| Next changeset 1:c0cedc12fcc5 (2020-01-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107 |
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added:
macros.xml mummerplot.xml test-data/1coords.txt test-data/1delta.txt test-data/delta-filter.txt test-data/delta.txt test-data/fplot.txt test-data/gnuplot.txt test-data/hplot.txt test-data/human_aqp3.fasta test-data/mcoords.txt test-data/mdelta.txt test-data/mouse_aqp3.fasta test-data/mummer.txt test-data/nucmer.txt test-data/plot.png test-data/qdiff.txt test-data/rdiff.txt test-data/report.txt test-data/rplot.txt test-data/show-coords.txt test-data/snps.txt |
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| diff -r 000000000000 -r e8c60daa41e0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,69 @@ +<macros> + <xml name="citation"> + <citations> + <citation type="bibtex"> + @misc{githubmummer, + author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg}, + year = {2012}, + title = {mummer4}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/mummer4/mummer}, + }</citation> + </citations> + </xml> + <token name="@MUMMER_VERSION@">4.0.0beta2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement> + <yield /> + </requirements> + </xml> + <xml name="mumplot_input" > + <yield /> + <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length" + help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" /> + <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." > + <option value="">Color</option> + <option value="-color">No color (-color)</option> + </param> + <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." > + <option value="">Dotplot</option> + <option value="-c">Coverage Plot (-c)</option> + </param> + <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter" + help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" /> + <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" /> + <conditional name="labels" > + <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." > + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + <when value="yes" > + <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" /> + <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" /> + </when> + <when value="no" /> + </conditional> + <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" > + <option value="small">Small</option> + <option value="medium">Medium</option> + <option value="large">Large</option> + </param> + <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" /> + <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" /> + <conditional name="range" > + <param name="custom" type="select" label="Choose custom X and Y axis ranges?" > + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + <when value="yes" > + <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" /> + <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" /> + <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" /> + <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" /> + </when> + <when value="no" /> + </conditional> + </xml> +</macros> |
