| Previous changeset 1:707216744193 (2019-04-12) |
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NFR.xml NFR_stats.xml nucDyn.xml nucDyn_stats.xml nucleR.xml nucleR_stats.xml periodicity.xml periodicity_stats.xml readBAM.xml stiffness.xml stiffness_stats.xml test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.bw test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.gff test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png test-data/NFR__cellcycleM_chrII.gff test-data/NFR__stats__cellcycleM_chrII.gw.csv test-data/NR__cellcycleM_chrII.gff test-data/NR__stats__cellcycleM_chrII.genes.csv test-data/NR__stats__cellcycleM_chrII.gw.csv test-data/P__cellcycleM_chrII.bw test-data/P__cellcycleM_chrII.gff test-data/P__stats__cellcycleM_chrII.genes.csv test-data/P__stats__cellcycleM_chrII.gw.csv test-data/STF__cellcycleM_chrII.gff test-data/STF__stats__cellcycleM_chrII.genes.csv test-data/STF__stats__cellcycleM_chrII.gw.csv test-data/STF__stats__cellcycleM_chrII.gw2.png test-data/TSS__cellcycleM_chrII.gff test-data/TSS__stats__cellcycleM_chrII.genes.csv test-data/TSS__stats__cellcycleM_chrII.gw.png test-data/TSS__stats__cellcycleM_chrII.gw2.png test-data/cellcycleM_chrII.bam test-data/readBAM__cellcycleM_chrII.RData test-data/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes test-data/refGenomes/R64-1-1/genes.gff txstart.xml txstart_stats.xml |
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| diff -r 707216744193 -r e88c806ddf3e NFR.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NFR.xml Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,51 @@ +<tool id="NFR" name="Nucleosome Free Regions" version="0.1"> +<description>: determine Nucleosome Free Regions from nucleR nucleosome calls</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics NFR --input $gff_file --output $output_gff_file --minwidth $minwidth --threshold $threshold +]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/> + <param name="minwidth" size="4" type="integer" value="110" label="Minimum Width" help="Minimum width for a linker fragment to be considered a nucleosome-free region." /> + <param name="threshold" size="4" type="integer" value="140" label="Maximum Width" help="Maximum width for a linker fragment to be considered a nucleosome-free region." /> +</inputs> + <outputs> + <data format="gff" name="output_gff_file" label="NFR__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="NR__cellcycleM_chrII.gff"/> + <param name="minwidth" value="110" /> + <param name="threshold" value="400" /> + <output name="output_gff_file" file="NFR__cellcycleM_chrII.gff" /> + </test> + </tests> + <help> + .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e NFR_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NFR_stats.xml Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,72 @@ +<tool id="NFR_stats" name="Nucleosome Free Regions Statistics" version="0.1"> + <description>: gather gene and genome-wide statistics on Nucleosome Free Regions</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> + <![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics NFR_stats --input $gff_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if + --out_gw $output_gw_csv_file + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome Free Regions (GFF)" help="Nucleosome Free Regions as annotated by NFR tool" /> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> +</inputs> + <outputs> + <data format="csv" name="output_gw_csv_file" label="NFR__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="NFR__cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <output name="output_gw_csv_file" file="NFR__stats__cellcycleM_chrII.gw.csv" /> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e nucDyn.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucDyn.xml Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,117 @@ +<tool id="nucDyn" name="Nucleosome Dynamics" version="0.1"> + <description>: detection of local changes in the position of nucleosomes, observed between two reference nucleosome maps </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + ln -f -s $output_bw_file $output_bw_file\.bw; + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics nucDyn --input1 $rdata_file --input2 $rdata_file2 --calls1 $gff_file --calls2 $gff_file2 --outputGff $output_gff_file --outputBigWig $output_bw_file\.bw + #if $assembly.source == "buildin": + --genome ${assembly.ref_chrom_sizes_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_chrom_sizes} + #end if + + #if $maxdiff + --maxDiff $maxdiff + #end if + #if $maxlen + --maxLen $maxlen + #end if + #if $minreads + --shift_min_nreads $minreads + #end if + #if $threshold + --shift_threshold $threshold + #end if + #if $minread + --indel_min_nreads $minread + #end if + #if $indthreshold + --indel_threshold $indthreshold + #end if + + --range $range --equal_size $equal --readSize $readsize ; + rm $output_bw_file\.bw +]]> + </command> + <inputs> + <param name="rdata_file" type="data" format="rdata" label="Condition 1: MNase-seq reference reads (Rdata)" help="Input BAM from MNase-seq in RData format for the initial state to be compared."/> + <param name="gff_file" type="data" format="gff" label="Condition 1: MNase-seq reference nucleosomes (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR for the initial state to be compared"/> + <param name="rdata_file2" type="data" format="rdata" label="Condition 2: MNase-seq final reads (Rdata)" help="Input BAM from MNase-seq in RData format for the final state to be compared. "/> + <param name="gff_file2" type="data" format="gff" label="Condition 2: MNase-seq final nucleosomes (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR for the final state to be compared."/> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_chrom_sizes_buildin" type="select" label="Select reference genome (Chrom sizes)" help="Select chromosome size for your reference genome. If your genome of interest is not listed, contact the Galaxy team"> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="3"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_chrom_sizes" type="data" format="txt" label="Reference genome (Chrom sizes)" help="Upload chromosome size for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> + <param name="range" type="text" value="All" label="Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome."/> + <param name="maxdiff" type="integer" value="70" label="Maximum Diff" optional="True" help="Maximum distance between the dyads of two reads that allows them to still be considered a *shift*. If unspecified but *readSize* is specified, it will be set to the half of readSize. If neither of them is specified, it will be set to 70."/> + <param name="maxlen" type="integer" value="140" label="Maximum Lenght" optional="True" help="Used in the preliminar filtering. Reads longer than this number will be filtered out."/> + <param name="minreads" type="integer" value="3" label="Shift minimum num. reads" optional="True" help="Minimum number of reads in a 'SHIFT +' or a 'SHIFT -' hotspot."/> + <param name="threshold" type="float" value="0.1" label="Shifts threshold" optional="True" help="Minimum score for a 'SHIFT +' or a 'SHIFT -' hotspot."/> + <param name="minread" type="integer" value="3" label="Indels minimum num. reads" optional="True" help="Minimum number of reads in an 'INCLUSION +' or a 'DELETION -' hotspot" /> + <param name="indthreshold" type="float" value="0.05" label="Indels threshold" optional="True" help="Minimum score for an 'INCLUSION' or a 'DELETION' hotspot." /> + <param name="equal" type="boolean" checked="false" label="Use Equal Size" optional="True" help="Set all fragments to the same size."/> + <param name="readsize" type="integer" value="140" label="Read Size" help="Length to which all reads will be set in case `equalSize` is `TRUE`. It is ignored when `equalSize` is set to `FALSE`." /> + </inputs> + <outputs> + <data format="gff" name="output_gff_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.gff"/> + <data format="bigwig" name="output_bw_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.bw"/> + </outputs> + <tests> + <test> + <param name="rdata_file" value="readBAM__cellcycleG2_chrII.RData" /> + <param name="rdata_file2" value="readBAM__cellcycleM_chrII.RData" /> + <param name="gff_file" value="NR__cellcycleG2_chrII.gff" /> + <param name="gff_file2" value="NR__cellcycleM_chrII.gff" /> + <param name="ref_chrom_sizes_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes" /> + <param name="range" value="All" /> + <param name="maxdiff" value="70" /> + <param name="maxlen" value="140" /> + <param name="minreads" value="3" /> + <param name="threshold" value="0.1" /> + <param name="minread" value="3" /> + <param name="indthreshold" value="0.05" /> + <output name="output_gff_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" /> + <output name="output_bw_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.bw" /> + </test> + </tests> + <help> + .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e nucDyn_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucDyn_stats.xml Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,75 @@ +<tool id="nucDyn_stats" name="Nucleosome Dynamics Statistics" version="0.1"> + <description>: statistics on Nucleosome Dynamics analysis</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + ln -f -s $output_gw_png_file $output_gw_png_file\.png; + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics nucDyn_stats --input $gff_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if + --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png; + rm $output_gw_png_file\.png +]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome Architecture (GFF)" help="Annotation of nucleosome changes as produced by Nucleosome Dynamics"/> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> +</inputs> + <outputs> + <data format="csv" name="output_genes_csv_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" /> + <data format="png" name="output_gw_png_file" label="ND__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" /> + </outputs> +<tests> + <test> + <param name="gff_file" value="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <output name="output_genes_csv_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv" /> + <output name="output_gw_png_file" file="ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png" /> + </test> +</tests> + <help> + .