGTGGTTAA +CAGAATGAGTCAACAGAGAACATATTTCCAAGAGACTGTAGTTTCTCTTCGCCAGCGTCT +AAGCCACATTGCTTTATGCACTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGA +GGGGAAAGAGAATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC +TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCACCTTCCCAAAA +TAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTCTCAACCAGTCAGCCAGCCTC +TTTCAGTGCATACAGCTTGAGGAGATCCCTTCTAAAGGTCCAATATAAATAGAAAAGTGG +GAGTAGAAAGGGCAATAATCTGATATCATCTGATTACATTCACACCTCAGGCTTGCACGC +TACAGGAAGAGTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT +AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAATCCTGGAGTA +GACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCATATATTACACATTGCTTTTTG +TACTTTGCATATAAAGTAGATGCTGATCTGCTATCTGCATATATAGTAGCTGCAGATAGC +ACTGTAACTACATCTACATATTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATG +CTGGACAACCTCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC +CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGTTCACCCAATA +GTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTACAAGCACCCATGCCTAAATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.align Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,104 @@ +18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0 1 + + scaffold_1 613 GTGTGTGTGTGTGTGTGTGT 632 + + (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 + +Matrix = Unknown +Transitions / transversions = 1.00 (0/0) +Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) + + +16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1 2 + + scaffold_1 780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824 + v - v - i v vv i + (ATAATA)n#Sim 1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45 + +Matrix = Unknown +Transitions / transversions = 0.40 (2/5) +Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) + + +12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2 3 + + scaffold_1 2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274 + - i v v iv -i vv v + (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46 + +Matrix = Unknown +Transitions / transversions = 0.50 (3/6) +Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) + + +15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3 4 + + scaffold_1 4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898 + v i i - vv vv i - - - + (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 + + scaffold_1 4899 -CTC 4901 + - + (TC)n#Simple_ 51 TCTC 54 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) + + +13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4 5 + + scaffold_1 6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278 + v i - v -i - i v - v v + (TAATTAA)n#Si 1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47 + + scaffold_1 6279 AAATAA 6284 + - + (TAATTAA)n#Si 48 -AATAA 52 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) + + +15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5 6 + + scaffold_1 6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597 + v i i viv i vi v -v i - + (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48 + + scaffold_1 6598 GACAGAGAG 6606 + v + (GACA)n#Simpl 49 GACAGACAG 57 + +Matrix = Unknown +Transitions / transversions = 0.86 (6/7) +Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) + + +67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 