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| diff -r 000000000000 -r e8c60daa41e0 mummerplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mummerplot.xml Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,139 @@ +<tool id="mummer_mummerplot" name="Mummerplot" version="@MUMMER_VERSION@"> + <description>Generate 2-D dotplot of aligned sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="5.2.3">gnuplot</requirement> + </expand> + <command detect_errors="exit_code"> + <![CDATA[ + ln -s $reference_sequence reference.fa && + ln -s $query_sequence query.fa && + mummerplot + -b '$breaklen' + $color + $coverage + $filter + $fat + #if str($labels.IDs) == 'yes': + -IdR '$labels.ref_id' + -IdQ '$labels.query_id' + #end if + #if str($sequences.seq_input) == 'yes': + -R '$reference_sequence' + -Q '$query_sequence' + $sequences.layout + #end if + -s '$size' + -terminal png + -title '$title' + $snp + #if $range.custom == 'yes': + -x [$range.min_x:$range.max_x] + -y [$range.min_y:$range.max_y] + #end if + '$delta' + ]]> + </command> + <inputs> + <param name="delta" type="data" format="tabular" label="Match File" /> + <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" /> + <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" /> + <expand macro="mumplot_input" > + <conditional name="sequences" > + <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" > + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + <when value="yes"> + <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" /> + </when> + <when value="no" /> + </conditional> + </expand> + <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" > + <option value="plot">Just the plot</option> + <option value="all">All outputs</option> + </param> + </inputs> + <outputs> + <data name="gnuplot" format="txt" from_work_dir="out.gp" label="${tool.name} on ${on_string}: gnuplot" > + <filter> extra_outs == 'all' </filter> + </data> + <data name="fplot" format="txt" from_work_dir="out.fplot" label="${tool.name} on ${on_string}: fplot" > + <filter> extra_outs == 'all' </filter> + </data> + <data name="rplot" format="txt" from_work_dir="out.rplot" label="${tool.name} on ${on_string}: rplot" > + <filter> extra_outs == 'all' </filter> + </data> + <data name="hplot" format="txt" from_work_dir="out.hplot" label="${tool.name} on ${on_string}: hplot" > + <filter> extra_outs == 'all' </filter> + </data> + <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" /> + </outputs> + <tests> + <test> + <param name="delta" ftype="txt" value="nucmer.txt" /> + <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> + <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" /> + <param name="seq_input" value="no" /> + <param name="extra_outs" value="all" /> + <output name="gnuplot" ftype="txt" compare="diff" value="gnuplot.txt" /> + <output name="fplot" ftype="txt" compare="diff" value="fplot.txt" /> + <output name="rplot" ftype="txt" compare="diff" value="rplot.txt" /> + <output name="hplot" ftype="txt" compare="diff" value="hplot.txt" /> + <output name="output_png" ftype="png" compare="sim_size" value="plot.png" /> + </test> + </tests> + <help><![CDATA[ +Mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer or nucmer. It can also color dotplots with an identity color gradient. + +**Outputs:** + * gnuplot: The gnuplot script + * fplot, rplot, hplot: The forward, reverse, and highlighted match information for plotting with gnuplot. + * plot: The plotted image file + +**Options:**:: + + + -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest + sequence end + + -color Color plot lines with a percent similarity gradient or turn off all plot color (default + color by match dir) If the plot is very sparse, edit the .gp script to plot with + 'linespoints' instead of 'lines' + + -c Generate a reference coverage plot (default for .tiling) + + --filter Only display .delta alignments which represent the "best" hit to any particular spot on + either sequence, i.e. a one-to-one mapping of reference and query subsequences + + --fat Layout sequences using fattest