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e nucleR.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucleR.xml Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,101 @@ +<tool id="nucleR" name="NucleR" version="0.1"> + <description>: analyze aligned BAM files from MNAse (in RData format)</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> + <![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics nucleR --input $rdata_file --output $output_gff_file --type $seq_type --width $width --minoverlap $minoverlap --dyad_length $dyad_length --hthresh $hthres --wthresh $wthres --pcKeepComp $pcKeepComp --fdrOverAmp $fdrOverAmp --trim $trim --fragmentLen $fragmentLen + #if $threshold.is == "absolute": + --thresholdValue ${threshold.thresholdValue} + #else if $threshold.is == "percentage": + --thresholdPercentage ${threshold.thresholdPercentage} + #end if + #if $chr + --chr $chr + #end if + #if $start + --start $start + #end if + #if $end + --end $end + #end if + #if $comp + --components $comp + #end if +]]> + </command> + <inputs> + <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM."/> + <param name="seq_type" type="select" label="Type of sequence reads"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <param name="width" size="4" type="integer" value="147" label="Width (bp)" help="Size of each nucleosome."/> + <param name="minoverlap" type="integer" value="80" label="Minimum Overlap (bp)" help="Minimum overlap between two nucleosomes for merging them."/> + <param name="dyad_length" type="integer" value="50" label="Dyad length (bp)" help="Lenght of the reads that should be used for nucleosome calling to define the dyad of the nucleosomes keeping the number of bases around the center of the read."/> + <param name="fragmentLen" type="integer" value="170" label="Fragment Length (bp)" help="Maximum fragment length allowed (bp)" optional="True" /> + <param name="chr" type="text" value="" label="Chromosome" optional="True" help="Chromosome to consider for the analysis in the given input file."/> + <param name="start" type="integer" value="" label="Start" optional="True" help="Start genomic position to consider for the analysis in the given input file."/> + <param name="end" type="integer" value="" label="End" optional="True" help="End genomic position to consider for the analysis in the given input file."/> + <param name="comp" type="integer" value="1" label="Components" optional="True" help="Number of negative binomials that will be used to filter duplicated reads."/> + <conditional name="threshold"> + <param name="is" type="select" label="Background threshold" help="Minimum number of reads (Coverage) to call a nucleosome. Can be given as a percentage, or an absolute number of reads."> + <option value="percentage" selected="True">use a percentage</option> + <option value="absolute">use a number of reads</option> + </param> + <when value="absolute"> + <param name="thresholdValue" type="integer" value="10" label="Bakground level (reads)" help="Absolute value to filter out nucleosome calls. It is the minimum number of reads (coverage) in a nucleosome call expressed as reads per million of mapped reads."/> + </when> + <when value="percentage"> + <param name="thresholdPercentage" type="float" value="35" label="Background level (%)" help="Percentile of coverage in the experiment used as threshold to filter out nucleosome calls (i.e., 25% would mean that only peaks with coverage in the 1st quantile would be considered)"/> + </when> + </conditional> + <param name="hthres" type="float" value="0.4" label="Height Threshold" help="Height threshold (between 0 and 1) to classify a nucleosome as fuzzy (class=F) or well-positioned ( class=W) according to the number of reads at the dyad. Nucleosomes below this value will be defined as fuzzy."/> + <param name="wthres" type="float" value="0.6" label="Width Threshold" help="Width threshold (between 0 and 1) to classify a nucleosome as fuzzy (class=F) or well-positioned (class=W) according to the dispersion of the reads around the dyad."/> + <param name="fdrOverAmp" type="float" value="0.05" label="fdrOverAmp" help="Threshold to filter over-amplified reads , as defined in filterDuplReads function of htSetqTools R package."/> + <param name="pcKeepComp" type="float" value="0.02" label="Coverage Smoothing" help="Parameter used in the smoothing when Fourier transformation is applied. Number of components to select with respect to the total size of the sample. Allowed values are numeric (in range 0:1) for manual setting, or auto for automatic detection."/> + <param name="trim" type="integer" value="50" label="Trim" help="Number of basepairs to keep from each read (or to extend in case it is larger than the read width)."/> + </inputs> + <outputs> + <data format="gff" name="output_gff_file" label="NR__${os.path.splitext(($rdata_file.name.split('__'))[1])[0]}.gff" /> +</outputs> + <tests> + <test> + <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" /> + <param name="seq_type" value="paired" /> + <param name="width" value="147" /> + <param name="minoverlap" value="80" /> + <param name="dyad_length" value="50" /> + <param name="thresholdPercentage" value="35" /> + <param name="hthres" value="0.4" /> + <param name="wthres" value="0.6" /> + <param name="pcKeepComp" value="0.02" /> + <output name="output_gff_file" file="NR__cellcycleM_chrII.gff" /> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {Github}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e nucleR_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucleR_stats.xml Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,73 @@ +<tool id="nucleR_stats" name="NucleR Statistics" version="0.1"> + <description>: gather gene and genome-wide statistics on NucleR results</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> + <![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics nucleR_stats --input $gff_file --out_genes $output_genes_csv_file --out_gw $output_gw_csv_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if; + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome Calls in GFF format as obtained from nucleR" /> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> +</inputs> + <outputs> + <data format="csv" name="output_genes_csv_file" label="NR__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" /> + <data format="csv" name="output_gw_csv_file" label="NR__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="NR__cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <output name="output_genes_csv_file" value="NR__stats__cellcycleM_chrII.genes.csv" /> + <output name="output_gw_csv_file" value="NR__stats__cellcycleM_chrII.gw.csv"/> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 707216744193 -r e88c806ddf3e periodicity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/periodicity.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,92 @@ +<tool id="periodicity" name="Periodicity" version="0.1"> + <description>: analyse nucleosome position phasing and periodicity within genes</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + ln -f -s $bwOutput_file $bwOutput_file\.bw; + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics periodicity --calls $gff_file --reads $rdata_file + #if $assembly.source == "buildin": + --chrom_sizes ${assembly.ref_chrom_sizes_buildin} --genes ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --chrom_sizes ${assembly.ref_chrom_sizes} --genes ${assembly.ref_genome_gff_history} + #end if + --gffOutput $output_gff_file --type $seq_type --bwOutput $bwOutput_file\.bw --periodicity $periodicity; + rm $bwOutput_file\.bw +]]> +</command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/> + <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM"/> + <param name="seq_type" type="select" label="Type of sequence reads"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes and their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_chrom_sizes_buildin" type="select" label="Select reference genome (Chrom sizes)" help="Select chromosome size for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="3"/> + </options> + </param> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_chrom_sizes" type="data" format="txt" label="Reference genome (Chrom sizes)" help="Upload chromosome size for your reference genome.Check below the documentation for learning about the file format."/> + <param name="ref_genome_gff_history" type="data" format="txt" label="Reference genome (Genes)" help=" Upload gene annotations for your reference genome. Check below the documentation for learning about the file format." /> + </when> + </conditional> + <param name="periodicity" size="4" type="integer" value="165" label="Period" help="Average distance between two consecutive nucleosomes (repeat length)." /> +</inputs> + <outputs> + <data format="gff" name="output_gff_file" label="P__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" /> + <data format="bigwig" name="bwOutput_file" label="P__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.bw" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="NR__cellcycleM_chrII.gff" /> + <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" /> + <param name="seq_type" value="paired" /> + <param name="ref_chrom_sizes_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <param name="periodicity" value="165" /> + <output name="output_gff_file" value="P__cellcycleM_chrII.gff" /> + <output name="bwOutput_file" value="P__cellcycleM_chrII.bw"/> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 707216744193 -r e88c806ddf3e periodicity_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/periodicity_stats.