7 + + scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029 + i i - + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 + + scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050 + + (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71 + +Matrix = Unknown +Transitions / transversions = 1.00 (2/0) +Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) + + +19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6 8 + + scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113 + v v i - i v + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37 + +Matrix = Unknown +Transitions / transversions = 0.67 (2/3) +Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.cat Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,103 @@ +18 0.00 0.00 0.00 scaffold_1 613 632 (13519) (GT)n#Simple_repeat 1 20 (0) m_b1s252i0 + + scaffold_1 613 GTGTGTGTGTGTGTGTGTGT 632 + + (GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGT 20 + +Matrix = Unknown +Transitions / transversions = 1.00 (0/0) +Gap_init rate = 0.00 (0 / 19), avg. gap size = 0.0 (0 / 0) + +16 18.30 2.22 2.22 scaffold_1 780 824 (13327) (ATAATA)n#Simple_repeat 1 45 (0) m_b1s252i1 + + scaffold_1 780 ATATTAAT-ATACTAAATAATGATAATATTAATTCTAATAATGATA 824 + v - v - i v vv i + (ATAATA)n#Sim 1 ATAATAATAATAAT-AATAATAATAATAATAATAATAATAATAATA 45 + +Matrix = Unknown +Transitions / transversions = 0.40 (2/5) +Gap_init rate = 0.05 (2 / 44), avg. gap size = 1.00 (2 / 2) + +12 23.88 4.55 0.00 scaffold_1 2231 2274 (11877) (CAGA)n#Simple_repeat 1 46 (0) m_b1s252i2 + + scaffold_1 2231 CAGA-AAACAGTCAGCCAATCAGA-GGACAGACTCAGAGACAGACA 2274 + - i v v iv -i vv v + (CAGA)n#Simpl 1 CAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACA 46 + +Matrix = Unknown +Transitions / transversions = 0.50 (3/6) +Gap_init rate = 0.05 (2 / 43), avg. gap size = 1.00 (2 / 2) + +15 18.42 10.20 0.00 scaffold_1 4853 4901 (9250) (TC)n#Simple_repeat 1 54 (0) m_b1s252i3 + + scaffold_1 4853 TCTATTTTTCTCTCTCTCTCT-TCGGTCAGTTTCTCT-TCT-TCTC-CTC 4898 + v i i - vv vv i - - - + (TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 50 + + scaffold_1 4899 -CTC 4901 + - + (TC)n#Simple_ 51 TCTC 54 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.10 (5 / 48), avg. gap size = 1.00 (5 / 5) + +13 19.07 1.82 7.69 scaffold_1 6230 6284 (7867) (TAATTAA)n#Simple_repeat 1 52 (0) m_b1s252i4 + + scaffold_1 6230 TAATGAGT-ATTACTAATTAATAATTGGATGAGTTTATGAATTCATCATT 6278 + v i - v -i - i v - v v + (TAATTAA)n#Si 1 TAATTAATAATTAATAATTAATAATT-AAT-AATTAAT-AATTAATAATT 47 + + scaffold_1 6279 AAATAA 6284 + - + (TAATTAA)n#Si 48 -AATAA 52 + +Matrix = Unknown +Transitions / transversions = 0.60 (3/5) +Gap_init rate = 0.09 (5 / 54), avg. gap size = 1.00 (5 / 5) + +15 28.31 0.00 3.51 scaffold_1 6548 6606 (7545) (GACA)n#Simple_repeat 1 57 (0) m_b1s252i5 + + scaffold_1 6548 GACAGAGAGATAAACAGACAGACATGGAAACAGAGGGACATAGAAAACAA 6597 + v i i viv i vi v -v i - + (GACA)n#Simpl 1 GACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGA-CAGAC-A 48 + + scaffold_1 6598 GACAGAGAG 6606 + v + (GACA)n#Simpl 49 GACAGACAG 57 + +Matrix = Unknown +Transitions / transversions = 0.86 (6/7) +Gap_init rate = 0.03 (2 / 58), avg. gap size = 1.00 (2 / 2) + +67 2.94 1.43 0.00 scaffold_1 11981 12050 (2170) (CT)n#Simple_repeat 1 71 (0) c_b1s251i0 + + scaffold_1 11981 CTCTCTCTCTCTCCCTCTCCCTCTC-CTCTCTCTCTCTCTCTCTCTCTCT 