alignment only + + -IdR Plot a particular reference sequence ID on the X-axis + + -IdQ Plot a particular query sequence ID on the Y-axis + + -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small') + + --SNP Highlight SNP locations in each alignment + + -title Specify the gnuplot plot title (default none) + + -x Set the xrange for the plot '[min:max]' + + -y Set the yrange for the plot '[min:max]' + + -R Plot an ordered set of reference sequences from Rfile + + -Q Plot an ordered set of query sequences from Qfile + + --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options + + ]]></help> + <expand macro="citation" /> +</tool> + + + |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/1coords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1coords.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,2 @@ +74 223 43 194 150 152 87.50 6480 5460 2.31 2.78 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5080 5599 4148 4658 520 511 86.18 6480 5460 8.02 9.36 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/1delta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1delta.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,20 @@ +reference.fa query.fa +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0 |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/delta-filter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta-filter.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,20 @@ +/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0 |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/delta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/delta.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,20 @@ +reference.fa query.fa +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0 |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/fplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fplot.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,13 @@ +#-- forward hits sorted by %sim +0 0 0 +0 0 0 + + +5080 4148 86.1804222648752 +5599 4658 86.1804222648752 + + +74 43 87.5 +223 194 87.5 + + |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/gnuplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gnuplot.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,23 @@ +set terminal png tiny size 800,800 +set output "out.png" +set title "Title" +set size 1,1 +set grid +unset key +set border 15 +set tics scale 0 +set xlabel "NG_007476.1:4960-11439" +set ylabel "NC_000070.6:c41098183-41092724" +set format "%.0f" +set mouse format "%.0f" +set mouse mouseformat "[%.0f, %.0f]" +if(GPVAL_VERSION < 5) { set mouse clipboardformat "[%.0f, %.0f]" } +set xrange [1:6480] +set yrange [1:5460] +set style line 1 lt 2 lw 3 pt 6 ps 1 +set style line 2 lt 2 lw 3 pt 6 ps 1 +set style line 3 lt 1 lw 3 pt 6 ps 1 +plot \ + "out.fplot" title "FWD" w lp ls 1, \ + "out.rplot" title "REV" w lp ls 2, \ + "out.hplot" title "HLT" w lp ls 3 \ No newline at end of file |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/hplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hplot.