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,73 @@ +<tool id="periodicity_stats" name="Periodicity Statistics" version="0.1"> + <description>: gather gene and genome-wide statistics on Nucleosome Gene Phasing</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> + <![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics periodicity_stats --input $gff_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if + --out_genes $output_genes_csv_file --out_gw $output_gw_csv_file + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Periodicity (GFF)" help="Nucleosome Gene Phasing as annotated by Periodicity tool."/> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> + </inputs> + <outputs> + <data format="csv" name="output_genes_csv_file" label="P__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" /> + <data format="csv" name="output_gw_csv_file" label="P__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="P__cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <output name="output_genes_csv_file" file="P__stats__cellcycleM_chrII.genes.csv" /> + <output name="output_gw_csv_file" file="P__stats__cellcycleM_chrII.gw.csv" /> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 707216744193 -r e88c806ddf3e readBAM.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readBAM.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,53 @@ +<tool id="readBAM" name="readBAM" version="0.1"> + <description>: convert aligned BAM files to RData format for NucleosomeDynamics</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ +docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics readBAM --input $bam_file --output $rdata_file --type $seq_type +]]> + </command> + <inputs> + <param name="bam_file" type="data" format="bam" label="MNase-seq / ATAC-seq BAM file" help="Upload your MNase-seq or ATAC-seq reads file in BAM format. Access sample data at 'Shared Data -> Data libraries" /> + <param name="seq_type" type="select" label="Type of sequence reads"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + </inputs> + <outputs> + <data format="rdata" name="rdata_file" label="readBAM__${os.path.splitext(os.path.basename($bam_file.name))[0]}.rdata" /> + </outputs> + <tests> + <test> + <param name="bam_file" value="cellcycleM_chrII.bam"/> + <param name="seq_type" value="paired" /> + <output name="rdata_file" file="readBAM__cellcycleM_chrII.RData"/> + </test> + </tests> + <help> + .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e stiffness.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stiffness.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,51 @@ +<tool id="stiffness" name="Stiffness" version="0.1"> + <description>: analyze stiffness of nucleosome positioning</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> + <![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics stiffness --calls $gff_file --reads $rdata_file --output $output_gff_file --range $range + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/> + <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM"/> + <param name="range" size="4" type="text" value="All" label="Genomic Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome ('chromosomeName:start-end)." /> +</inputs> + <outputs> + <data format="gff" name="output_gff_file" label="STF__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="NR__cellcycleM_chrII.gff" /> + <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" /> + <param name="range" value="All" /> + <output name="output_gff_file" file="STF__cellcycleM_chrII.gff" /> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 707216744193 -r e88c806ddf3e stiffness_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stiffness_stats.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,77 @@ +<tool id="stiffness_stats" name="Stiffness Statistics" version="0.1"> + <description>: gather gene and genome-wide statistics on nucleosome position stiffness</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + ln -f -s $output_gw2_png_file $output_gw2_png_file\.png; + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics stiffness_stats --input $gff_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if + --out_genes $output_genes_csv_file --out_gw $output_gw_csv_file --out_gw2 $output_gw2_png_file\.png; + rm $output_gw2_png_file\.png + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Stiffness (GFF)" help="Stiffness as annotated by Stiffness tool." /> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> +</inputs> + <outputs> + <data format="csv" name="output_genes_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" /> + <data format="csv" name="output_gw_csv_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" /> + <data format="png" name="output_gw2_png_file" label="STF__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw2.png" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="STF__cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <output name="output_genes_csv_file" file="STF__stats__cellcycleM_chrII.genes.csv" /> + <output name="output_gw_csv_file" file="STF__stats__cellcycleM_chrII.gw.csv" /> + <output name="output_gw2_png_file" file="STF__stats__cellcycleM_chrII.gw2.png" /> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
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| diff -r 707216744193 -r e88c806ddf3e test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.bw |
| b |
| Binary file test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.bw has changed |
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| diff -r 707216744193 -r e88c806ddf3e test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ND__cellcycleG2_chrII_cellcycleM_chrII.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,722 @@\n+chrII\tNucleosomeDynamics\tNucleosome change\t 12453\t 12686\t0.0145905861502489\t.\t.\tnreads=3.35583137722519;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 16527\t 16679\t0.0116178639233301\t.\t.\tnreads=3.32010826742652;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 17813\t 17978\t0.00244022288092387\t.\t.\tnreads=3.76846113314784;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 37509\t 37662\t0.0188279663158348\t.\t.\tnreads=3.0026735322627;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 37680\t 37965\t0.000449408121787405\t.\t.\tnreads=4.90937327810431;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 42220\t 42420\t0.00515117881707874\t.\t.\tnreads=3.62446352577001;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 48952\t 49138\t0.0174820397546826\t.\t.\tnreads=3.12224345105165;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 60041\t 60213\t0.00752990883595927\t.\t.\tnreads=3.46115105617404;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 63974\t 64184\t0.0204239568573379\t.\t.\tnreads=3.26787918041301;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 66137\t 66370\t0.00693722416549654\t.\t.\tnreads=3.75995674495063;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 67666\t 67853\t0.0130522050957899\t.\t.\tnreads=3.27843468004489;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 83543\t 83768\t0.00784042922041864\t.\t.\tnreads=3.76569634817574;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t 84503\t 84695\t0.00565162083864906\t.\t.\tnreads=3.51913948422993;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t100895\t101079\t0.00328559494434197\t.\t.\tnreads=3.49612711163579;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t102972\t103183\t0.016066352618141\t.\t.\tnreads=3.13361957497686;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t111868\t112024\t0.00827526598026395\t.\t.\tnreads=3.28236436923612;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t112026\t112197\t0.00711596807380461\t.\t.\tnreads=3.319806541034;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t113316\t113539\t0.0156579178808079\t.\t.\tnreads=3.26569919496744;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t129897\t130126\t0.00723063033856206\t.\t.\tnreads=3.51596796674879;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t130219\t130416\t0.00899578220783154\t.\t.\tnreads=3.2723888779058;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome change\t132392\t132606\t0.00173707815491035\t.\t.\tnreads=4.02662169323612;class=INCLUSION\n+chrII\tNucleosomeDynamics\tNucleosome 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| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.genes.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
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TFC2),0,0,0,0\n+YPR187W (RPO26 RPB6),0,0,0,0\n+YPR188C (MLC2),0,0,0,0\n+YPR189W (SKI3 SKI5),0,0,0,0\n+YPR190C (RPC82 RPC3),0,0,0,0\n+YPR191W (QCR2 COR2 UCR2),0,0,0,0\n+YPR192W (AQY1),0,0,0,0\n+YPR193C (HPA2),0,0,0,0\n+YPR194C (OPT2),0,0,0,0\n+YPR195C,0,0,0,0\n+YPR196W,0,0,0,0\n+YPR198W (SGE1 NOR1),0,0,0,0\n+YPR199C (ARR1 ACR1 YAP8),0,0,0,0\n+YPR201W (ARR3 ACR3),0,0,0,0\n' |
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| diff -r 707216744193 -r e88c806ddf3e test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png |
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| Binary file test-data/ND__stats__cellcycleG2_chrII_cellcycleM_chrII.gw.png has changed |