12029 + i i - + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 50 + + scaffold_1 12030 CTCTCTCTCTCTCTCTCTCTC 12050 + + (CT)n#Simple_ 51 CTCTCTCTCTCTCTCTCTCTC 71 + +Matrix = Unknown +Transitions / transversions = 1.00 (2/0) +Gap_init rate = 0.01 (1 / 69), avg. gap size = 1.00 (1 / 1) + +19 15.37 2.78 0.00 scaffold_1 12078 12113 (2107) (CT)n#Simple_repeat 1 37 (0) m_b1s252i6 + + scaffold_1 12078 CTCGCTCTCTCACTCTCTCCCTCTCTC-CCCACTCTC 12113 + v v i - i v + (CT)n#Simple_ 1 CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC 37 + +Matrix = Unknown +Transitions / transversions = 0.67 (2/3) +Gap_init rate = 0.03 (1 / 35), avg. gap size = 1.00 (1 / 1) + +## Total Sequences: 1 +## Total Length: 14220 +## Total NonMask ( excluding >20bp runs of N/X bases ): 14220 +## Total NonSub ( excluding all non ACGT bases ):14220 +RepeatMasker version open-4.0.7 , default mode +run with rmblastn version 2.2.27+ +RepeatMasker Combined Database: Dfam_Consensus-20170127
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.gff Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,11 @@ +##gff-version 2 +##date 2018-04-21 +##sequence-region dataset_12.dat +scaffold_1 RepeatMasker similarity 613 632 0.0 + . Target "Motif:(GT)n" 1 20 +scaffold_1 RepeatMasker similarity 780 824 18.3 + . Target "Motif:(ATAATA)n" 1 45 +scaffold_1 RepeatMasker similarity 2231 2274 23.9 + . Target "Motif:(CAGA)n" 1 46 +scaffold_1 RepeatMasker similarity 4853 4901 18.4 + . Target "Motif:(TC)n" 1 54 +scaffold_1 RepeatMasker similarity 6230 6284 19.1 + . Target "Motif:(TAATTAA)n" 1 52 +scaffold_1 RepeatMasker similarity 6548 6606 28.3 + . Target "Motif:(GACA)n" 1 57 +scaffold_1 RepeatMasker similarity 11981 12050 2.9 + . Target "Motif:(CT)n" 1 71 +scaffold_1 RepeatMasker similarity 12078 12113 15.4 + . Target "Motif:(CT)n" 1 37
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.log Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,10 @@ +SW score % div. % del. % ins. query sequence pos in query: begin end (left) repeat class/family pos in repeat: begin end (left) ID + +18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) 1 +16 18.3 2.2 2.2 scaffold_1 780 824 (13396) (ATAATA)n Simple_repeat 1 45 (0) 2 +12 23.9 4.5 0.0 scaffold_1 2231 2274 (11946) (CAGA)n Simple_repeat 1 46 (0) 3 +15 18.4 10.2 0.0 scaffold_1 4853 4901 (9319) (TC)n Simple_repeat 1 54 (0) 4 +13 19.1 1.8 7.7 scaffold_1 6230 6284 (7936) (TAATTAA)n Simple_repeat 1 52 (0) 5 +15 28.3 0.0 3.5 scaffold_1 6548 6606 (7614) (GACA)n Simple_repeat 1 57 (0) 6 +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0) 7 +19 15.4 2.8 0.0 scaffold_1 12078 12113 (2107) (CT)n Simple_repeat 1 37 (0) 8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.masked Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,286 @@ +>scaffold_1 +TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATC +CAATATATTCCTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGAC +ATCCTCAGTGATTGAAGTGACAAAAAGTGGAGCGCACGCAGTGGTCATTA +CCCTCCAATGGTACTTCTAATTAAGGAAAGATTTTTTGCATTCACTGAGC +AAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGGGTCCATTAAA +CAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT +AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGC +CCCAAATTGTCTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATA +ATTGTGTTTCTCTCTAGATGTGCGGTGTCCATCAAGACACTGGATGTCAC +GTGGTCACTCCTGTGAAGAGCGAACTGTGTGGAACCCGAAGTACTGTGTG +GTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGGTGGTGAGAGC +AGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC +TCTCATCTGCTCNNNNNNNNNNNNNNNNNNNNCCTTGTCAATGTCATTAC +ACAATTTATGTTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACAT +CTACTTTCTGTCACCTGATACCTCATACTTTACACTCTAATCCCTTTTTC +CTTTCTAACTGCTGCTGTGTTAAGCTGTCNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNGTGAATGGAGATTCACAATGAAGAAA +CACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT +TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCA +AGGCTGAGTCTGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGG +ATTATGCTAGTTTGTGTGAGATTAGAGGTCCTGTTGTTACGAGCAAATCA +GCAGTCAGCAGGGTAATCTAAATTACATTGTTCTGTCGGCAATATCCTCT +CCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCCCCACAGTAGT +GCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT +ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTG +TGATTGTTGGTGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGAT +CTCCTGGGATTTTCACACACGGCATTCTCTAGAGTTTACTCAGAACGGTG +TGGAAAGCAAAAAAACATCCCGCGAGCTGCAATCCTGCGGATGGAAACAC +CTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGATCAATCTGACA +GAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA +AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTAC +AGCAGCAGATGAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACAT +CTCAGACTGCACAGGACACCAAAACAAAAACACATCCTGTTTTCTACTGG +TGGTAGAGTCACAATTTGGCAATAAGATAAATCCATGGACCCAACTTGCC +TTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATGTTTTCTTTAC +ACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG +TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGA +TACCTGCGGCAATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTAT +TATAGAGAGTAATTTCACTGTCCATGTCTTTTTTGATCATAAAGCAGGTC +TAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCAGGTCTAGGTGC +TGTATACAACACTGTATTGAAATGCTGAAGCCAATATATCAATCTATCTG +TCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT +GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCAC +CACAGCATTTACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGT +TACCTGTTATTGGCCTGGCTCTATGGCATGNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNCAAAGTGCCCTGTTCTTGTTAGAGCA +GAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGATGGTTTTTTG +GTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA +AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGT +TTCGTAGTTCTAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTA +AAGCGGCTACATGTAGAATTTGACCCACTTTGGTGCCCACATATGGTAAC +TAAAACACTACAGACAGTATGCACTCCAACCCTATATAATTTATGTCCTT +CAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGATTAATACCTAG +AATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG +AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAA +CCTGGTCATTCCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCT +CCTGCTGTGGGTGCCAATAGCTCATGCAAGTTGGTGTCTTTCAACTAAGG +CCACTATGTGAGGACCATCAGCAGCAAATTAAATTAGAAGTGCCTTGGAG +TTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGACAGAACAGTG +CCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT +GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAA +GGCATAGTTACTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGC +TGGAACTTGGAACATGTAGCCTAAGTTTCCCTTTGTCTGCAATTACTGAG +GTATGCCATGTTGAAATAGAACAATAATTGCAGGGAGGAATTATTCCAAT +CGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTTCACAGCAACA +AAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT +CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAA +GCGATGATACAGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACA +TGGTTTAAACAAGCTCAGTTAAATGGATCAGAGCATCAACTGCTGTGAAC +AAGCAATCACACGGTCAAGGTCAAACATTTACACTTCTGAGAGATCTGGA +GAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTAACTGATTACG +CCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA +TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCAT +GCAGCCTAATTTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATG +TTTTAGGCAGTTTTAGGCACTAAAGGTGAACTGAGGATGCAGTCCCACGA +TTAATTTTTATTCATCAGTTAACCTCATGTGAAGTGTAGTAAACAGAAAA +AACCTAAATCAGATCAGTATTTCTTATGACCCCCCTCCCCTACCACCCAT +CTTTAAAACAGCTCCAGTTCTCCTCAATCCCCCTGTACTTAGGTAGTTTT +TTTCTAGCGTCTTGGAGAAGTTGCCTCAGTTCTTCTGTGGATTTTAGGCT +GTCTCTGTGTCTTCTGTCTCCTCATGTATTCTCAGACTGACTCCATGATG +TTGAGATCAGGGCTCTGTGGTGGGGGGGTCAGACCATCTGTTGCGGGACT +CCTTGTTCTTCTTGTCTCTGAGGATAGTTCTTTATGATGCTGACTGTGTG +ATTGGACTCATTGTCCTGCTGCAGAATTAATCTGGGACTGATCAGACATC +TCCCTGATTGTACTGACAAAGGATAAGAGCAAAAACCTGTAGACTGCCTA +AAACTTCTGCACAGTACTGCACAATACTGTATGTATGTGTGATAATACTC +AGAAGTGATATAGAGTGGTTCAGGAGAAGCCTTAACTTACTTGTTCTTCT +TTTCCCTATGATGCAATTTCTCTCCAAGCAAACAGTACATAATGAAATAT +GTCTAAGAAAACACTAGCTGTTTGTCTTTTTGAAACACATTTAATAATTC +AGATTTAGCCACAAATTAAAAATGAGCTTATACTTTGAACTTGCCCATTG +GTTTTGATGTATGAAGCTGACAGATTTAGTCCACTGCATACTGCACTTTT +TTGGATAGTGAAATAAATTAATTTATTATGCAGCATTTAAGCATATTGCT +GTTATCTAGAATTTTATATATTAATAGGTATATATTATATTAACTCTTCA +TTTGCTTAAATTTGGCCTGTATATTCCTCCATTTTATACAACCTTTAGAA +AACACTGGAGTGAACAAAAATGTGAGGTTCAAAAGTGAGAGGAAAGAAAA +ATCAGTGTGTGCAGCAAGACTGTAAGAGTCCCTGAACAAAAGTGTTGATT +TATTGTTGGCTGTGAAAGTTTTTGCTGCAGGGGTTTTTGTAAACAGTGAC +TCTTCTTTATGTCTTTGTTTCTATCTTTTTGTGTTTTCTTTTTTCATCTT +ATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NATACTCATGCTTCTCTTTTACTCTAATGGAAAACATAGAATTGAGGTGC +AGTATCACTGAGAACAGCCAATGCTGATACTGTCATTTGTTATAGGATGT +TTACTTAAGAAATGATTGTGGCCTTATTTGCCAAAGACGATTAGGCCCTG +AGCCATTTGTACAGCCAATGTGACACCTCCGTAACCATAAGAAAAATTAT +GCTTCCACAAACAGAAAGAGAGACAAATACAGACAGTGAAAGCAAAACTA +TGAGAGAAGGGATAGCCATCTCAGCATTCAGCCAGTGTGTCACATGTCCA +GAGGGCTGCAATATGAAGCCAATAAACTGAGAGAAAGGTGTGATTCCAGA +GGGCTTTCCGGACTTTAAACTTTTCTCATTTTCACCTTCAGCTCGTTGTG +AAGCCTTCAATTGTTCCTTGGTCACATGAAGCCCCCTGTGTGTAAAATTG +ACATTCAGCTTATTACTCTCATCTACATCTCTAAAGTTGCACATGACTGC +CAGTAGAGGGTGCTCATGATTTGAGACAAGTAACTTTTCTGTGCTTGTGT +CAACAGTTAAAAATTCCCTATGGATACTTGAAAGAAATGCACCAGTGTTT +AAATTTAGACTCAGTCCAAGTAGGCTTTGCCATTTGCTTTACTGTTGTAA +TCAAATCAGTGCTCACAGTACATCAGTGGCAAAAGCAATTAGCTTAATTG +AGTTAGTAGGGAGTGAAAAGATAGATCACTATTTCCTGGCAGCGATATAT +TTTTCTCAGTTAACCTTCTCACAGAAAATTAGTTAGATGAGTTTCTTATC +TCATTAGAACCATTGTTGTTTATTATTTAAACCTGACCTTTATCCAGAGA +ATGTTTTTCACAGTAAGCATGTGTTTCACTCCAGCTCATACAGACACACC +TTGTGGCCAGTCAGGGAATGTGCATTAAAACTAATGTTCTCTCTGGTAGA +GCCATTCTGCCTATTCTGTTATTCACCAAAACTTTCCTGCCCAGATTTTT +CCATCTAGTCAGGGGACTTTTTCCTCAGCTGAACTGTCAGTAGCCAGCTG +CTCTGACCTTTACTCACCTCAGAGATTACTCATTCAAGTTATTTTACCAA +TGATGGAATAAAGTGAATACACACATCGTGACTTCATCATACTTTCCCTC +CTTTACCGTACTTTCCTAACATCAGTTAGCAAATTATACACTTAAATATG +CTAAAATAGAGATTTGTTTCAAATTGAAGAGCAACACAGGACACATTTGC +TTACACAAGTGACTCTATCTTATTTTTTAAGTGGCTGTCATCCTCAATAT +CATCAATATTTTAGGCATGTGAATGTAGGNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATTATTATGATAAAG +CTACACATTATACTGCAATTCCGGGCCAACACTATTGTTTCGCCCTTACA +GTACAGGACTGTACATATCACTGTCACTACAAATTGTTTCAGTGAGGCTC +AGATTACAGCTCATCTTGCTTAGTCATTACGGCTCAGACCACCAGACAAT +GTCTTTACGTCAGAGAAAGTCTGAGTGAGAGCTGTCCTTAAAACCAAGTC +CCATGAGGCAAGTAAAGAGGTGACTCGCTGAGAGGATCAGGGAGAGGNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNGGTGCTGCATTGAGTCGAGAGGTGTGAGGATGTTCGATAAGCCA +TTATCACTCTGCTCGGAGGACGTCAGGCCCTATCCTTTTTTCTTTGAGTC +ACCACTTTCTCACCACAGCCATCCTTCTTCCTTTGTCTGTTTAATCTTTT +GCAGCCAAACATTTGGTATGCAAACTATAGGAAGATATGGTCTGACACCG +ACTGATGTGATGCTAATGCCTTCTCTGTTTTATCCAATGACTCCTCATTT +ATCAGGACCAATCCAGCTATTGTGTGCTATTGGCCCAACACAGCATTAAA +CATGGTGACCAGAATAGCCACAGCAAAATAAATAACGGGCCTCTGTGACT +ATTGTATGTGCATTTCTTACAGCTGTCATTTTTCTTTTCTGTTAGCTTTC +ATTCTACTGTGCGTGCTCTCTATCTGCCTACGTTGTATCTGTGCCTTTTG +TTAAATTCATTCAGCCTTTTATCTGTCTTGAATTTCTTTCTCTGTGTCCT +CCTTTCCCTCTCTGTCTCAGCAGATCCGTCCCTTGTTTTTGCAGGAGAAG +CGCTCTGCGTCATGCAAGGTCCATCTTCTGCGACGCACCATCAGCGTTCC +AGTGGAAACACAGTTTCCAGAACTCCATAGCCAGCTGTCCACTGAGAGCG +GTGAGTAGCCTGAGGACATGCCTCTGCTGTGATTAGCATGCATCATTATT +TCCATACACACACTGGAAATCTTTTAATCGTTTTTCTTGACACAATTTAA +TTAATTTAAATAATTAATAACATTGAAATCAACTGTTAAACACTTGTTCA +ACATGGTTGTGGACAAAATCATCATAATGACTGTGGAGACTAAGGAGAAA +CAATGCTTTGTTAAAATCTTTGCTCTGGTTTTGGCTTTTTCTATATTCTA +TTTGTGTGTGCAGTGCTGCTAAACATCATCTTAGTCAGAGTCAAACTTGA +GCACTCATGCAGATGCTTGTTCTATTCAGTGGTCAAATGGGCAGTGTAGC +TTAGGAGAAGCACTTCTTTCCGCTCCTCAGTGACATAACCAGTCACACAC +TCACACAGGCAAGTGAGCCTTTTAAAATTGCTGATACTATTTTTTTCTAC +TTCATATCCACTAGATGGAGAGCTTGGTGCTTTGTAGCACTCCAGTGTAC +TTGGAATGTTTCATCATAACCACTAAGGCAGACATTGATAAAGGCTTCGG +TCTCTTTCAAACTGCAGGTGTCATGTTGCACTCTCCCTATTGCTTTTATG +AAAATGTAGTGCCGGTAATATAACACAGTTACTCTCTGCATATATCACTA +TGTACACTTACTTCTATGGAAAAGATGGAGCGCCACAGTGAAAACTGTTT +TGAGTCTGTGAGGGGAAAACACAGCATCAGTCACAGTGAAACACTAGGTG +GCACTCAGGTTTGACATTCAAGCATTTGTATCCCACAGTTACTGTTGCTG +GGTTGTTGGCTGGCATGCAACTTAATATGATCTATCTTTAAATCAGTGTG +TGCAGTGGTTATTTAGTTTAAGTGCTTTTTAATGATGTCACAACATTATT +TTGTCTACACCCTGCATACAGCACAGTATATTAAATTTAGGTTTTATTAA +GTTAAGTAATGTTCTGAGGTGGCATTGCCCTCAGGTATATATCCCTCAGG +CAGTGTTACTGGACAGCATATAGATTGTAATGTTGTGTAAGCAGTGTTGT +GTAAGCTTTTTTAACCAAAATGCTCTCATGTTTCTTTGTTACCACAGTGG +TTTTAGTGATGTTTTGTGCTGTGAACAGAATCATGATTTCTGCAGACACT +CCACATCTGTTTAAACAGTGATTTTCACATCTGTCTGTAACTGAGTCAGT +CAGTTTGTGGTTGGATTGATGTGTAGTGGGATCTACAGATCATCAACCCT +CGGGGAAGCCATTTAGTTCTGTGTTAAATAAAAATACAACTTTTGAGCAC +TGTTTTTTCATATTTTTCTTCATCCCTTAGTTGATATTAAAGGTGCTATA +TGTAGATTTTTGCTATCACTACATAGCCAATGTTAGGATTAAGAACCCCA +GCAACCCGAATGTTAACTCGTACTTTGCTTCTATTTCTATTACATATTTT +CTTCTATGGAAGTTAGGATGTTAACCAGCTAACCCCAGGTCATCTCATAA +TACCACTTGGCAATAGTCAGTCACTGTTGCATTCAGTCTGCCCCTCCAGC +ATGAAAGGATGAAGAAGTACCGCTACCCAGAAGGCGTAGTCTAACCCCTT +GTCTTGTAAACACAGCAATGGCTGAAGCTCTTGGTAAGTAAACAGCTGTT +AATGTCAGTGTTGGCTACATAGCTAAAACTTACACATAGCACCGTTAAAA +AAATAAATGGTAAGTTTTTGTCCTTTTAGTTAAAGCATGTAAATGTCAGT +TAAAACAATTTAGAAAATTTCTCATTCAAATAGTCATTTTATTTTGTGTG +CTATAAATACCTTCAGTTTTTTTTCTTGTACTTTATTTTAAACTCTTGTC +TTTCTCTTATGCCCCTTATCTACCAGGAGAGGTCACACTCTTGTTGATAG +CATGATAAGGAAATGAGCAGAGATGTCCTTATTTCTCCTCAAAGTTATTC +CCTGCATAGCACATATTTGACTTTAAAAATACAAAGACTACAGGTGCTAA +ATCACACACACAACACCCAAAAGAATAGAGGACTTTTAAATATGTGCATC +CCATTTTCTAATCTATATTCACCACTGATACAAGTGATGACACGGTGATG +AGAAAATAACGTAACATACATTATTATACAAGATTGGTATGATTGCTGTA +GGTTGGTTTTGTTTATCTGAGAAGGGACAGAGGCTAAAAGAATAAACAAA +GTCTGCCAGCTACTTCACTAATTACAGAGTACCCCTGCAACTCTGCCAAT +GACATTCTGAAACTTTTCCATGACTATTATGTAAGATAATTTTTGAATCA +CTGATTCAGATTTCCATAGCCAAGATACACTATTCTGCATGTTGGCTAGA +ATACATTACAATACATTAATATATTACTGTAGTGGTTATTATGTCAGCCA +TTTAAACATAATTTCATACTTTCAGCTGTTCGCAGGGCAAACTTTTTATT +TTTGTCACCTGAATCCAGTTGCATTTGGATTTGAATTCAGTGGTGACTGC +CAATGAAAAATAACTCACAGGGGCACTTAGAGATCTGAGGCGGCATTGAC +TGAACATCGAAGGGCTACTATTACAGAAATGCAAGTGGAAAAAGAATCTG +ATATGATACTTGCCAGTATGAAAAGCATAATTAGGACTTTAAATGCATGT +TTTAAATGTTTTTGTGAACCATAATTTCAGTGTAAAAGTTCCAGTTATAT +TTTAAAAGGAACTCCAAATATCCAGTGGTAGCATCAAGGTAACCTGAGAT +AAGTGAAAAGTAATTCTAAATTAATCAGTATGTTGAAATATCAGACATTT +GTGTGCATTATTGTTAGTGTGACCATGGTGGGATACTTCAAACACACTTG +TTCATTGGCAAAATAATTGTCACATGAATTAACACAAGTGACACTTTCAG +TATCATACTGACAGAATGTTTGTTGTTAACTTTATCCCTGAAAACAAACA +CTAATACATGTTCTTGTCGCCCCTTCAGTGCCTAACCTTTAAAATTGTGC +TTGTGAGTGTGTGTATGTGAGCGCACCTGTATGGTTTTCAAATAATGTTC +CACATCACAACACTACAAACACTCACATGGTCTATGTTTTACTAAATTAT +TCATTGGCGTAGGCCCCACCTGCTCTTGTCCTTGTGTGACACAGGCTCTA +AATAAGCAGCATGATGAATAAAAATGACACTGAGATGAATAGGAATCCAC +AGCAAATCAGAGAGCACTCTCATCTCGTCTCATCCTCCGACTGAATAGCG +AGCGGCTGCCTCCTTTATTCTTTTGAACTCTTCGCGGTTTTGGCACAAAC +ATGCCAGAGACAGAGAGCGCTGTTACGCTCCCACCAGAGCAACTACGCTT +AATTTTACTGAGGTGAAAGTTTTTTTTTTTTTTCTGGATAAAGCTTTGGA +AAAGTTCTCAACTGTTGCTTCTTTAAAGATGCTGGGGCATATTCTGCCCT +ATTTTCCAGTTTTTTACATCTCCCATAAATATTTTCACAAGCTGTAACAT +TTTAGACAGGATTAAATTGAACTAGATAACTGACCAAAGGCTGCTAAATT +ATTTTTATGTGCCTTGTAGCACAAATACTGTCTCACATATATTTTAAGTA +TCTTAATATTCCCTCTGATGTTTAATTTAACAAAGCTGTCCTTCCCTCCA +TCTCTCTCCTCATAGTTTTTCATTACAATTAGCTCTCATTAGATAGAATT +GTATTTGTTGTCTTTGTGCCAGTCACTCCAGTCTATTTTGCCAGCACACA +ACTAAATAATTGTTTTGCCTTGTCAGTGTCTTGTTTTACAGTTTTAATGA +TGAGCCCAAAACATGTCAAATATGAGGAACTATAACTTATCAAGAAAGTG +GGGTAGTTGAGATAAAACTGTTTCCGAGGTGGAGGTTGGCTGAGCTCCAT +TTGGCCACAAAATGTAGCTGAAAGGGCAGAGAAACCCACTTTAATGGAGT +ACAGGTTGCATATGAGCTGGTAGGAAAGATATAGAATCATTATCAGCTGA +TAATCTAACAGTAGCAGTCAGTGTAGATGCTGTGCTAACGCAAAGTTGTG +AAACTACTGTCTGTAAGCAACTCATCCAATTGTTATTGCTGCCAAGCTTA +AGTATTTTAACAGCTTTTAGGTGTTGTTAGCACAGTACTCGTTTGGATCC +GGCCATGACAAGAAATCTTTATCGGCCACTAATTTAATTAATCATCTTTT +TTCAAGCAAAAATCACAAACTTTCTTTGGTTCCACTTTTTCTCATTGTAG +ATTAAATATCTTTTGGGTTTTGGCACAGGCTGGACAAAAAAACCTCTGAG +ACGCTGTGATAAGAATTTATTTTCACATTTTTTTTACTTTTCAGGGACTA +CACAATTATTTGGTGATGAAAATAATATTTTGTTGCAGCCCAAATGTTAA +CTTGCCACTCAAGCTGTCAATTCAAGAAGGCAAAAGCAACAAATACTGCT +TTGCCGAGCTGAAATGAGAGTAGAAACCATGCCCGGGCCAGCTCAGCCTG +GTCAGGTTTTTGAGTCCATCTATTGTTAACATTCAGGTTGCAGCACAAGG +GAAGTTCCTAAATTCTTCTGGCATGTTAATGTTTTCCAAACTGATGTTAC +CAAGTCCTCGTTATGATGAGAAAAAAATATGCTGAGAGTGAAATTGATCA +AAGTGGAAACATTAAGCACTGCCACAGTCCCCTCCACCCATCTTTCTCCC +TCTCTCTCCACCGCAACGTGGAAACTGCTCNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +CTCCCTCCCATTCTGTGCTCCGGTATANNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNCAGAGAGGGGTTCAGTCAGACAGATGTAACACAGCAG +TAGAAGCCTGAGCTGAGCTGGCAGGCTGCGGAGGCCAGACCAGAGCCAGC +AGCTCTGACTGGAGAGAACAGCGAAGAGGTGACGGCAGCAGCGGCAGCAC +AGGGGATAAAACAGTAGTTGTAGTAGCAGTTTCAGTAGTTGTACTTCAGT +TACAGAGCTGACTTTACCTCAGGATATGGGTGTGTTGATCTGGGCGCTCA +TCACCCTGTGAATTTAACATGGACCCTGACACCAGCACCCATCCAGAGAC +ACAACATGGTGAGTGAGATTTGAAGGAGGAAAAGATTAGAAACAATGAGA +GTGATACTGTGGGAAAAGTTGAGGAGCGTGTTAGTGAACAAGGGAGTCAG +GTCACATGGTTTTCCCGTTAGGGTTGCTATTATGACTAGGCTCTCCATTT +GGCTCTAAAGCTGTTGACTAGGGCCTCTGTGGTCAAATGAATAGGACTTC +AGTCTGTTCTGTTGAGTAGGGGGTGAAGGGGTGAGGGGTGTTACATGGCA +ATGTGATGAAATCAACTGCCTGCTTAAGACATTTTGCTCTAATGACCCTC +TTGTCATTACTTTAACAGGGTTGTAAAGTTTTTTTTGCTTTTTTGTAGCT +AAGAAAGTTGAGAATTGTTTTGTCTGAACTCTCTCTGGGATTTGTCTTGT +CGGTTTTTGGCTGGTTTTTGGTGTGAGCTTCACAGAGCAGGAAGCTCTCC +TCCTGCTCTTTGAATGGAATAATTAACTGTGAGGGCCGTGGGTGTACCAT +TTCTGCTCAAAAGCAGCAAGATAATTTGATGGTTATGTGAATCTGTATAT +TTGTATGCTGTGTAGTGGTGCTGCATGTGGGTGTTTGTGTTAGAGACACA +GAGGGGCACCAAAGAATGAAAGTGGGAGACAGAGGGAACGAGAAGGGGAG +AGACCGAGAGAGAAGGACTTATGTACACAAATAAATCCAGGGGGATCTAG +ACTGCACTGTAGGCCAGTGCGAATGCTCACTCTTTCTCTTCCCCCTCATT +TTCCGCTGCCTCTTTTTTTTCCTCCACTGCTCCAAATGTTGGAGCCCAAA +CTAGATAGTTAAAAGGCAGAAAAAAATGGTGTGTTATTAACTGGGCCAGA +AAAGACGATGTTTTGTCTTCATGGCCGATGGGAAGGACTCTGCTGTGCTG +CTGATGAAGAATGTGGTTAACAGAATGAGTCAACAGAGAACATATTTCCA +AGAGACTGTAGTTTCTCTTCGCCAGCGTCTAAGCCACATTGCTTTATGCA +CTGGGCTCTCTGCCATGACGGCGAAGGAGAGACAAAGAGAGGGGAAAGAG +AATCGCTAAAGATAAAACTCTGTTTTTATCCATCTCCTGAGACACAAAAC +TTCTGTTAGCAATCTAACCAAATAAGCGAGAACATTAAGCTTCTTCTCAC +CTTCCCAAAATAAAATGTCAACTTCATGCAGTAATACTCACTCTCTTCTC +TCAACCAGTCAGCCAGCCTCTTTCAGTGCATACAGCTTGAGGAGATCCCT +TCTAAAGGTCCAATATAAATAGAAAAGTGGGAGTAGAAAGGGCAATAATC +TGATATCATCTGATTACATTCACACCTCAGGCTTGCACGCTACAGGAAGA +GTTCACGCTTCCCAAGGCTTGCAGGCATCACTTTTCACTCATTCTCAGAT +AGACACACAAACACATGCACAGAAATATCATTGCTGTTGTTTGCAACAAA +TCCTGGAGTAGACTACTTTGCATTGAATTTCTATATGCATGTGTTTTCAT +ATATTACACATTGCTTTTTGTACTTTGCATATAAAGTAGATGCTGATCTG +CTATCTGCATATATAGTAGCTGCAGATAGCACTGTAACTACATCTACATA +TTTCTTGTTTGTATCTACATCAAGCAGATAGTTGCTGATGCTGGACAACC +TCTTCCGATATTCATTATTTTGGAAAAAAAAATATCAATGGCATTCCTAC +CTTACAACTTAAATTAAAAGTGGTCACTTGAGTAACTGCAGAACATGTGT +TCACCCAATAGTTTTTTTTAGAGAGTGTCACTCAAAGTATTCCTCCTTAC +AAGCACCCATGCCTAAATCA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.poly Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,2 @@ +18 0.0 0.0 0.0 scaffold_1 613 632 (13588) (GT)n Simple_repeat 1 20 (0) +67 2.9 1.4 0.0 scaffold_1 11981 12050 (2170) (CT)n Simple_repeat 1 71 (0)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fasta.stats Wed May 02 20:18:11 2018 -0400 @@ -0,0 +1,51 @@ +================================================== +file name: dataset_12.dat +sequences: 1 +total length: 14220 bp (14220 bp excl N/X-runs) +GC level: 39.94 % +bases masked: 378 bp ( 2.66 %) +================================================== + number of length percentage + elements* occupied of sequence +-------------------------------------------------- +SINEs: 0 0 bp 0.00 % + ALUs 0 0 bp 0.00 % + MIRs 0 0 bp 0.00 % + +LINEs: 0 0 bp 0.00 % + LINE1 0 0 bp 0.00 % + LINE2 0 0 bp 0.00 % + L3/CR1 0 0 bp 0.00 % + +LTR elements: 0 0 bp 0.00 % + ERVL 0 0 bp 0.00 % + ERVL-MaLRs 0 0 bp 0.00 % + ERV_classI 0 0 bp 0.00 % + ERV_classII 0 0 bp 0.00 % + +DNA elements: 0 0 bp 0.00 % + hAT-Charlie 0 0 bp 0.00 % + TcMar-Tigger 0 0 bp 0.00 % + +Unclassified: 0 0 bp 0.00 % + +Total interspersed repeats: 0 bp 0.00 % + + +Small RNA: 0 0 bp 0.00 % + +Satellites: 0 0 bp 0.00 % +Simple repeats: 8 378 bp 2.66 % +Low complexity: 0 0 bp 0.00 % +================================================== + +* most repeats fragmented by insertions or deletions + have been counted as one element + + +The query species was assumed to be homo +RepeatMasker Combined Database: Dfam_Consensus-20170127 + +run with rmblastn version 2.2.27+ +The query was compared to unclassified sequences in ".../dataset_2.dat" +