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,13 @@ +#-- highlighted hits sorted by %sim +0 0 0 +0 0 0 + + +5080 4148 86.1804222648752 +5599 4658 86.1804222648752 + + +74 43 87.5 +223 194 87.5 + + |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/human_aqp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_aqp3.fasta Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,95 @@ +>NG_007476.1:4960-11439 Homo sapiens aquaporin 3 (Gill blood group) (AQP3), RefSeqGene on chromosome 9 +AGCGCTCCTATAAAGGGAGCCACCAGCGCTGGAGGCCGCTGCTCGCTGCGCCACCGCCTCCCGCCACCCC +TGCCCGCCCGACAGCGCCGCCGCCTGCCCCGCCATGGGTCGACAGAAGGAGCTGGTGTCCCGCTGCGGGG +AGATGCTCCACATCCGCTACCGGCTGCTCCGACAGGCGCTGGCCGAGTGCCTGGGGACCCTCATCCTGGT +GGTGAGTGGAGGGAGCCGGGGAAGCCCTTCTCTCTCCAGCCCTTGCACTCCCCAAACTCTCACTTCCCCG +AAGGGGCTGTGTTTTCCAAGGTAGCCTGGACCCACCTCCCCAGCTGTGACCCCCACGCTTAACCGCGGAG +GATCAAGCTGACTTCCAAAGTCCTCTTCCCCACGGTTCTAACCCCCTCTCTGACAGCTCCGACTCTTGCC +AGAATGACAGCTGTTACTCCCCAGTGATAGTGCCGATCGTTTACCCTCCCACAAGTGACTCAGCCAACAG +GCTGGGGGCAGCGGTCACGCTTGCAGTCTGGGACAGCCAGCCACTTCCCCTGCCTCCCACACCCCTCCAG +ATTCCCAGAATCCCAGCCCCCAGATGTAGGGGAGGGGGCGGAGGCAAATGAGCCATTATTAGGTTATTTG +GGTCCTGGGTGTCTGGCCTCTAATGAATAATTAAGCCTCAAAAAGTCCAAAGGTTGAAGTGAGTGAGGAC +AGTTTGCACGAGTGGGGGCAGAGGGTGCAGGCCACATGGGCTGCGAACAGCGAAGTGGGAAGGGAGGCAG +ATTCTGACGGTAGAAGGGTGGGAGGAAGCTAGGCCCAGGCACAGAGGACGCGTGTCTAAAGTTGCTCACC +TGGTGCTCAGCGACTCCCAGGCCCTGTCTGTTATCCAGACAGATGCTGTCAGCGTCTGTGCAGAAGACGA +CAAGCATTCTGGTTACTCCCTGGCCTCTTGGTTACTCTGTGGGTTCTCTGAGTGAGCATTTCCCTGCCTG +AGTTACTCCTCAGTCCTAGTTACTCCTTGGTCACACCAGTTTCACCCTGGTTTTGTTCTGAGTGACTCTG +TTTGCACTTCTTAGGTCTGGCAGACCCACCAGTTATGTTCTATTTCCTGTCCCAGTTACTCTGATTTTTC +AGCCGCTCATGTGGTTACACCTGTTTTCCTCTGTGTTCAGTTGCTACATTGCAGTGAGTGGGTTACTCCG +TTCCTGCCCCAGCCCTGGGTAGTACAGACCAGCTGGCCCACTGTGGACTAGGAAGCCTAACTAAGGGCAA +GTAGGGATCCCCAAATGGTTGAGGATCAGGATCTATGGGCAGAGGAGGGCTGAAACCCACTTCTGGCTTC +CAAGAATAGGAAGTGGGGAAGCCACAGGGGGCATTTTATCCACAGCCTCCCATAAGATTAGTCGTCCTAT +CAGCCAGCCCTAGCCCCTCTCTCCTGTGCCAAGAAGGCAATAGGAGGTGGCCTTTATCACTCTCCTGCCT +CGGAGCCCTCACTCCTATCGGAGTCCTGAGTCCAGCCACCTGTTTTAGAGCAGCCAGGCTAGGGGAGGAT +GATGTCTTCTATTTTCCTAGAGGGGCCTCCTCATTCCCTCCCAAGTCTCAGTTCACTCTCTCACAAAGGA +GCCGTTAGTCCTCCCACTGAGCCCCAGGATCATCAGGCTTATCCCAGACCACAAAAGAAGAGTGTTAAAT +TTTAGGGGAAGGGTTGCAGACTCAGATGGATGTGAGGTATTGGATATCAGTGAGAAGCAGAACTTCAAGG +ACTGCATGAACTGGAGGGGCAGGCCTGGGGATCCCTTTGTAGTGGGTGAGTGCCTGCCTGCCTACCTGCG +TGTTGGGAGCCTAGGCCTGCAGTGGCAGAATCAGGGTTGGCTTTGGGGTGAGGAAAGCCCCTTTCTCTGA +GATACCTGGTGTGAGGGCAGGGGGCGGTGCTGGCCGAGAACTCAGGGCAGGGGTTGGGGGAGGAAGAGGA +AGATTAGCCCCAAGGTGGTGGAACTGGCTCTGACAGCTCCTCCCTCCAAGGCGTCCTGGGATGGAGCCAG +GTCTGAGCCTTTGGCAGGCAAGGAGCTGCTGCCAGGGCCTCCCAAGCAGGGCAGGGCGCCTCAGACCCTC +ACGTGCCTGTCTCCCACCACCCCTCCTCACACATACACCTGCAATCTCTGATCTTTGCTCTCACCTGCCT +GCACACCTTTGCCCCATGTCATTGCCGCTGGCTTCTCCGTTATCTCTTGGTCTTTCTGGGATGATAATCA +AAATGCTTAACTATCCAGTACAACAGGCACTGACCCGTCAGAATAAACAAGGTCTGTAGCACAGGTCCTG +GAAACTGCCTGCTCTGTGGGCATAAAACCTTTAGTTATGGGCAGGTGGGAGAGGAGACCAGGGCAAGGCA +TTGGAGCAGCTTTGAGGGACACTCAGGGGGCTCAGGGCAACAATGCTTTACAGCTGCTGCAGAAGTATTT +TCAGGCTTGAACAAGGGGAACAGACATAGTACGTTCTTTTTCTTTTTTAAATAGAGACAAAGTCTCACTA +TGTTGCCCAGGCTGTTCTCAAACTCCTGGGTTCAAGATCCTCCCATCTCAGCCTCCAAAGTGCTGGGATT +ACAGGTGTGAGCCACCACAGCTGGCTCCAGTATGTTCTATATTTGTAGAACACCAGGGCTCTTAGTCTCT +TTTAGTTCCCCCATTTTTGGCAGAAAGTTTAGAACCGATCTCCCCATTTCTACAGCCCTGGGTCCCGGGC +TGGGGATAGTGAGAGGAGCCACACAGATCCCTGTCTGTAGGACCTCCAAATCTGAGTGGGGAATCTGGAC +CCCTGAGAGCAGAGAGGTCATGGGTGGAGAGAGGAGACGCTGGGACAGGGACAGGTAAAGGAAGGGGAGG +TTGTTGAGGGGGACATGGTGAAGGCTGGGGCTCTGGCATCCTGGACTCAGGAGAAGTGGATTCAACCTCA +CTTCTGGTCTCCTCCCTATTTATTTATGCCGCCCATTGCCACCACTACCACCACCACATGAGCTTTTCTT +TTCAACTCTTTTTTTTTTTTTTTTGAGATGGAGTCCCGCTCTGTCGCCCAGGCTGAAGTGCAGTGGCGCA +ATCTTGGCTCACTGCAACATCTGCCTCCCATTTTCAAGTGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG +GGATTACAGGCACCTGCCACCACGCCTGGCTAATTTTTGTACTTTTAGTAGAGATGGGGTTTCACTATGT +TGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTACCAAAGTGCTGGGATT +ACAGTGTGAGCCACTGCACCGGGCCTACATGAGCTTTTCTTTGGGGCAGCTGGGGGATGAGTGAGAGGCT +TCCCACCTTTATGGTCCAGGCCTGAAGGGCTGTGGAGAAACTTGTGCTAAGGTGAAAGCTGTTCCCCTAC +ACCTACGCCTGCTGAAATTCAAGGAAAATCAGTGAAGATGGTTCAGTCATCTTCTAGGATCCCAGTCGCA +GACCCTGCTTCCAGCCCTTTCCATAGGGCCCTCTCATATTAGAGTTGGGACAGTGGGGTGGGAAGGCATG +TGTCCTTTTTCTGGAAAGTGCAATTACAGCAGAAGGGGTTTGGGCTGGGTTCCAGGAAGCGCCTCTAGTC +CTCCCAGTGGTGGCGAGTGGGCATGTTGCTGGCTTCACCCCTTCCTTCTGGAGTGAGAGTTGCTGGTCCT +CACCCTCCCTGCCTGTTCTTCTTCCTGACAGATGTTTGGCTGTGGCTCCGTGGCCCAGGTTGTGCTCAGC +CGGGGCACCCACGGTGGTTTCCTCACCATCAACCTGGCCTTTGGCTTTGCTGTCACTCTGGGCATCCTCA +TCGCTGGCCAGGTCTCTGGTAAGGCCTTAACCCTGCCCCCAGCCCTTGGCCCTCAATAGCATTCCCACTA +GGTGTCCTGGCATTCCTAAGGGCAGGTCACAGCTGTGGCCTCTGCTTTGGCCCCTTGGGAAAGGAGGGTG +GAGAAGAAACTTGACACTTAGAACTTTCGACTCTCACCTTGGAATCAGAGATTATCAGCTGACCTGTTAC +ATAGACCAACCGCCATCCTGTGCAAGAAACCCCTCTCTGCACCCCTTCTCAGGGGACCCTAGCCTGCCGA +CTGTGGCAGGCTGCAGCTAATAGGTCCCTTGTCCCCTCTGCCCAGGGGCCCACCTGAACCCTGCCGTGAC +CTTTGCCATGTGCTTCCTGGCTCGTGAGCCCTGGATCAAGCTGCCCATCTACACCCTGGCACAGACGCTG +GGAGCCTTCTTGGGTGCTGGAATAGTTTTTGGGCTGTATTATGGTAAGCATTCCCCACCCTGTCCTCCTC +CACTACCCCCGTCCCTCTGTTCAGGACCTGCTGGCACCAGGCCTTTTGATGACAGACGGCTAGGACCTGC +CCAGGCCCCGGGCTCATGACTCACTCATTCACGCACAGGGTCAAGGTAGGGGGCACGAAGGGAAAGAAAC +AAGTTGGGCAATAACAGAGTCTCAGGCCCTCCACCCCACCCCACGCCACCCCCTCTGCCTGCTGCAATAC +AGCAGTATTGCTACTTACCCATAACTCATGGGAGGGTGGGGAGGGCACACCTGAGAGGGAAGTCTGGGCT +CAGGCCTCTCCCCCGACTCACTGTGTGTCTAATCTGTCACCAGATGCAATCTGGCACTTCGCCGACAACC +AGCTTTTTGTTTCGGGCCCCAATGGCACAGCCGGCATCTTTGCTACCTACCCCTCTGGACACTTGGATAT +GATCAATGGCTTCTTTGACCAGGTATGGGCTGGGGACGTGTGAGGGGAACGCAGGGAGGGGACCGAGTTG +CCTTGGTAGCTCATGGGCTGGTTGGGGGACAGGACTCCTCGACTGTAGCAGGGTTTCTCCAATCTGTGGG +GTAACCCGCATCAGAACATGGTGGCAAGTACTTACAAAACATGCGGCTCTCCAGCGGGTTCTTGTCACGC +AGACATTCTAGCACCATTGCTTTCAGGAGAAGAGCATGGGCGGGCGCTGACAAGAGTTTAAGAGCTAGAG +GGAAGACGGGGGATGGAAGGAGGGGTCAGAGAAAGGGAGGGAGCTGCAGCTCACCCTGTTCTCCCCACTC +CCCAGTTCATAGGCACAGCCTCCCTTATCGTGTGTGTGCTGGCCATTGTTGACCCCTACAACAACCCCGT +CCCCCGAGGCCTGGAGGCCTTCACCGTGGGCCTGGTGGTCCTGGTCATTGGCACCTCCATGGGCTTCAAC +TCCGGCTATGCCGTCAACCCTGCCCGGGACTTTGGCCCCCGCCTTTTTACAGCCCTTGCGGGCTGGGGCT +CTGCAGTCTTCACGTGAGTACAGCCCCCACCCAGCTCACCCCAGCCTGCCTCTCCTCTGCCCTGCCCCCC +ATGTCCCTGACTATGAGTGTCTGTCCCCCCAGGACCGGCCAGCATTGGTGGTGGGTGCCCATCGTGTCCC +CACTCCTGGGCTCCATTGCGGGTGTCTTCGTGTACCAGCTGATGATCGGCTGCCACCTGGAGCAGCCCCC +ACCCTCCAACGAGGAAGAGAATGTGAAGCTGGCCCATGTGAAGCACAAGGAGCAGATCTGAGTGGGCAGG +GGCCATCTCCCCACTCCGCTGCCCTGGCCTTGAGCATCCACTGACTGTCCAAGGGCCACTCCCAAGAAGC +CCCCTTCACGATCCACCCTTTCAGGCTAAGGAGCTCCCTATCTACCCTCACCCCACGAGACAGCCCCTTC +AGGATTTCCACTGGACCTTGCCCAAATAGCACCTTAGGCCACTGCCCCTAAGCTGGGGTGGAACCGGAAT +TTGGGTCAATACATCCTTTTGTCTCCCAAGGGAAGAGAATGGGCAGCAGGTATGTGTGTGTGTGCATGTG +TGTGCATGTGTGTGCATGTGTGTGCAGGGGTGTGTGTGTGTGGGGGGGGTTCCCAGATATTCAGGGCAAG +GGACCAGTCGGAAGGGATTCTGGCTATTGGGGGAGCCCAGAGACAGGGGAAGGCAGCCTGTCCATCTGTG +CATAAGGAGAGGAAAGTTCCAGGGTGTGTATGTTTCAGGGGCTTCACATGGAGGAGCTGCAGATAGATAT +GTGTTTCTGTGTATGTGTATGTCTGCCTTTTTTTCTAAGTGGGGGCTTCTACAGGCTTTTGGGAAGTAGG +GTGGATGTGGGTAGGGCTGGGAGGAGGGGGCCACAGCTTAGGTTTGGAGCTCTGGATGTACATACATAAG +TAGGAGCAGTGGGACGTGTTTCTGTCATAATGCAGGCATGAAGGGTGGAGTGAAGTCAGGTCATAAGTTT +CATGTTTGCTTTTGTTTTGTTTTGTTTTTAATGTATGTAGCAGATGTTACAGTCTTAGGGATCCGGGATG +GGAGACCCCACTTTAGAAAGGGTCGTCACTCCTTTAATCCTCTACTCAACAATGTACTCTTTTACTTTTA +TATTAAAAAAAATAAAATAAATATGTGCCTAAAACCTCCA + |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/mcoords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcoords.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,2 @@ +74 223 43 194 150 152 87.50 6480 5460 2.31 2.78 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5080 5599 4148 4658 520 511 86.18 6480 5460 8.02 9.36 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 |