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| diff -r 707216744193 -r e88c806ddf3e test-data/NFR__cellcycleM_chrII.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NFR__cellcycleM_chrII.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,363 @@\n+chrII\tnucleR\tNucleosome Free Region\t 2206\t 5855\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 6260\t 6591\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 7454\t 8280\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 9206\t 9365\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 9513\t 9735\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 10575\t 10705\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 13814\t 13994\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 17977\t 18128\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 23821\t 23963\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 28660\t 28787\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 28935\t 29055\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 29707\t 29937\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 30138\t 33133\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 33281\t 35636\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 35947\t 36170\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 36318\t 36698\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 38703\t 38857\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 40592\t 40741\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 43102\t 43225\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 45053\t 45250\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 45398\t 45587\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 46364\t 46567\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 59610\t 59780\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 60814\t 61165\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 63548\t 63685\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 69585\t 69716\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 71682\t 71868\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 74764\t 74905\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t 75053\t 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Free Region\t116921\t117083\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t117231\t117396\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t119162\t119442\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t124852\t125015\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t127599\t127741\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t132229\t132388\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t133791\t133998\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t135758\t136052\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t136200\t136324\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t138217\t138343\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t140400\t140872\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t141020\t141181\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t141934\t142145\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t142919\t143037\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t143647\t143979\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t145828\t146076\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t146981\t147101\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t150286\t150446\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t151263\t151411\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t153713\t153888\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t158494\t158642\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t159739\t160081\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t161467\t161652\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t162733\t162928\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Fre'..b'\tNucleosome Free Region\t645916\t646202\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t647265\t647433\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t650112\t650273\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t651165\t651282\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free 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Region\t687748\t687922\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t691766\t691909\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t694561\t694978\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t697460\t697842\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t697990\t698120\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t700118\t700229\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t702208\t702407\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t704330\t704473\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t708016\t708163\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t711418\t711538\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t712776\t712980\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t714530\t714666\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t716571\t716717\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t718198\t718379\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t721201\t721315\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t722455\t722567\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t723064\t723198\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t728166\t728304\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t728452\t728566\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t730199\t730311\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t734674\t734797\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t736098\t736213\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t738398\t738517\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t739655\t739797\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t741157\t741269\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t741970\t742158\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t742614\t742756\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t744698\t744808\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t746091\t746213\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t751207\t751423\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t760919\t761190\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t764749\t764901\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t770619\t770819\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t773646\t773888\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t774372\t774666\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t776330\t776483\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t782402\t782555\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t784678\t784804\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t788762\t788885\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t789033\t789242\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t792111\t792330\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t792644\t792777\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t796554\t796691\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t798957\t799178\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t800280\t800453\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t804919\t805257\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t805405\t807476\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t808869\t809288\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t809436\t809606\t.\t.\t.\t.\n+chrII\tnucleR\tNucleosome Free Region\t809754\t809910\t.\t.\t.\t.\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/NFR__stats__cellcycleM_chrII.gw.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NFR__stats__cellcycleM_chrII.gw.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +NFR,Value +Total,363 +Mean width,264.22 +Std. Dev. width,469.59 |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/NR__cellcycleM_chrII.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NR__cellcycleM_chrII.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,4856 @@\n+chrII\tnucleR\tNucleosome\t 1604\t 1750\t0.759294809783929\t*\t.\tscore_width=0.52157252172839;score_height=0.997017097839469;class=F\n+chrII\tnucleR\tNucleosome\t 1700\t 1846\t0.421390436543631\t*\t.\tscore_width=0.25256457172844;score_height=0.590216301358822;class=F\n+chrII\tnucleR\tNucleosome\t 1770\t 1916\t0.756903479351746\t*\t.\tscore_width=0.51426906014978;score_height=0.999537898553711;class=F\n+chrII\tnucleR\tNucleosome\t 1868\t 2080\t0.737461892010131\t*\t.\tscore_width=0.476852408461523;score_height=0.998071375558739;class=F\n+chrII\tnucleR\tNucleosome\t 2059\t 2205\t0.60668872634879\t*\t.\tscore_width=0.98431878691199;score_height=0.22905866578559;class=F\n+chrII\tnucleR\tNucleosome\t 5856\t 6002\t0.225748168309391\t*\t.\tscore_width=0.300138070767553;score_height=0.151358265851229;class=F\n+chrII\tnucleR\tNucleosome\t 5960\t 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|
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/NR__stats__cellcycleM_chrII.genes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NR__stats__cellcycleM_chrII.genes.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,5681 @@\n+Name,Total Nucleosomes,Total Well-Positioned,Total Fuzzy,Total Uncertain\n+Q0080 (ATP8 AAP1),0,0,0,0\n+Q0085 (ATP6 OLI2 OLI4 PHO1),0,0,0,0\n+Q0130 (OLI1 ATP9 OLI3),0,0,0,0\n+Q0275 (COX3 OXI2),0,0,0,0\n+YAL001C (TFC3 FUN24 TSV115),0,0,0,0\n+YAL002W (VPS8 FUN15 VPL8 VPT8),0,0,0,0\n+YAL003W (EFB1 TEF5),0,0,0,0\n+YAL004W,0,0,0,0\n+YAL005C (SSA1 YG100),0,0,0,0\n+YAL007C (ERP2),0,0,0,0\n+YAL008W (FUN14),0,0,0,0\n+YAL009W (SPO7),0,0,0,0\n+YAL010C (MDM10 FUN37),0,0,0,0\n+YAL011W (SWC3 SWC1),0,0,0,0\n+YAL012W (CYS3 CYI1 FUN35 STR1),0,0,0,0\n+YAL013W (DEP1 FUN54),0,0,0,0\n+YAL014C (SYN8 SLT2 UIP2),0,0,0,0\n+YAL015C (NTG1 FUN33 SCR1 ogg2),0,0,0,0\n+YAL016C-B,0,0,0,0\n+YAL016W (TPD3 FUN32),0,0,0,0\n+YAL017W (PSK1 FUN31),0,0,0,0\n+YAL018C,0,0,0,0\n+YAL019W (FUN30),0,0,0,0\n+YAL020C (ATS1 FUN28 KTI13),0,0,0,0\n+YAL021C (CCR4 FUN27 NUT21),0,0,0,0\n+YAL022C (FUN26),0,0,0,0\n+YAL023C (PMT2 FUN25),0,0,0,0\n+YAL024C (LTE1 MSI2),0,0,0,0\n+YAL025C (MAK16),0,0,0,0\n+YAL026C (DRS2 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(ACH1),15,8,7,0\n+YBL016W (FUS3 DAC2),8,8,0,0\n+YBL017C (PEP1 VPS10 VPT1),38,15,23,0\n+YBL018C (POP8),5,3,2,0\n+YBL019W (APN2 ETH1),12,6,6,0\n+YBL020W (RFT1),11,9,2,0\n+YBL021C (HAP3),4,4,0,0\n+YBL022C (PIM1 LON1),28,10,18,0\n+YBL023C (MCM2),21,9,12,0\n+YBL024W (NCL1 TRM4),17,8,9,0\n+YBL025W (RRN10),6,4,2,0\n+YBL026W (LSM2 SMX5 SNP3),5,3,2,0\n+YBL027W (RPL19B),6,2,3,1\n+YBL028C,4,1,3,0\n+YBL029C-A,3,3,0,0\n+YBL029W,9,3,6,0\n+YBL030C (PET9 AAC2 ANC2 OP1),9,1,8,0\n+YBL031W (SHE1),7,5,2,0\n+YBL032W (HEK2 KHD1),10,6,4,0\n+YBL033C (RIB1),7,7,0,0\n+YBL034C (STU1),33,16,17,0\n+YBL035C (POL12),16,8,8,0\n+YBL036C,6,4,2,0\n+YBL037W (APL3),22,9,12,1\n+YBL038W (MRPL16),6,4,2,0\n+YBL039C (URA7),13,10,3,0\n+YBL039W-B (YBL039W-A),3,2,1,0\n+YBL040C (ERD2),5,5,0,0\n+YBL041W (PRE7 PRS3),5,5,0,0\n+YBL042C (FUI1),15,3,12,0\n+YBL043W (ECM13),8,5,3,0\n+YBL045C (COR1 QCR1),12,6,6,0\n+YBL046W (PSY4),9,5,4,0\n+YBL047C (EDE1 BUD15),31,10,20,1\n+YBL049W (MOH1),7,2,5,0\n+YBL050W (SEC17 RNS3),8,7,1,0\n+YBL051C (PIN4 MDT1),19,8,11,0\n+YBL052C (SAS3),18,8,10,0\n+YBL054W (TOD6 PBF1),11,8,3,0\n+YBL055C (Tat-D),11,9,2,0\n+YBL056W (PTC3),12,7,5,0\n+YBL057C (PTH2),7,4,3,0\n+YBL058W ('..b',0,0\n+YPR032W (SRO7 SNI1 SOP1),0,0,0,0\n+YPR033C (HTS1 TSM4572),0,0,0,0\n+YPR034W (ARP7 RSC11 SWP61),0,0,0,0\n+YPR035W (GLN1),0,0,0,0\n+YPR036W (VMA13 CLS11),0,0,0,0\n+YPR036W-A,0,0,0,0\n+YPR037C (ERV2),0,0,0,0\n+YPR040W (TIP41),0,0,0,0\n+YPR041W (TIF5 SUI5),0,0,0,0\n+YPR042C (PUF2),0,0,0,0\n+YPR043W (RPL43A),0,0,0,0\n+YPR044C (OPI11),0,0,0,0\n+YPR045C (THP3 MNI2),0,0,0,0\n+YPR046W (MCM16),0,0,0,0\n+YPR047W (MSF1),0,0,0,0\n+YPR048W (TAH18),0,0,0,0\n+YPR049C (ATG11 CVT9),0,0,0,0\n+YPR050C,0,0,0,0\n+YPR051W (MAK3 NAA30),0,0,0,0\n+YPR052C (NHP6A),0,0,0,0\n+YPR053C,0,0,0,0\n+YPR054W (SMK1),0,0,0,0\n+YPR055W (SEC8),0,0,0,0\n+YPR056W (TFB4),0,0,0,0\n+YPR057W (BRR1),0,0,0,0\n+YPR058W (YMC1),0,0,0,0\n+YPR059C,0,0,0,0\n+YPR060C (ARO7 HGS1 OSM2 TYR7),0,0,0,0\n+YPR061C (JID1),0,0,0,0\n+YPR062W (FCY1 yCD),0,0,0,0\n+YPR063C,0,0,0,0\n+YPR065W (ROX1 REO1),0,0,0,0\n+YPR067W (ISA2),0,0,0,0\n+YPR068C (HOS1),0,0,0,0\n+YPR069C (SPE3),0,0,0,0\n+YPR070W (MED1),0,0,0,0\n+YPR071W,0,0,0,0\n+YPR072W (NOT5),0,0,0,0\n+YPR073C (LTP1),0,0,0,0\n+YPR074C (TKL1),0,0,0,0\n+YPR075C (OPY2),0,0,0,0\n+YPR076W,0,0,0,0\n+YPR077C,0,0,0,0\n+YPR078C,0,0,0,0\n+YPR079W (MRL1),0,0,0,0\n+YPR080W (TEF1 EF-1%20alpha),0,0,0,0\n+YPR081C (GRS2),0,0,0,0\n+YPR082C (DIB1 SNU16),0,0,0,0\n+YPR083W (MDM36),0,0,0,0\n+YPR084W,0,0,0,0\n+YPR085C (ASA1),0,0,0,0\n+YPR086W (SUA7 SOH4),0,0,0,0\n+YPR088C (SRP54 SRH1),0,0,0,0\n+YPR089W (YPR090W),0,0,0,0\n+YPR091C,0,0,0,0\n+YPR093C (ASR1),0,0,0,0\n+YPR094W (RDS3),0,0,0,0\n+YPR095C (SYT1),0,0,0,0\n+YPR097W,0,0,0,0\n+YPR098C,0,0,0,0\n+YPR100W (MRPL51),0,0,0,0\n+YPR101W (SNT309 NTC25),0,0,0,0\n+YPR102C (RPL11A),0,0,0,0\n+YPR103W (PRE2 DOA3 PRG1 SRR2),0,0,0,0\n+YPR104C (FHL1 SPP42),0,0,0,0\n+YPR105C (COG4 COD1 SEC38 SGF1),0,0,0,0\n+YPR106W (ISR1),0,0,0,0\n+YPR107C (YTH1),0,0,0,0\n+YPR108W (RPN7),0,0,0,0\n+YPR109W,0,0,0,0\n+YPR110C (RPC40 RPC5),0,0,0,0\n+YPR111W (DBF20),0,0,0,0\n+YPR112C (MRD1),0,0,0,0\n+YPR113W (PIS1),0,0,0,0\n+YPR114W,0,0,0,0\n+YPR115W (RGC1 GCA1),0,0,0,0\n+YPR116W (RRG8),0,0,0,0\n+YPR117W,0,0,0,0\n+YPR118W (MRI1),0,0,0,0\n+YPR119W (CLB2),0,0,0,0\n+YPR120C (CLB5),0,0,0,0\n+YPR121W (THI22),0,0,0,0\n+YPR122W (AXL1 FUS5 STE22),0,0,0,0\n+YPR124W (CTR1),0,0,0,0\n+YPR125W (YLH47 MRS7),0,0,0,0\n+YPR126C,0,0,0,0\n+YPR127W,0,0,0,0\n+YPR128C (ANT1),0,0,0,0\n+YPR129W (SCD6 LSM13),0,0,0,0\n+YPR131C (NAT3 NAA20),0,0,0,0\n+YPR132W (RPS23B),0,0,0,0\n+YPR133C (SPN1 IWS1),0,0,0,0\n+YPR133W-A (TOM5 MOM8A),0,0,0,0\n+YPR134W (MSS18),0,0,0,0\n+YPR135W (CTF4 CHL15 POB1),0,0,0,0\n+YPR137W (RRP9),0,0,0,0\n+YPR138C (MEP3),0,0,0,0\n+YPR139C (VPS66),0,0,0,0\n+YPR140W (TAZ1),0,0,0,0\n+YPR141C (KAR3 OSR11),0,0,0,0\n+YPR143W (RRP15),0,0,0,0\n+YPR144C (NOC4 UTP19),0,0,0,0\n+YPR145C-A,0,0,0,0\n+YPR145W (ASN1),0,0,0,0\n+YPR147C,0,0,0,0\n+YPR148C,0,0,0,0\n+YPR149W (NCE102 NCE2),0,0,0,0\n+YPR150W,0,0,0,0\n+YPR151C (SUE1),0,0,0,0\n+YPR152C (URN1),0,0,0,0\n+YPR153W,0,0,0,0\n+YPR154W (PIN3 LSB2),0,0,0,0\n+YPR155C (NCA2),0,0,0,0\n+YPR156C (TPO3),0,0,0,0\n+YPR157W,0,0,0,0\n+YPR158W (CUR1),0,0,0,0\n+YPR159W (KRE6 CWH48),0,0,0,0\n+YPR160W (GPH1),0,0,0,0\n+YPR161C (SGV1 BUR1),0,0,0,0\n+YPR162C (ORC4),0,0,0,0\n+YPR163C (TIF3 RBL3 STM1),0,0,0,0\n+YPR164W (MMS1 RTT108 SLM6),0,0,0,0\n+YPR165W (RHO1),0,0,0,0\n+YPR166C (MRP2),0,0,0,0\n+YPR167C (MET16),0,0,0,0\n+YPR169W (JIP5),0,0,0,0\n+YPR169W-A,0,0,0,0\n+YPR170C,0,0,0,0\n+YPR170W-A,0,0,0,0\n+YPR170W-B,0,0,0,0\n+YPR171W (BSP1),0,0,0,0\n+YPR172W,0,0,0,0\n+YPR173C (VPS4 CSC1 DID6 END13 GRD13 VPL4 VPT10),0,0,0,0\n+YPR174C,0,0,0,0\n+YPR175W (DPB2),0,0,0,0\n+YPR176C (BET2),0,0,0,0\n+YPR178W (PRP4 RNA4),0,0,0,0\n+YPR179C (HDA3 PLO1),0,0,0,0\n+YPR180W (AOS1 RHC31),0,0,0,0\n+YPR181C (SEC23),0,0,0,0\n+YPR182W (SMX3),0,0,0,0\n+YPR183W (DPM1 SED3),0,0,0,0\n+YPR184W (GDB1),0,0,0,0\n+YPR185W (ATG13 APG13),0,0,0,0\n+YPR186C (PZF1 TFC2),0,0,0,0\n+YPR187W (RPO26 RPB6),0,0,0,0\n+YPR188C (MLC2),0,0,0,0\n+YPR189W (SKI3 SKI5),0,0,0,0\n+YPR190C (RPC82 RPC3),0,0,0,0\n+YPR191W (QCR2 COR2 UCR2),0,0,0,0\n+YPR192W (AQY1),0,0,0,0\n+YPR193C (HPA2),0,0,0,0\n+YPR194C (OPT2),0,0,0,0\n+YPR195C,0,0,0,0\n+YPR196W,0,0,0,0\n+YPR198W (SGE1 NOR1),0,0,0,0\n+YPR199C (ARR1 ACR1 YAP8),0,0,0,0\n+YPR201W (ARR3 ACR3),0,0,0,0\n' |
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| diff -r 707216744193 -r e88c806ddf3e test-data/NR__stats__cellcycleM_chrII.gw.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NR__stats__cellcycleM_chrII.gw.csv Fri Apr 12 05:28:43 2019 -0400 |
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| @@ -0,0 +1,5 @@ +Class,Frequency +Fuzzy,2410 +Uncertain,38 +Well-positioned,2408 +Total,4856 |
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| diff -r 707216744193 -r e88c806ddf3e test-data/P__cellcycleM_chrII.bw |
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| Binary file test-data/P__cellcycleM_chrII.bw has changed |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/P__cellcycleM_chrII.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/P__cellcycleM_chrII.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,388 @@\n+chrII\tnucleR\tnucleosome periodicity\t237064\t237512\t.\t-\t.\tid=YBL001C (ECM15);nucleosome_first=237471;nucleosome_last=237301;score_phase=5;score_autocorrelation=0.123614194749145\n+chrII\tnucleR\tnucleosome periodicity\t236439\t237087\t.\t+\t.\tid=YBL002W (HTB2);nucleosome_first=236547;nucleosome_last=236862;score_phase=15;score_autocorrelation=0.247507999824661\n+chrII\tnucleR\tnucleosome periodicity\t235199\t235827\t.\t-\t.\tid=YBL003C (HTA2 H2A2);nucleosome_first=235732;nucleosome_last=235351;score_phase=51;score_autocorrelation=0.441909852056576\n+chrII\tnucleR\tnucleosome periodicity\t227535\t235175\t.\t+\t.\tid=YBL004W (UTP20);nucleosome_first=227593;nucleosome_last=235168;score_phase=15;score_autocorrelation=0.76519955820537\n+chrII\tnucleR\tnucleosome periodicity\t217408\t220685\t.\t+\t.\tid=YBL005W (PDR3 AMY2 TPE2);nucleosome_first=217419;nucleosome_last=220654;score_phase=65;score_autocorrelation=0.670940499713206\n+chrII\tnucleR\tnucleosome periodicity\t216405\t217150\t.\t-\t.\tid=YBL006C (LDB7 RSC14);nucleosome_first=217109;nucleosome_last=216652;score_phase=38;score_autocorrelation=0.564457737503059\n+chrII\tnucleR\tnucleosome periodicity\t212548\t216418\t.\t-\t.\tid=YBL007C (SLA1);nucleosome_first=216367;nucleosome_last=212765;score_phase=28;score_autocorrelation=0.691116663680679\n+chrII\tnucleR\tnucleosome periodicity\t209588\t212256\t.\t+\t.\tid=YBL008W (HIR1);nucleosome_first=209623.5;nucleosome_last=212224;score_phase=39.5;score_autocorrelation=0.691806742832004\n+chrII\tnucleR\tnucleosome periodicity\t207160\t209350\t.\t+\t.\tid=YBL009W (ALK2);nucleosome_first=207212;nucleosome_last=209210;score_phase=18;score_autocorrelation=0.687513706741524\n+chrII\tnucleR\tnucleosome periodicity\t205899\t206969\t.\t-\t.\tid=YBL010C;nucleosome_first=206905;nucleosome_last=205909;score_phase=6;score_autocorrelation=0.780206289308176\n+chrII\tnucleR\tnucleosome periodicity\t203445\t206022\t.\t+\t.\tid=YBL011W (SCT1 GAT2);nucleosome_first=203514;nucleosome_last=205909;score_phase=80;score_autocorrelation=0.706908721063669\n+chrII\tnucleR\tnucleosome periodicity\t198947\t201777\t.\t-\t.\tid=YBL014C (RRN6);nucleosome_first=201728;nucleosome_last=199095;score_phase=7;score_autocorrelation=0.701109612182642\n+chrII\tnucleR\tnucleosome periodicity\t194037\t195953\t.\t+\t.\tid=YBL015W (ACH1);nucleosome_first=194110;nucleosome_last=195908;score_phase=17;score_autocorrelation=0.792438187561268\n+chrII\tnucleR\tnucleosome periodicity\t192430\t193647\t.\t+\t.\tid=YBL016W (FUS3 DAC2);nucleosome_first=192558;nucleosome_last=193565;score_phase=17;score_autocorrelation=0.781841750938207\n+chrII\tnucleR\tnucleosome periodicity\t186771\t191767\t.\t-\t.\tid=YBL017C (PEP1 VPS10 VPT1);nucleosome_first=191720;nucleosome_last=186923;score_phase=12;score_autocorrelation=0.760365182667541\n+chrII\tnucleR\tnucleosome periodicity\t185933\t186515\t.\t-\t.\tid=YBL018C (POP8);nucleosome_first=186470;nucleosome_last=185986;score_phase=11;score_autocorrelation=0.526887749169972\n+chrII\tnucleR\tnucleosome periodicity\t184307\t186027\t.\t+\t.\tid=YBL019W (APN2 ETH1);nucleosome_first=184356;nucleosome_last=185986;score_phase=20;score_autocorrelation=0.655433571862553\n+chrII\tnucleR\tnucleosome periodicity\t182342\t184205\t.\t+\t.\tid=YBL020W (RFT1);nucleosome_first=182353;nucleosome_last=183983;score_phase=20;score_autocorrelation=0.800020689491276\n+chrII\tnucleR\tnucleosome periodicity\t181490\t182126\t.\t-\t.\tid=YBL021C (HAP3);nucleosome_first=182064;nucleosome_last=181623;score_phase=54;score_autocorrelation=0.364407455724596\n+chrII\tnucleR\tnucleosome periodicity\t177798\t181394\t.\t-\t.\tid=YBL022C (PIM1 LON1);nucleosome_first=181363;nucleosome_last=177830;score_phase=68;score_autocorrelation=0.76974359485396\n+chrII\tnucleR\tnucleosome periodicity\t174739\t177601\t.\t-\t.\tid=YBL023C (MCM2);nucleosome_first=177564;nucleosome_last=174930;score_phase=6;score_autocorrelation=0.827482730083788\n+chrII\tnucleR\tnucleosome periodicity\t172511\t174713\t.\t+\t.\tid=YBL024W (NCL1 TRM4);nucleosome_first=172550;nucleosome_last=174655;score_phase=40;score_autocorrelation=0.7128510998952\n+chrII\tnucleR\tnucleosome periodicity\t17'..b'score_phase=15;score_autocorrelation=0.640911293945197\n+chrII\tnucleR\tnucleosome periodicity\t760139\t761048\t.\t-\t.\tid=YBR277C;nucleosome_first=760845;nucleosome_last=760327;score_phase=23;score_autocorrelation=0.508434144278625\n+chrII\tnucleR\tnucleosome periodicity\t760269\t760991\t.\t+\t.\tid=YBR278W (DPB3);nucleosome_first=760327;nucleosome_last=760845;score_phase=23;score_autocorrelation=0.508434144278625\n+chrII\tnucleR\tnucleosome periodicity\t761219\t762741\t.\t+\t.