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| diff -r 000000000000 -r e8c60daa41e0 test-data/mdelta.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mdelta.txt Wed Dec 05 02:36:43 2018 -0500 |
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| @@ -0,0 +1,20 @@ +reference.fa query.fa +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0 |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/mouse_aqp3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mouse_aqp3.fasta Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,80 @@ +>NC_000070.6:c41098183-41092724 Mus musculus strain C57BL/6J chromosome 4, GRCm38.p4 C57BL/6J +ACCGCTCTCGGTGCCTTGCGCTAGCTACTTTGCACTCGTACGCCGCCGGACCTCGCCGCTGCCTGCCTCG +CGCCATGGGTCGACAGAAGGAGTTGATGAATCGTTGTGGGGAGATGCTTCACATCCGCTACCGGCTGCTT +CGCCAGGCGCTGGCGGAGTGCCTGGGGACCCTCATCCTTGTGGTGAGTGCAGGGTAGTGAGCAGTCCTAT +CTATTTCAGGCCCCGTGGTCCCCAACTCCTTATTCACTCCAGGGACAGTTTTCCAGGCAGACACGACCAG +TTCCCCAGCTCTGCTCCCGAGGCTTAACCCTCAGGGTCAAGCTGACCTCCAAAGCCTTCAACAGTCTTGA +CAGTTCTAACTCAACTTGTGACAGTGCTACTTACCCAAGAACAGCTCTGCTATTTTGCCTTTCCCCCTGG +AGACAGAGACCAAGGCTGCGGAGGGTCACCCCTTAGTGTGGGACCTCCCACACGTTTCCTGGCTTCCCAA +CTTTCCCAGGGCTCCAACCTCAGGACACAGCAGAGAAAGGCAAATGGACACCCCTATTAAGTTATTTGGG +TCTTGGGTGTCTGGCCCCTAATGAATAATTAAGCCTCAGAAAGTCCAAAAGTTGCAGTGAAGTGAGGGCG +GATTACGGCAGGTAGGGGCAGAGGGCGCAGATTTCTTGGGCTGTAAGCAGCAAAATCGGAAGAACGGAGA +TTGTGGAAGGAAACAGAGCCTAACAGAACAGTGGGCGCGTCTAAATGTGTTGTGCACACGCTGTAGGAGT +CCTTCGGATCCTGCGACCCAGATGCTTCCAGCGTCTTTGCTGGCCTTTTGATCCCCCCTCTGCCTCTCCT +CTCAATGGCCCCTGGTGAACCCCCAGATCTCAGGCTTCTGCAGTTTTGCCCCGAGTTCTGGTTAACTTGG +CGCACTTCTTGATCAGACAGACACTATGGCTTTCATTTCCTGTCCCAGTTACTCTGATTTTCAGCCACTG +ACTTGTTTTTCTGAGTCTCTTCTCAATTCCGGTGTCCCTTTTTGCAGTGGGGTGGGTTACTTGAGTTCCA +GCAACAGCCTCAGTCTTGGGTAGTGCAGATCAGTCAACTGGCGAGGGAACATGGTGGGGCAGGCTACACA +TGGAGAAAGGGGGCCCAAATGTGCCTCTGACTTCATAGACTAGTGGCCTATCAGTTGTCCCCACTCCCTC +CTGCCTCGGTGGTTCCCTGTTTCCTATCTTGATTTGTGAGTCTGGCCACCTGTTCGGTTGAGAGCAGCAA +GAGGACAAGGGAGGGTGTCTTACAGTTTCAAAATGGGGCCCCCTCATCCCGTCCCAGTTCTCAGAGCCTA +TTCCTCTGTAAAAGAACAGTCAGTCCCCCCACTGAGTCCCAGGATCACTTGGCTTAGCCTAGACCACAAA +AAGAGGGTTCTGGATTTGTGGTGAAGGCTTTCAGGCTCAGGTAGATGCGAGAGATCAGGTGTCAGGGAAA +AGCTTGAGGAGAGGGGAGAGCAAGCCTAGTGGATCCCCTGATGACTGAGGGCCTGCTCGTGTCCCTGTGT +TGGGGACTTGAGACCTCTGTGTCAGGATCCAGGTTGACTTTGGGGTGAGGAAAGCCCCCTTTTTTCTGAG +GTATATAGTTGGGTGGTATATGGGGTGAGGGGCTGGCTAAGAACCTGCAGCTGGGTGAAAGTGCAGGATA +AGGAAGAGGAAAGATTAGCCCCAAGGTGGTGGAACTGGCTTTGACAGCCTCCTCCTCCGGAGGCCCCTTG +GCACGGAGCCAAGTCTGGGCCTCAGGCAAAGAGCTCAGGCCAGGGTCTGACTGGACATAGTGCCCGGGAC +GGCCACATGCCTCCACCCCTTGCTCTTACAATCTCTGACCTTTGCTCTCACCTGCCGGAACACCTTTGAC +CTACATCGCTGCCACTGGCCTCCCTGCCTCATCTTCCCGAGTGATAATAATCAGTGCTTAACAACCCAGC +ACCCAGGCTTGGACCCATTAGAGTTAATGAGGCACAGCTTGCTGCTGGCCAGCGTAGCACTTACTTGTTT +GTGAGACCCCGGGTCTCCTTCGCCCTAGTCCTTGGCTGTTCTAGAACTCACTCTGTAGACCAGGCTGGTC +TCTCTGCCTCGAGAGTGCAGGGATCAGGCCTGGCTCAGCATAGCACTGGTTCAGTTATGGAGAACTGAGA +AAGGAGTCCCAGGGCCGGGCTGGAGGAGCGTGGAGGGCCACTAGAGACTTGAGGCAACAGCACTTAACAG +TTGGTGGAGAGTATTCACACTTGAACATATGTCTGTCTGTCCCTGCCGATCCTGAGGCACCTTTTAGTCC +CTCTATCCCAGGGTTAGAACAGATCTCACGGGACCTAGAGGGAAGAGCTGCTTAAAACCTTCTATTTAGG +ACTCTACAGATCAGAGTGGAAATCCTGGAGACAGCGGGCTGGAGAAGGAAGAGGAAAAGTGGCCTGGGGA +GGGACCGGCAGGGACAGATGTGAACAGGGAGGCTATAATGAGGAACACGTGAGGACCAGATACGCAGACA +TTTCTCCATGCAGGAGTAGATTCAACTTCTCTTTTGATCTCTCTCCGTGGCCCCCACCTCCTCCACTATG +ACCTGGGCTTTGGAAGAGTCCAGGACGATGGGGTATTTCCTACCTCTGTGTGCCAAATCTGGAGGACGGG +CAGAAACTGCTGTAGTGATAGCTCCCTTCTGTGCCCTTCCCGGATTCAAGAAAAACCAGTGGATGTCATT +TAACCACCTGGGTCCCCAGTCATGTACCCATTACTGATTCCCCCCCATCCCCCCATGAGGCTCTGCACGT +CTCCTCTTTCTGGGACTTAAGGAGGGATTTGGGTTATATCCCAGGAAGCACCTTCAGTGGTGTCAGGCAT +GTCTGATCTCAGTGGGACTTCACTTGCTTTGTTTTCCGACAGATGTTTGGCTGTGGCTCCGTGGCTCAGG +TGGTGCTCAGCCGTGGCACCCATGGTGGCTTCCTCACCATCAACTTGGCTTTTGGCTTCGCTGTCACCCT +TGGCATCTTGGTGGCTGGCCAGGTGTCTGGTAAGGCCTCAACCCCAGCTTCAGTTTTCAGCCCTCACCAG +CATTTCCAACAAGTATCTGCCTAGAGAGCAGAGGGGGAGGAACAACTCCAACCAAGGACGCACACTAACA +GCACCTCAGCTTTGGGCCCTTTGGAGGCAAGGGTGGAAGAGACTTCACAGAACCTTTGACTTTCACCTTG +GAATCAAAGATCAGTCTGTGACATAGTCCAACTGCCATCCAGGCTAAGAAAACCTACCTACACCCCAGAA +AGGAAGAGCCCAAGGTGGCAGGCTGTAACTAATGGATGCTATCTCCTCTTCGCAGGTGCCCACTTGAACC +CCGCTGTGACCTTCGCAATGTGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTATGCACTGGC +ACAGACACTGGGGGCCTTCTTGGGCGCTGGGATTGTTTTTGGGCTGTACTACGGTAAGCATTCCCCATCC +CGCCCTCCCTTCTCCACACTTTCCCTCTTTAAGTACTTGTTGGCACCAAGCCCACTGATGACAACCGGGG +CCTGCCCAGGCCCAGGGCCCGTGACTCATTCACGAACACTCAGGCCCAGGTTGGGGGCCTAGGGGAAAGA +AACGAGTTGGGCAACAACAGAATCTCAGGTCCTCCACCCCGCCCCACCCCCTGAGCCTCTACAGTCATAT +GCTTACCCATGACCCCTGGCGGGGTGGGGAGGGCAGCTCTGAGAGGAGAGGCTCTGCCCTCACTCACAAT +GGCTCTAATCTGTCACCAGATGCAATCTGGGCCTTTGCCAACAATGAGCTTTTCGTCTCTGGCCCCAACG +GCACAGCTGGAATCTTTGCCACCTATCCCTCTGGACACTTGGACATGGTCAATGGCTTCTTTGATCAGGT +ATGGACTAGGGACATGTGAAGTAAAGGTAGAGGGAGGAACAGTCTTGTTTTGGACAACGCTCCTTGATTG +TAGCAGGATTTCTTCTCAGTTCGTGAGAACCCCAACCTCAGAACATGGTGGTGGCGTTGTCTTTTATAAA +GCATGGCGCTTCCCAGTGAGTTCTTGGTTTTGCGATCATCCTAGAGTCAGGATGGTCTCTAGCGTGGAGG +ACTGGAGCGTGGGAGAAGGAGCTGGCCCTCACCGTGCTCTCTCCCCTCTCCCAGTTCATAGGCACAGCCG +CCCTTATTGTGTGTGTACTGGCCATCGTTGACCCTTATAACAACCCTGTGCCCCGTGGCCTGGAGGCTTT +CACTGTGGGCCTGGTGGTCCTGGTCATTGGAACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCT +GCCCGTGACTTTGGACCTCGCCTCTTCACCGCCCTGGCTGGCTGGGGCTCAGAAGTCTTCACGTGAGTAC +AGTCCCCACTCCCCAGCTTGCCTCCCCTCTTCCTGCCGACCTGTCTCTGATTTCCGGTGTTCTCCCTCCA +GGACTGGCCGGCACTGGTGGTGGGTACCCATTGTCTCCCCACTCCTGGGTTCCATCGCTGGTGTCTTCGT +GTACCAGCTCATGATTGGTTGCCACCTGGAGCAGCCCCCACCCTCCACCGAGGAAGAGAATGTGAAGCTG +GCCCACATGAAACACAAGGAGCAGATCTGAGTGGGCAGCAGCCCCCCTCCCCCACTGTGCACTCTCCTGA +GTGTCCACTGACTGTGTGGGGACCAGTCCCCGAAAGCCCTTTGTGATGCCTCTCTCGGGCTAAACCGCTC +CCTGTGTCCACCCCTGCTGGATGGGCCCTCCAGAATTTCTATGAACTCTGCCCATTAGGGCATTAGGTTC +CCACCCACCTTTAAGCCAAGGTAGGATAGCAAATAAGATGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA +GAGAGAGAGAGAGAATGAATGTGTACATGTGTGCTGTTTTCTAAGCTGAATGATGCAAAGGCAAGGGACC +AAGTTTTCAAAACAAACTGTAGCAGCTCAGGGGAAGGGAGCCCAGGGGAAGGGAGAAAGTGAGTCAGGAA +TGTGCCAGAGTGTGCATGCTTCAGGGACTCCTCCATGTGGAGGTGGACCCAGAAGTGAGTTTCTAAGTAT +GCGTGTGCCTACTGTTTTTTTTTTTTTTTTTGAAATGGACTTCTAGGCTTGGGGAGGGGGAAGGGATAAG +AAGGGTGTAGCTCACATCTGGAGCTATGACCCTTGACTGGGGGCTGTGTAATATGTTTCTGTTATAAGAT +AGACATTGGGAGGGGCTGAAGTCCAGGTCGTAAGTTTCATAATTTGTTTTTTAAATATATAAATATATAC +ATACATATATGTTACAGCCCTAGGAATAGGGGTGGGAAACTCCACTTTTTAAAAGGGGTTTCCTTTCTTT +AATCCTCCAATCAACAATGTACTGTTGCCTTTTATATATAAAAAAGAATAAAACGTATACATGCTACAGG + |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/mummer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mummer.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,19 @@ +> NC_000070.6:c41098183-41092724 + 100 71 22 + 149 120 20 + 185 156 23 + 650 578 21 + 1092 945 27 + 1861 1578 21 + 1960 1691 30 + 3737 2908 28 + 4226 3396 26 + 4648 3784 27 + 5111 4180 20 + 5206 4275 26 + 5254 4323 23 + 5481 4540 20 + 5511 4570 28 + 5540 4599 27 + 5574 4633 26 +> NC_000070.6:c41098183-41092724 Reverse |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/nucmer.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nucmer.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,20 @@ +reference.fa query.fa +NUCMER +>NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 6480 5460 +74 223 43 194 19 19 0 +-26 +-2 +0 +5080 5599 4148 4658 72 72 0 +-32 +240 +1 +1 +1 +1 +3 +1 +21 +12 +20 +0 |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/plot.png |
| b |
| Binary file test-data/plot.png has changed |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/qdiff.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/qdiff.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,3 @@ +NC_000070.6:c41098183-41092724 BRK 1 42 42 +NC_000070.6:c41098183-41092724 GAP 195 4147 3953 4856 -903 +NC_000070.6:c41098183-41092724 BRK 4659 5460 802 |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/rdiff.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdiff.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,3 @@ +NG_007476.1:4960-11439 BRK 1 73 73 +NG_007476.1:4960-11439 GAP 224 5079 4856 3953 903 +NG_007476.1:4960-11439 BRK 5600 6480 881 |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report.txt Wed Dec 05 02:36:43 2018 -0500 |
| [ |
| @@ -0,0 +1,87 @@ + + + + + + + + + + + + [REF] [QRY] +.A 0(0.00%) 0(0.00%) +.A 0(0.00%) 3(23.08%) +.C 0(0.00%) 0(0.00%) +.C 0(0.00%) 5(38.46%) +.G 0(0.00%) 0(0.00%) +.G 1(7.69%) 2(15.38%) +.T 0(0.00%) 0(0.00%) +.T 2(15.38%) 0(0.00%) +/Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/human_aqp3.fasta /Users/nickeener/GalaxyProjects/tools-iuc/tools/mummer4/test-data/mouse_aqp3.fasta +1-to-1 2 2 +A. 0(0.00%) 0(0.00%) +A. 3(23.08%) 0(0.00%) +AC 6(7.69%) 5(6.41%) +AC 1(100.00%) 0(0.00%) +AG 0(0.00%) 0(0.00%) +AG 2(2.56%) 5(6.41%) +AT 0(0.00%) 0(0.00%) +AT 2(2.56%) 2(2.56%) +AlignedBases 670(10.34%) 663(12.14%) +AlignedSeqs 1(100.00%) 1(100.00%) +AvgIdentity 86.48 86.48 +AvgIdentity 86.48 86.48 +AvgLength 335.00 331.50 +AvgLength 335.00 331.50 +Breakpoints 4 4 +C. 0(0.00%) 0(0.00%) +C. 5(38.46%) 0(0.00%) +CA 0(0.00%) 1(100.00%) +CA 5(6.41%) 6(7.69%) +CG 0(0.00%) 0(0.00%) +CG 6(7.69%) 6(7.69%) +CT 0(0.00%) 0(0.00%) +CT 28(35.90%) 9(11.54%) +G. 0(0.00%) 0(0.00%) +G. 2(15.38%) 1(7.69%) +GA 0(0.00%) 0(0.00%) +GA 5(6.41%) 2(2.56%) +GC 0(0.00%) 0(0.00%) +GC 6(7.69%) 6(7.69%) +GT 0(0.00%) 0(0.00%) +GT 5(6.41%) 2(2.56%) +InsertionAvg 1936.67 1599.00 +InsertionSum 5810 4797 +Insertions 3 3 +Inversions 0 0 +M-to-M 2 2 +NUCMER +Relocations 0 0 +T. 0(0.00%) 0(0.00%) +T. 0(0.00%) 2(15.38%) +TA 0(0.00%) 0(0.00%) +TA 2(2.56%) 2(2.56%) +TC 0(0.00%) 0(0.00%) +TC 9(11.54%) 28(35.90%) +TG 0(0.00%) 0(0.00%) +TG 2(2.56%) 5(6.41%) +TandemIns 0 0 +TandemInsAvg 0.00 0.00 +TandemInsSum 0 0 +TotalBases 6480 5460 +TotalGIndels 0 0 +TotalGSNPs 1 1 +TotalIndels 13 13 +TotalLength 670 663 +TotalLength 670 663 +TotalSNPs 78 78 +TotalSeqs 1 1 +Translocations 0 0 +UnalignedBases 5810(89.66%) 4797(87.86%) +UnalignedSeqs 0(0.00%) 0(0.00%) +[Alignments] +[Bases] +[Feature Estimates] +[SNPs] +[Sequences] |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/rplot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rplot.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,5 @@ +#-- reverse hits sorted by %sim +0 0 0 +0 0 0 + + |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/show-coords.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/show-coords.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +74 223 43 194 150 152 87.50 6480 5460 2.31 2.78 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 +5080 5599 4148 4658 520 511 86.18 6480 5460 8.02 9.36 NG_007476.1:4960-11439 NC_000070.6:c41098183-41092724 |
| b |
| diff -r 000000000000 -r e8c60daa41e0 test-data/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snps.txt Wed Dec 05 02:36:43 2018 -0500 |
| b |
| b'@@ -0,0 +1,91 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