\tid=YBR279W (PAF1);nucleosome_first=761264;nucleosome_last=762544;score_phase=40;score_autocorrelation=0.615867301203239\n+chrII\tnucleR\tnucleosome periodicity\t762619\t764720\t.\t-\t.\tid=YBR280C (SAF1);nucleosome_first=764675;nucleosome_last=762778;score_phase=82;score_autocorrelation=0.779107062672397\n+chrII\tnucleR\tnucleosome periodicity\t764860\t767647\t.\t-\t.\tid=YBR281C (DUG2);nucleosome_first=767602;nucleosome_last=764975;score_phase=13;score_autocorrelation=0.718078349933465\n+chrII\tnucleR\tnucleosome periodicity\t768209\t768768\t.\t+\t.\tid=YBR282W (MRPL27);nucleosome_first=768242;nucleosome_last=768643;score_phase=71;score_autocorrelation=0.225237372533772\n+chrII\tnucleR\tnucleosome periodicity\t768791\t770559\t.\t-\t.\tid=YBR283C (SSH1);nucleosome_first=770545;nucleosome_last=768971;score_phase=76;score_autocorrelation=0.738444654887431\n+chrII\tnucleR\tnucleosome periodicity\t770878\t773843\t.\t+\t.\tid=YBR284W;nucleosome_first=770893;nucleosome_last=773572;score_phase=39;score_autocorrelation=0.647711214702801\n+chrII\tnucleR\tnucleosome periodicity\t773867\t774497\t.\t+\t.\tid=YBR285W;nucleosome_first=773962;nucleosome_last=774298;score_phase=6;score_autocorrelation=0.42386245522976\n+chrII\tnucleR\tnucleosome periodicity\t774680\t776385\t.\t+\t.\tid=YBR286W (APE3 APY1);nucleosome_first=774740;nucleosome_last=776256;score_phase=31;score_autocorrelation=0.652304146352848\n+chrII\tnucleR\tnucleosome periodicity\t776530\t777974\t.\t+\t.\tid=YBR287W (ZSP1);nucleosome_first=776557;nucleosome_last=777796.5;score_phase=80.5;score_autocorrelation=0.710558142988998\n+chrII\tnucleR\tnucleosome periodicity\t777927\t779498\t.\t-\t.\tid=YBR288C (APM3 YKS6);nucleosome_first=779458;nucleosome_last=778040;score_phase=67;score_autocorrelation=0.586202358233777\n+chrII\tnucleR\tnucleosome periodicity\t779645\t782442\t.\t+\t.\tid=YBR289W (SNF5 HAF4 SWI10 TYE4);nucleosome_first=779708;nucleosome_last=782328;score_phase=20;score_autocorrelation=0.723591201923921\n+chrII\tnucleR\tnucleosome periodicity\t782576\t783664\t.\t+\t.\tid=YBR290W (BSD2);nucleosome_first=782629;nucleosome_last=783577;score_phase=42;score_autocorrelation=0.596334221652069\n+chrII\tnucleR\tnucleosome periodicity\t783604\t784608\t.\t-\t.\tid=YBR291C (CTP1);nucleosome_first=784604;nucleosome_last=783740;score_phase=39;score_autocorrelation=0.656245602514189\n+chrII\tnucleR\tnucleosome periodicity\t786653\t788651\t.\t+\t.\tid=YBR293W (VBA2);nucleosome_first=786833;nucleosome_last=788516;score_phase=33;score_autocorrelation=0.727296447408856\n+chrII\tnucleR\tnucleosome periodicity\t789128\t791892\t.\t+\t.\tid=YBR294W (SUL1 SFP2);nucleosome_first=789316;nucleosome_last=791881;score_phase=75;score_autocorrelation=0.83425538568721\n+chrII\tnucleR\tnucleosome periodicity\t792812\t796635\t.\t+\t.\tid=YBR295W (PCA1 CAD2 PAY2);nucleosome_first=792851;nucleosome_last=796480;score_phase=1;score_autocorrelation=0.720477880816592\n+chrII\tnucleR\tnucleosome periodicity\t796558\t798588\t.\t-\t.\tid=YBR296C (PHO89 ITN1);nucleosome_first=798550.5;nucleosome_last=796765;score_phase=29.5;score_autocorrelation=0.62949228432078\n+chrII\tnucleR\tnucleosome periodicity\t800477\t802166\t.\t+\t.\tid=YBR297W (MAL33 MAL3R MALR);nucleosome_first=800527;nucleosome_last=802003;score_phase=9;score_autocorrelation=0.735386126838853\n+chrII\tnucleR\tnucleosome periodicity\t802538\t804872\t.\t-\t.\tid=YBR298C (MAL31 MAL3T MALT);nucleosome_first=804845;nucleosome_last=802661;score_phase=39;score_autocorrelation=0.817387712298236\n+chrII\tnucleR\tnucleosome periodicity\t805323\t807234\t.\t+\t.\tid=YBR299W (MAL32 MAL3S MALS);nucleosome_first=805331;nucleosome_last=805331;score_phase=0;score_autocorrelation=NA\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/P__stats__cellcycleM_chrII.genes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/P__stats__cellcycleM_chrII.genes.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,5681 @@\n+Name,Score phase,Score autocorrelation\n+Q0080 (ATP8 AAP1),NA,NA\n+Q0085 (ATP6 OLI2 OLI4 PHO1),NA,NA\n+Q0130 (OLI1 ATP9 OLI3),NA,NA\n+Q0275 (COX3 OXI2),NA,NA\n+YAL001C (TFC3 FUN24 TSV115),NA,NA\n+YAL002W (VPS8 FUN15 VPL8 VPT8),NA,NA\n+YAL003W (EFB1 TEF5),NA,NA\n+YAL004W,NA,NA\n+YAL005C (SSA1 YG100),NA,NA\n+YAL007C (ERP2),NA,NA\n+YAL008W (FUN14),NA,NA\n+YAL009W (SPO7),NA,NA\n+YAL010C (MDM10 FUN37),NA,NA\n+YAL011W (SWC3 SWC1),NA,NA\n+YAL012W (CYS3 CYI1 FUN35 STR1),NA,NA\n+YAL013W (DEP1 FUN54),NA,NA\n+YAL014C (SYN8 SLT2 UIP2),NA,NA\n+YAL015C (NTG1 FUN33 SCR1 ogg2),NA,NA\n+YAL016C-B,NA,NA\n+YAL016W (TPD3 FUN32),NA,NA\n+YAL017W (PSK1 FUN31),NA,NA\n+YAL018C,NA,NA\n+YAL019W (FUN30),NA,NA\n+YAL020C (ATS1 FUN28 KTI13),NA,NA\n+YAL021C (CCR4 FUN27 NUT21),NA,NA\n+YAL022C (FUN26),NA,NA\n+YAL023C (PMT2 FUN25),NA,NA\n+YAL024C (LTE1 MSI2),NA,NA\n+YAL025C (MAK16),NA,NA\n+YAL026C (DRS2 FUN38 SWA3),NA,NA\n+YAL027W (SAW1),NA,NA\n+YAL028W (FRT2 HPH2),NA,NA\n+YAL029C (MYO4 FUN22 SHE1),NA,NA\n+YAL030W (SNC1),NA,NA\n+YAL031C (GIP4 FUN21),NA,NA\n+YAL032C (PRP45 FUN20),NA,NA\n+YAL033W (POP5 FUN53),NA,NA\n+YAL034C (FUN19),NA,NA\n+YAL034C-B (YAL035C-A),NA,NA\n+YAL034W-A (MTW1 DSN3 NSL2),NA,NA\n+YAL035W (FUN12 yIF2),NA,NA\n+YAL036C (RBG1 FUN11),NA,NA\n+YAL037C-A,NA,NA\n+YAL037C-B,NA,NA\n+YAL037W,NA,NA\n+YAL038W (CDC19 PYK1),NA,NA\n+YAL039C (CYC3),NA,NA\n+YAL040C (CLN3 DAF1 FUN10 WHI1),NA,NA\n+YAL041W (CDC24 CLS4),NA,NA\n+YAL042W (ERV46 FUN9),NA,NA\n+YAL043C (PTA1 FUN39),NA,NA\n+YAL044C (GCV3),NA,NA\n+YAL044W-A,NA,NA\n+YAL045C,NA,NA\n+YAL046C (AIM1),NA,NA\n+YAL047C (SPC72 LDB4),NA,NA\n+YAL047W-A,NA,NA\n+YAL048C (GEM1 GON1),NA,NA\n+YAL049C (AIM2),NA,NA\n+YAL051W (OAF1 YAF1),NA,NA\n+YAL053W (FLC2 HUF2),NA,NA\n+YAL054C (ACS1 FUN44),NA,NA\n+YAL055W (PEX22 YAF5),NA,NA\n+YAL056W (GPB2 KRH1),NA,NA\n+YAL058W (CNE1 FUN48),NA,NA\n+YAL059W (ECM1),NA,NA\n+YAL060W (BDH1 BDH),NA,NA\n+YAL061W (BDH2),NA,NA\n+YAL062W (GDH3 FUN51),NA,NA\n+YAL064W-B,NA,NA\n+YAL067C (SEO1),NA,NA\n+YAR002C-A (ERP1),NA,NA\n+YAR002W (NUP60),NA,NA\n+YAR003W (SWD1 CPS50 FUN16 SAF49),NA,NA\n+YAR007C (RFA1 BUF2 FUN3 RPA1),NA,NA\n+YAR008W (SEN34 FUN4),NA,NA\n+YAR014C (BUD14),NA,NA\n+YAR015W (ADE1),NA,NA\n+YAR018C (KIN3 FUN52 NPK1),NA,NA\n+YAR019C (CDC15 LYT1),NA,NA\n+YAR023C,NA,NA\n+YAR027W (UIP3),NA,NA\n+YAR028W,NA,NA\n+YAR029W,NA,NA\n+YAR033W (MST28),NA,NA\n+YAR035W (YAT1),NA,NA\n+YAR042W (SWH1 OSH1 YAR044W),NA,NA\n+YAR066W,NA,NA\n+YBL001C (ECM15),5,0.123614194749145\n+YBL002W (HTB2),15,0.247507999824661\n+YBL003C (HTA2 H2A2),51,0.441909852056576\n+YBL004W (UTP20),15,0.76519955820537\n+YBL005W (PDR3 AMY2 TPE2),65,0.670940499713206\n+YBL006C (LDB7 RSC14),38,0.564457737503059\n+YBL007C (SLA1),28,0.691116663680679\n+YBL008W (HIR1),39.5,0.691806742832004\n+YBL009W (ALK2),18,0.687513706741524\n+YBL010C,6,0.780206289308176\n+YBL011W (SCT1 GAT2),80,0.706908721063669\n+YBL014C (RRN6),7,0.701109612182642\n+YBL015W (ACH1),17,0.792438187561268\n+YBL016W (FUS3 DAC2),17,0.781841750938207\n+YBL017C (PEP1 VPS10 VPT1),12,0.760365182667541\n+YBL018C (POP8),11,0.526887749169972\n+YBL019W (APN2 ETH1),20,0.655433571862553\n+YBL020W (RFT1),20,0.800020689491276\n+YBL021C (HAP3),54,0.364407455724596\n+YBL022C (PIM1 LON1),68,0.76974359485396\n+YBL023C (MCM2),6,0.827482730083788\n+YBL024W (NCL1 TRM4),40,0.7128510998952\n+YBL025W (RRN10),49,0.549023316643203\n+YBL026W (LSM2 SMX5 SNP3),74,0.470003560122776\n+YBL027W (RPL19B),25.5,0.65598709431213\n+YBL028C,60,0.540653461844549\n+YBL029C-A,2,0.0584438750689197\n+YBL029W,4,0.352468609844477\n+YBL030C (PET9 AAC2 ANC2 OP1),70,0.758870853516898\n+YBL031W (SHE1),57,0.635814710010918\n+YBL032W (HEK2 KHD1),82,0.687525205516002\n+YBL033C (RIB1),41,0.786673372809983\n+YBL034C (STU1),3,0.780953657968117\n+YBL035C (POL12),9,0.735078345800086\n+YBL036C,9,0.516546221938709\n+YBL037W (APL3),67,0.644970987429556\n+YBL038W (MRPL16),68,0.678573732421623\n+YBL039C (URA7),51,0.809398370503164\n+YBL039W-B (YBL039W-A),69,0.201892861103923\n+YBL040C (ERD2),34,0.51366761254049\n+YBL041W (PRE7 PRS3),55,0.605360453248349\n+YBL042C (FUI1),70,0.787600076710142\n+YBL043W (ECM13),53,0.614659989917182\n+YBL045C (C'..b'1),NA,NA\n+YPR019W (MCM4 CDC54 HCD21),NA,NA\n+YPR020W (ATP20),NA,NA\n+YPR021C (AGC1),NA,NA\n+YPR022C,NA,NA\n+YPR023C (EAF3),NA,NA\n+YPR024W (YME1 OSD1 YTA11),NA,NA\n+YPR025C (CCL1),NA,NA\n+YPR026W (ATH1),NA,NA\n+YPR027C,NA,NA\n+YPR028W (YOP1 YIP2),NA,NA\n+YPR029C (APL4),NA,NA\n+YPR030W (CSR2 ART8 MRG19),NA,NA\n+YPR031W (NTO1),NA,NA\n+YPR032W (SRO7 SNI1 SOP1),NA,NA\n+YPR033C (HTS1 TSM4572),NA,NA\n+YPR034W (ARP7 RSC11 SWP61),NA,NA\n+YPR035W (GLN1),NA,NA\n+YPR036W (VMA13 CLS11),NA,NA\n+YPR036W-A,NA,NA\n+YPR037C (ERV2),NA,NA\n+YPR040W (TIP41),NA,NA\n+YPR041W (TIF5 SUI5),NA,NA\n+YPR042C (PUF2),NA,NA\n+YPR043W (RPL43A),NA,NA\n+YPR044C (OPI11),NA,NA\n+YPR045C (THP3 MNI2),NA,NA\n+YPR046W (MCM16),NA,NA\n+YPR047W (MSF1),NA,NA\n+YPR048W (TAH18),NA,NA\n+YPR049C (ATG11 CVT9),NA,NA\n+YPR050C,NA,NA\n+YPR051W (MAK3 NAA30),NA,NA\n+YPR052C (NHP6A),NA,NA\n+YPR053C,NA,NA\n+YPR054W (SMK1),NA,NA\n+YPR055W (SEC8),NA,NA\n+YPR056W (TFB4),NA,NA\n+YPR057W (BRR1),NA,NA\n+YPR058W (YMC1),NA,NA\n+YPR059C,NA,NA\n+YPR060C (ARO7 HGS1 OSM2 TYR7),NA,NA\n+YPR061C (JID1),NA,NA\n+YPR062W (FCY1 yCD),NA,NA\n+YPR063C,NA,NA\n+YPR065W (ROX1 REO1),NA,NA\n+YPR067W (ISA2),NA,NA\n+YPR068C (HOS1),NA,NA\n+YPR069C (SPE3),NA,NA\n+YPR070W (MED1),NA,NA\n+YPR071W,NA,NA\n+YPR072W (NOT5),NA,NA\n+YPR073C (LTP1),NA,NA\n+YPR074C (TKL1),NA,NA\n+YPR075C (OPY2),NA,NA\n+YPR076W,NA,NA\n+YPR077C,NA,NA\n+YPR078C,NA,NA\n+YPR079W (MRL1),NA,NA\n+YPR080W (TEF1 EF-1%20alpha),NA,NA\n+YPR081C (GRS2),NA,NA\n+YPR082C (DIB1 SNU16),NA,NA\n+YPR083W (MDM36),NA,NA\n+YPR084W,NA,NA\n+YPR085C (ASA1),NA,NA\n+YPR086W (SUA7 SOH4),NA,NA\n+YPR088C (SRP54 SRH1),NA,NA\n+YPR089W (YPR090W),NA,NA\n+YPR091C,NA,NA\n+YPR093C (ASR1),NA,NA\n+YPR094W (RDS3),NA,NA\n+YPR095C (SYT1),NA,NA\n+YPR097W,NA,NA\n+YPR098C,NA,NA\n+YPR100W (MRPL51),NA,NA\n+YPR101W (SNT309 NTC25),NA,NA\n+YPR102C (RPL11A),NA,NA\n+YPR103W (PRE2 DOA3 PRG1 SRR2),NA,NA\n+YPR104C (FHL1 SPP42),NA,NA\n+YPR105C (COG4 COD1 SEC38 SGF1),NA,NA\n+YPR106W (ISR1),NA,NA\n+YPR107C (YTH1),NA,NA\n+YPR108W (RPN7),NA,NA\n+YPR109W,NA,NA\n+YPR110C (RPC40 RPC5),NA,NA\n+YPR111W (DBF20),NA,NA\n+YPR112C (MRD1),NA,NA\n+YPR113W (PIS1),NA,NA\n+YPR114W,NA,NA\n+YPR115W (RGC1 GCA1),NA,NA\n+YPR116W (RRG8),NA,NA\n+YPR117W,NA,NA\n+YPR118W (MRI1),NA,NA\n+YPR119W (CLB2),NA,NA\n+YPR120C (CLB5),NA,NA\n+YPR121W (THI22),NA,NA\n+YPR122W (AXL1 FUS5 STE22),NA,NA\n+YPR124W (CTR1),NA,NA\n+YPR125W (YLH47 MRS7),NA,NA\n+YPR126C,NA,NA\n+YPR127W,NA,NA\n+YPR128C (ANT1),NA,NA\n+YPR129W (SCD6 LSM13),NA,NA\n+YPR131C (NAT3 NAA20),NA,NA\n+YPR132W (RPS23B),NA,NA\n+YPR133C (SPN1 IWS1),NA,NA\n+YPR133W-A (TOM5 MOM8A),NA,NA\n+YPR134W (MSS18),NA,NA\n+YPR135W (CTF4 CHL15 POB1),NA,NA\n+YPR137W (RRP9),NA,NA\n+YPR138C (MEP3),NA,NA\n+YPR139C (VPS66),NA,NA\n+YPR140W (TAZ1),NA,NA\n+YPR141C (KAR3 OSR11),NA,NA\n+YPR143W (RRP15),NA,NA\n+YPR144C (NOC4 UTP19),NA,NA\n+YPR145C-A,NA,NA\n+YPR145W (ASN1),NA,NA\n+YPR147C,NA,NA\n+YPR148C,NA,NA\n+YPR149W (NCE102 NCE2),NA,NA\n+YPR150W,NA,NA\n+YPR151C (SUE1),NA,NA\n+YPR152C (URN1),NA,NA\n+YPR153W,NA,NA\n+YPR154W (PIN3 LSB2),NA,NA\n+YPR155C (NCA2),NA,NA\n+YPR156C (TPO3),NA,NA\n+YPR157W,NA,NA\n+YPR158W (CUR1),NA,NA\n+YPR159W (KRE6 CWH48),NA,NA\n+YPR160W (GPH1),NA,NA\n+YPR161C (SGV1 BUR1),NA,NA\n+YPR162C (ORC4),NA,NA\n+YPR163C (TIF3 RBL3 STM1),NA,NA\n+YPR164W (MMS1 RTT108 SLM6),NA,NA\n+YPR165W (RHO1),NA,NA\n+YPR166C (MRP2),NA,NA\n+YPR167C (MET16),NA,NA\n+YPR169W (JIP5),NA,NA\n+YPR169W-A,NA,NA\n+YPR170C,NA,NA\n+YPR170W-A,NA,NA\n+YPR170W-B,NA,NA\n+YPR171W (BSP1),NA,NA\n+YPR172W,NA,NA\n+YPR173C (VPS4 CSC1 DID6 END13 GRD13 VPL4 VPT10),NA,NA\n+YPR174C,NA,NA\n+YPR175W (DPB2),NA,NA\n+YPR176C (BET2),NA,NA\n+YPR178W (PRP4 RNA4),NA,NA\n+YPR179C (HDA3 PLO1),NA,NA\n+YPR180W (AOS1 RHC31),NA,NA\n+YPR181C (SEC23),NA,NA\n+YPR182W (SMX3),NA,NA\n+YPR183W (DPM1 SED3),NA,NA\n+YPR184W (GDB1),NA,NA\n+YPR185W (ATG13 APG13),NA,NA\n+YPR186C (PZF1 TFC2),NA,NA\n+YPR187W (RPO26 RPB6),NA,NA\n+YPR188C (MLC2),NA,NA\n+YPR189W (SKI3 SKI5),NA,NA\n+YPR190C (RPC82 RPC3),NA,NA\n+YPR191W (QCR2 COR2 UCR2),NA,NA\n+YPR192W (AQY1),NA,NA\n+YPR193C (HPA2),NA,NA\n+YPR194C (OPT2),NA,NA\n+YPR195C,NA,NA\n+YPR196W,NA,NA\n+YPR198W (SGE1 NOR1),NA,NA\n+YPR199C (ARR1 ACR1 YAP8),NA,NA\n+YPR201W (ARR3 ACR3),NA,NA\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/P__stats__cellcycleM_chrII.gw.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/P__stats__cellcycleM_chrII.gw.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +Type,Count +Phased genes,118 +Not-phased genes,138 +Other genes,131 |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/STF__cellcycleM_chrII.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/STF__cellcycleM_chrII.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,4856 @@\n+chrII\tnucleR\tStiffness estimation\t 1604\t 1750\t0.171287013248063\t*\t.\tnucleR_class=F;k.chrII=129;gauss_sd=59.9853027808279;gauss_m=1691.51461988304\n+chrII\tnucleR\tStiffness estimation\t 1700\t 1846\t0.0778687448224189\t*\t.\tnucleR_class=F;k.chrII=129;gauss_sd=88.966291255314;gauss_m=1770.03212851406\n+chrII\tnucleR\tStiffness estimation\t 1770\t 1916\t0.0929606973513573\t*\t.\tnucleR_class=F;k.chrII=157;gauss_sd=81.4249287385646;gauss_m=1862.416\n+chrII\tnucleR\tStiffness estimation\t 1868\t 2080\t0.0799728957279602\t*\t.\tnucleR_class=F;k.chrII=161;gauss_sd=87.7881026559271;gauss_m=1943.059566787\n+chrII\tnucleR\tStiffness estimation\t 2059\t 2205\t0.176066692915104\t*\t.\tnucleR_class=F;k.chrII=73;gauss_sd=59.1654906194994;gauss_m=2055.12987012987\n+chrII\tnucleR\tStiffness estimation\t 5856\t 6002\t0.26213857792046\t*\t.\tnucleR_class=F;k.chrII=96;gauss_sd=48.4888187287537;gauss_m=6012.73148148148\n+chrII\tnucleR\tStiffness estimation\t 5960\t 6106\t0.167305958540268\t*\t.\tnucleR_class=W;k.chrII=110;gauss_sd=60.6947838870543;gauss_m=6049.29370629371\n+chrII\tnucleR\tStiffness estimation\t 6113\t 6259\t0.126486205841288\t*\t.\tnucleR_class=W;k.chrII=93;gauss_sd=69.8048327578829;gauss_m=6152.10211267606\n+chrII\tnucleR\tStiffness estimation\t 6592\t 6738\t0.235729313563203\t*\t.\tnucleR_class=W;k.chrII=41;gauss_sd=51.1328827438375;gauss_m=6685.19791666667\n+chrII\tnucleR\tStiffness estimation\t 6756\t 6968\t0.115859982374092\t*\t.\tnucleR_class=F;k.chrII=70;gauss_sd=72.9357317625726;gauss_m=6876.59677419355\n+chrII\tnucleR\tStiffness estimation\t 6913\t 7059\t0.0882017243942026\t*\t.\tnucleR_class=W;k.chrII=34;gauss_sd=83.592735171046;gauss_m=6962.74107142857\n+chrII\tnucleR\tStiffness estimation\t 7086\t 7232\t0.189221731160958\t*\t.\tnucleR_class=F;k.chrII=25;gauss_sd=57.0717997138748;gauss_m=7131.40322580645\n+chrII\tnucleR\tStiffness estimation\t 7307\t 7453\t0.846283969590719\t*\t.\tnucleR_class=F;k.chrII=17;gauss_sd=26.9866524742271;gauss_m=7372.17647058824\n+chrII\tnucleR\tStiffness estimation\t 8281\t 8427\t0.464949627047333\t*\t.\tnucleR_class=F;k.chrII=65;gauss_sd=36.4086119226317;gauss_m=8449.35915492958\n+chrII\tnucleR\tStiffness estimation\t 8390\t 8536\t0.337912617334092\t*\t.\tnucleR_class=W;k.chrII=74;gauss_sd=42.7075707990642;gauss_m=8462.90476190476\n+chrII\tnucleR\tStiffness estimation\t 8585\t 8731\t0.122860780671672\t*\t.\tnucleR_class=W;k.chrII=55;gauss_sd=70.8272595435151;gauss_m=8685.24074074074\n+chrII\tnucleR\tStiffness estimation\t 8727\t 8873\t0.174228125640712\t*\t.\tnucleR_class=W;k.chrII=47;gauss_sd=59.4768475266222;gauss_m=8789.14285714286\n+chrII\tnucleR\tStiffness estimation\t 8883\t 9029\t0.439225959750987\t*\t.\tnucleR_class=W;k.chrII=34;gauss_sd=37.4595946342019;gauss_m=8942.01388888889\n+chrII\tnucleR\tStiffness estimation\t 9059\t 9205\t0.615408719530882\t*\t.\tnucleR_class=F;k.chrII=16;gauss_sd=31.6464683390317;gauss_m=9125.21875\n+chrII\tnucleR\tStiffness estimation\t 9366\t 9512\t0.883174906848997\t*\t.\tnucleR_class=W;k.chrII=43;gauss_sd=26.4170131895827;gauss_m=9443.27777777778\n+chrII\tnucleR\tStiffness estimation\t 9736\t 9882\t0.25663895908982\t*\t.\tnucleR_class=W;k.chrII=44;gauss_sd=49.0056079223913;gauss_m=9828.01960784314\n+chrII\tnucleR\tStiffness estimation\t 9914\t 10060\t0.20118063423879\t*\t.\tnucleR_class=W;k.chrII=42;gauss_sd=55.34953633681;gauss_m=9983.20192307692\n+chrII\tnucleR\tStiffness estimation\t 10072\t 10253\t0.169981495167321\t*\t.\tnucleR_class=F;k.chrII=60;gauss_sd=60.2152163551851;gauss_m=10173.1842105263\n+chrII\tnucleR\tStiffness estimation\t 10236\t 10382\t0.0870436968174149\t*\t.\tnucleR_class=F;k.chrII=35;gauss_sd=84.1469559525384;gauss_m=10256.9019607843\n+chrII\tnucleR\tStiffness estimation\t 10428\t 10574\t0.348184787275007\t*\t.\tnucleR_class=W;k.chrII=69;gauss_sd=42.072873788434;gauss_m=10488.7012987013\n+chrII\tnucleR\tStiffness estimation\t 10706\t 10852\t0.117470754475156\t*\t.\tnucleR_class=F;k.chrII=23;gauss_sd=72.4339542693372;gauss_m=10812.6142857143\n+chrII\tnucleR\tStiffness estimation\t 10865\t 11011\t0.314765259840438\t*\t.\tnucleR_class=W;k.chrII=76;gauss_sd=44.2500409223469;gauss_m=10934.511904761'..b'8213924153;gauss_m=802937.653846154\n+chrII\tnucleR\tStiffness estimation\t803010\t803207\t0.0872246878042238\t*\t.\tnucleR_class=F;k.chrII=77;gauss_sd=84.0596082666074;gauss_m=803103.42\n+chrII\tnucleR\tStiffness estimation\t803159\t803305\t0.079813257723264\t*\t.\tnucleR_class=F;k.chrII=56;gauss_sd=87.8758532206824;gauss_m=803234.172897196\n+chrII\tnucleR\tStiffness estimation\t803257\t803464\t0.0818131005500517\t*\t.\tnucleR_class=F;k.chrII=63;gauss_sd=86.7951879035538;gauss_m=803363.004201681\n+chrII\tnucleR\tStiffness estimation\t803406\t803552\t0.0878491396189522\t*\t.\tnucleR_class=F;k.chrII=48;gauss_sd=83.7603179833568;gauss_m=803458.517441861\n+chrII\tnucleR\tStiffness estimation\t803535\t803681\t0.107658254499785\t*\t.\tnucleR_class=F;k.chrII=39;gauss_sd=75.6629738119022;gauss_m=803600.28030303\n+chrII\tnucleR\tStiffness estimation\t803610\t803756\t0.100775911055734\t*\t.\tnucleR_class=F;k.chrII=39;gauss_sd=78.2039531924754;gauss_m=803677.809523809\n+chrII\tnucleR\tStiffness estimation\t803689\t803835\t0.0829027609519688\t*\t.\tnucleR_class=F;k.chrII=44;gauss_sd=86.2228902220612;gauss_m=803786.598684211\n+chrII\tnucleR\tStiffness estimation\t803775\t803921\t0.154673929428804\t*\t.\tnucleR_class=F;k.chrII=57;gauss_sd=63.1245818458975;gauss_m=803870.435064935\n+chrII\tnucleR\tStiffness estimation\t803926\t804072\t0.145214982903291\t*\t.\tnucleR_class=F;k.chrII=51;gauss_sd=65.1480407872489;gauss_m=803964.856164384\n+chrII\tnucleR\tStiffness estimation\t804110\t804256\t0.160190058209618\t*\t.\tnucleR_class=W;k.chrII=76;gauss_sd=62.0282164959036;gauss_m=804194.576086957\n+chrII\tnucleR\tStiffness estimation\t804293\t804439\t0.248891858307867\t*\t.\tnucleR_class=W;k.chrII=77;gauss_sd=49.7624470495939;gauss_m=804367.5\n+chrII\tnucleR\tStiffness estimation\t804446\t804592\t0.0890275482536271\t*\t.\tnucleR_class=W;k.chrII=46;gauss_sd=83.2041267490654;gauss_m=804513.528571429\n+chrII\tnucleR\tStiffness estimation\t804616\t804762\t0.216995930487667\t*\t.\tnucleR_class=W;k.chrII=50;gauss_sd=53.2943634093125;gauss_m=804684.482758621\n+chrII\tnucleR\tStiffness estimation\t804772\t804918\t0.221652231000117\t*\t.\tnucleR_class=W;k.chrII=45;gauss_sd=52.7316086329595;gauss_m=804828.25\n+chrII\tnucleR\tStiffness estimation\t805258\t805404\t0.279091588656617\t*\t.\tnucleR_class=F;k.chrII=17;gauss_sd=46.9930572156206;gauss_m=805310.235294118\n+chrII\tnucleR\tStiffness estimation\t807477\t807623\t0.624350856132532\t*\t.\tnucleR_class=W;k.chrII=38;gauss_sd=31.4190260142085;gauss_m=807559.217948718\n+chrII\tnucleR\tStiffness estimation\t807659\t807805\t0.153404528749141\t*\t.\tnucleR_class=W;k.chrII=60;gauss_sd=63.3852172494957;gauss_m=807749.493333333\n+chrII\tnucleR\tStiffness estimation\t807812\t807958\t0.152032186983978\t*\t.\tnucleR_class=F;k.chrII=40;gauss_sd=63.6706527389348;gauss_m=807863.772727273\n+chrII\tnucleR\tStiffness estimation\t807975\t808121\t0.193057774608677\t*\t.\tnucleR_class=W;k.chrII=40;gauss_sd=56.5019486042599;gauss_m=808035.568627451\n+chrII\tnucleR\tStiffness estimation\t808171\t808317\t0.200012285781477\t*\t.\tnucleR_class=F;k.chrII=26;gauss_sd=55.5109598788083;gauss_m=808236.5\n+chrII\tnucleR\tStiffness estimation\t808352\t808498\t0.562561957976046\t*\t.\tnucleR_class=W;k.chrII=53;gauss_sd=33.0995350538224;gauss_m=808429.857142857\n+chrII\tnucleR\tStiffness estimation\t808502\t808709\t0.0613448802207351\t*\t.\tnucleR_class=F;k.chrII=27;gauss_sd=100.234657841752;gauss_m=808582.41\n+chrII\tnucleR\tStiffness estimation\t808722\t808868\t0.319394760333917\t*\t.\tnucleR_class=W;k.chrII=28;gauss_sd=43.9281769376335;gauss_m=808777.551724138\n+chrII\tnucleR\tStiffness estimation\t809289\t809435\t1.44114315185158\t*\t.\tnucleR_class=W;k.chrII=69;gauss_sd=20.6801418063837;gauss_m=809357.528985507\n+chrII\tnucleR\tStiffness estimation\t809607\t809753\t0.554081915535382\t*\t.\tnucleR_class=W;k.chrII=33;gauss_sd=33.3518620517249;gauss_m=809676.823529412\n+chrII\tnucleR\tStiffness estimation\t809911\t810057\t0.252814159026492\t*\t.\tnucleR_class=F;k.chrII=19;gauss_sd=49.3749168208635;gauss_m=810004.782608696\n+chrII\tnucleR\tStiffness estimation\t810075\t810221\t0.246352731009941\t*\t.\tnucleR_class=W;k.chrII=57;gauss_sd=50.0182373499813;gauss_m=810152.553030303\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/STF__stats__cellcycleM_chrII.genes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/STF__stats__cellcycleM_chrII.genes.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,5681 @@\n+Name,Mean_STF,StdDev_STF\n+Q0080 (ATP8 AAP1),NA,NA\n+Q0085 (ATP6 OLI2 OLI4 PHO1),NA,NA\n+Q0130 (OLI1 ATP9 OLI3),NA,NA\n+Q0275 (COX3 OXI2),NA,NA\n+YAL001C (TFC3 FUN24 TSV115),NA,NA\n+YAL002W (VPS8 FUN15 VPL8 VPT8),NA,NA\n+YAL003W (EFB1 TEF5),NA,NA\n+YAL004W,NA,NA\n+YAL005C (SSA1 YG100),NA,NA\n+YAL007C (ERP2),NA,NA\n+YAL008W (FUN14),NA,NA\n+YAL009W (SPO7),NA,NA\n+YAL010C (MDM10 FUN37),NA,NA\n+YAL011W (SWC3 SWC1),NA,NA\n+YAL012W (CYS3 CYI1 FUN35 STR1),NA,NA\n+YAL013W (DEP1 FUN54),NA,NA\n+YAL014C (SYN8 SLT2 UIP2),NA,NA\n+YAL015C (NTG1 FUN33 SCR1 ogg2),NA,NA\n+YAL016C-B,NA,NA\n+YAL016W (TPD3 FUN32),NA,NA\n+YAL017W (PSK1 FUN31),NA,NA\n+YAL018C,NA,NA\n+YAL019W (FUN30),NA,NA\n+YAL020C (ATS1 FUN28 KTI13),NA,NA\n+YAL021C (CCR4 FUN27 NUT21),NA,NA\n+YAL022C (FUN26),NA,NA\n+YAL023C (PMT2 FUN25),NA,NA\n+YAL024C (LTE1 MSI2),NA,NA\n+YAL025C (MAK16),NA,NA\n+YAL026C (DRS2 FUN38 SWA3),NA,NA\n+YAL027W (SAW1),NA,NA\n+YAL028W (FRT2 HPH2),NA,NA\n+YAL029C (MYO4 FUN22 SHE1),NA,NA\n+YAL030W (SNC1),NA,NA\n+YAL031C (GIP4 FUN21),NA,NA\n+YAL032C (PRP45 FUN20),NA,NA\n+YAL033W (POP5 FUN53),NA,NA\n+YAL034C (FUN19),NA,NA\n+YAL034C-B (YAL035C-A),NA,NA\n+YAL034W-A (MTW1 DSN3 NSL2),NA,NA\n+YAL035W (FUN12 yIF2),NA,NA\n+YAL036C (RBG1 FUN11),NA,NA\n+YAL037C-A,NA,NA\n+YAL037C-B,NA,NA\n+YAL037W,NA,NA\n+YAL038W (CDC19 PYK1),NA,NA\n+YAL039C (CYC3),NA,NA\n+YAL040C (CLN3 DAF1 FUN10 WHI1),NA,NA\n+YAL041W (CDC24 CLS4),NA,NA\n+YAL042W (ERV46 FUN9),NA,NA\n+YAL043C (PTA1 FUN39),NA,NA\n+YAL044C (GCV3),NA,NA\n+YAL044W-A,NA,NA\n+YAL045C,NA,NA\n+YAL046C (AIM1),NA,NA\n+YAL047C (SPC72 LDB4),NA,NA\n+YAL047W-A,NA,NA\n+YAL048C (GEM1 GON1),NA,NA\n+YAL049C (AIM2),NA,NA\n+YAL051W (OAF1 YAF1),NA,NA\n+YAL053W (FLC2 HUF2),NA,NA\n+YAL054C (ACS1 FUN44),NA,NA\n+YAL055W (PEX22 YAF5),NA,NA\n+YAL056W (GPB2 KRH1),NA,NA\n+YAL058W (CNE1 FUN48),NA,NA\n+YAL059W (ECM1),NA,NA\n+YAL060W (BDH1 BDH),NA,NA\n+YAL061W (BDH2),NA,NA\n+YAL062W (GDH3 FUN51),NA,NA\n+YAL064W-B,NA,NA\n+YAL067C (SEO1),NA,NA\n+YAR002C-A (ERP1),NA,NA\n+YAR002W (NUP60),NA,NA\n+YAR003W (SWD1 CPS50 FUN16 SAF49),NA,NA\n+YAR007C (RFA1 BUF2 FUN3 RPA1),NA,NA\n+YAR008W (SEN34 FUN4),NA,NA\n+YAR014C (BUD14),NA,NA\n+YAR015W (ADE1),NA,NA\n+YAR018C (KIN3 FUN52 NPK1),NA,NA\n+YAR019C (CDC15 LYT1),NA,NA\n+YAR023C,NA,NA\n+YAR027W (UIP3),NA,NA\n+YAR028W,NA,NA\n+YAR029W,NA,NA\n+YAR033W (MST28),NA,NA\n+YAR035W (YAT1),NA,NA\n+YAR042W (SWH1 OSH1 YAR044W),NA,NA\n+YAR066W,NA,NA\n+YBL001C (ECM15),0.3369411758228,0.100615077867832\n+YBL002W (HTB2),0.213710366326179,0.131151391750773\n+YBL003C (HTA2 H2A2),0.156460236777274,0.0717510350855517\n+YBL004W (UTP20),0.116326701052992,0.0418018350724186\n+YBL005W (PDR3 AMY2 TPE2),0.134920655083122,0.0438512962087054\n+YBL006C (LDB7 RSC14),0.165874720912654,0.0690080665165947\n+YBL007C (SLA1),0.130978609539888,0.0537530558213459\n+YBL008W (HIR1),0.145438488779706,0.0646874638976448\n+YBL009W (ALK2),0.145316801517486,0.0898470870985948\n+YBL010C,0.180186147594529,0.110486833113724\n+YBL011W (SCT1 GAT2),0.124306283612217,0.0468689760692884\n+YBL014C (RRN6),0.15410596481712,0.119717904776735\n+YBL015W (ACH1),0.119187674655864,0.0344531509832448\n+YBL016W (FUS3 DAC2),0.182637891161528,0.0753806720438713\n+YBL017C (PEP1 VPS10 VPT1),0.138245268209903,0.0825478286204092\n+YBL018C (POP8),0.135662716961552,0.0552393790508817\n+YBL019W (APN2 ETH1),0.175073629705323,0.126265300513864\n+YBL020W (RFT1),0.196033278965994,0.0964425732935458\n+YBL021C (HAP3),0.168394121009678,0.0861697214027815\n+YBL022C (PIM1 LON1),0.149045087748445,0.115957596784023\n+YBL023C (MCM2),0.127984551820798,0.0370044009835167\n+YBL024W (NCL1 TRM4),0.135485491942239,0.0725727932306564\n+YBL025W (RRN10),0.135532557689103,0.0590450749529365\n+YBL026W (LSM2 SMX5 SNP3),0.286037631306212,0.272568874739717\n+YBL027W (RPL19B),0.115126308998334,0.0599624292952761\n+YBL028C,0.177467451636151,0.0309971811400936\n+YBL029C-A,0.247487322389232,0.117414578594309\n+YBL029W,0.230914365084067,0.195685302431977\n+YBL030C (PET9 AAC2 ANC2 OP1),0.122939445980811,0.0390871106712527\n+YBL031W (SHE1),0.293537297603728,0.265098586482323\n+YBL032W (HEK2 KHD1),0.158739995277577,0.07'..b'1),NA,NA\n+YPR019W (MCM4 CDC54 HCD21),NA,NA\n+YPR020W (ATP20),NA,NA\n+YPR021C (AGC1),NA,NA\n+YPR022C,NA,NA\n+YPR023C (EAF3),NA,NA\n+YPR024W (YME1 OSD1 YTA11),NA,NA\n+YPR025C (CCL1),NA,NA\n+YPR026W (ATH1),NA,NA\n+YPR027C,NA,NA\n+YPR028W (YOP1 YIP2),NA,NA\n+YPR029C (APL4),NA,NA\n+YPR030W (CSR2 ART8 MRG19),NA,NA\n+YPR031W (NTO1),NA,NA\n+YPR032W (SRO7 SNI1 SOP1),NA,NA\n+YPR033C (HTS1 TSM4572),NA,NA\n+YPR034W (ARP7 RSC11 SWP61),NA,NA\n+YPR035W (GLN1),NA,NA\n+YPR036W (VMA13 CLS11),NA,NA\n+YPR036W-A,NA,NA\n+YPR037C (ERV2),NA,NA\n+YPR040W (TIP41),NA,NA\n+YPR041W (TIF5 SUI5),NA,NA\n+YPR042C (PUF2),NA,NA\n+YPR043W (RPL43A),NA,NA\n+YPR044C (OPI11),NA,NA\n+YPR045C (THP3 MNI2),NA,NA\n+YPR046W (MCM16),NA,NA\n+YPR047W (MSF1),NA,NA\n+YPR048W (TAH18),NA,NA\n+YPR049C (ATG11 CVT9),NA,NA\n+YPR050C,NA,NA\n+YPR051W (MAK3 NAA30),NA,NA\n+YPR052C (NHP6A),NA,NA\n+YPR053C,NA,NA\n+YPR054W (SMK1),NA,NA\n+YPR055W (SEC8),NA,NA\n+YPR056W (TFB4),NA,NA\n+YPR057W (BRR1),NA,NA\n+YPR058W (YMC1),NA,NA\n+YPR059C,NA,NA\n+YPR060C (ARO7 HGS1 OSM2 TYR7),NA,NA\n+YPR061C (JID1),NA,NA\n+YPR062W (FCY1 yCD),NA,NA\n+YPR063C,NA,NA\n+YPR065W (ROX1 REO1),NA,NA\n+YPR067W (ISA2),NA,NA\n+YPR068C (HOS1),NA,NA\n+YPR069C (SPE3),NA,NA\n+YPR070W (MED1),NA,NA\n+YPR071W,NA,NA\n+YPR072W (NOT5),NA,NA\n+YPR073C (LTP1),NA,NA\n+YPR074C (TKL1),NA,NA\n+YPR075C (OPY2),NA,NA\n+YPR076W,NA,NA\n+YPR077C,NA,NA\n+YPR078C,NA,NA\n+YPR079W (MRL1),NA,NA\n+YPR080W (TEF1 EF-1%20alpha),NA,NA\n+YPR081C (GRS2),NA,NA\n+YPR082C (DIB1 SNU16),NA,NA\n+YPR083W (MDM36),NA,NA\n+YPR084W,NA,NA\n+YPR085C (ASA1),NA,NA\n+YPR086W (SUA7 SOH4),NA,NA\n+YPR088C (SRP54 SRH1),NA,NA\n+YPR089W (YPR090W),NA,NA\n+YPR091C,NA,NA\n+YPR093C (ASR1),NA,NA\n+YPR094W (RDS3),NA,NA\n+YPR095C (SYT1),NA,NA\n+YPR097W,NA,NA\n+YPR098C,NA,NA\n+YPR100W (MRPL51),NA,NA\n+YPR101W (SNT309 NTC25),NA,NA\n+YPR102C (RPL11A),NA,NA\n+YPR103W (PRE2 DOA3 PRG1 SRR2),NA,NA\n+YPR104C (FHL1 SPP42),NA,NA\n+YPR105C (COG4 COD1 SEC38 SGF1),NA,NA\n+YPR106W (ISR1),NA,NA\n+YPR107C (YTH1),NA,NA\n+YPR108W (RPN7),NA,NA\n+YPR109W,NA,NA\n+YPR110C (RPC40 RPC5),NA,NA\n+YPR111W (DBF20),NA,NA\n+YPR112C (MRD1),NA,NA\n+YPR113W (PIS1),NA,NA\n+YPR114W,NA,NA\n+YPR115W (RGC1 GCA1),NA,NA\n+YPR116W (RRG8),NA,NA\n+YPR117W,NA,NA\n+YPR118W (MRI1),NA,NA\n+YPR119W (CLB2),NA,NA\n+YPR120C (CLB5),NA,NA\n+YPR121W (THI22),NA,NA\n+YPR122W (AXL1 FUS5 STE22),NA,NA\n+YPR124W (CTR1),NA,NA\n+YPR125W (YLH47 MRS7),NA,NA\n+YPR126C,NA,NA\n+YPR127W,NA,NA\n+YPR128C (ANT1),NA,NA\n+YPR129W (SCD6 LSM13),NA,NA\n+YPR131C (NAT3 NAA20),NA,NA\n+YPR132W (RPS23B),NA,NA\n+YPR133C (SPN1 IWS1),NA,NA\n+YPR133W-A (TOM5 MOM8A),NA,NA\n+YPR134W (MSS18),NA,NA\n+YPR135W (CTF4 CHL15 POB1),NA,NA\n+YPR137W (RRP9),NA,NA\n+YPR138C (MEP3),NA,NA\n+YPR139C (VPS66),NA,NA\n+YPR140W (TAZ1),NA,NA\n+YPR141C (KAR3 OSR11),NA,NA\n+YPR143W (RRP15),NA,NA\n+YPR144C (NOC4 UTP19),NA,NA\n+YPR145C-A,NA,NA\n+YPR145W (ASN1),NA,NA\n+YPR147C,NA,NA\n+YPR148C,NA,NA\n+YPR149W (NCE102 NCE2),NA,NA\n+YPR150W,NA,NA\n+YPR151C (SUE1),NA,NA\n+YPR152C (URN1),NA,NA\n+YPR153W,NA,NA\n+YPR154W (PIN3 LSB2),NA,NA\n+YPR155C (NCA2),NA,NA\n+YPR156C (TPO3),NA,NA\n+YPR157W,NA,NA\n+YPR158W (CUR1),NA,NA\n+YPR159W (KRE6 CWH48),NA,NA\n+YPR160W (GPH1),NA,NA\n+YPR161C (SGV1 BUR1),NA,NA\n+YPR162C (ORC4),NA,NA\n+YPR163C (TIF3 RBL3 STM1),NA,NA\n+YPR164W (MMS1 RTT108 SLM6),NA,NA\n+YPR165W (RHO1),NA,NA\n+YPR166C (MRP2),NA,NA\n+YPR167C (MET16),NA,NA\n+YPR169W (JIP5),NA,NA\n+YPR169W-A,NA,NA\n+YPR170C,NA,NA\n+YPR170W-A,NA,NA\n+YPR170W-B,NA,NA\n+YPR171W (BSP1),NA,NA\n+YPR172W,NA,NA\n+YPR173C (VPS4 CSC1 DID6 END13 GRD13 VPL4 VPT10),NA,NA\n+YPR174C,NA,NA\n+YPR175W (DPB2),NA,NA\n+YPR176C (BET2),NA,NA\n+YPR178W (PRP4 RNA4),NA,NA\n+YPR179C (HDA3 PLO1),NA,NA\n+YPR180W (AOS1 RHC31),NA,NA\n+YPR181C (SEC23),NA,NA\n+YPR182W (SMX3),NA,NA\n+YPR183W (DPM1 SED3),NA,NA\n+YPR184W (GDB1),NA,NA\n+YPR185W (ATG13 APG13),NA,NA\n+YPR186C (PZF1 TFC2),NA,NA\n+YPR187W (RPO26 RPB6),NA,NA\n+YPR188C (MLC2),NA,NA\n+YPR189W (SKI3 SKI5),NA,NA\n+YPR190C (RPC82 RPC3),NA,NA\n+YPR191W (QCR2 COR2 UCR2),NA,NA\n+YPR192W (AQY1),NA,NA\n+YPR193C (HPA2),NA,NA\n+YPR194C (OPT2),NA,NA\n+YPR195C,NA,NA\n+YPR196W,NA,NA\n+YPR198W (SGE1 NOR1),NA,NA\n+YPR199C (ARR1 ACR1 YAP8),NA,NA\n+YPR201W (ARR3 ACR3),NA,NA\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/STF__stats__cellcycleM_chrII.gw.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/STF__stats__cellcycleM_chrII.gw.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Statistic,Value +Mean stiffness,0.1681 +Std. Dev. stiffness,0.1499 |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/STF__stats__cellcycleM_chrII.gw2.png |
| b |
| Binary file test-data/STF__stats__cellcycleM_chrII.gw2.png has changed |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/TSS__cellcycleM_chrII.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TSS__cellcycleM_chrII.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,389 @@\n+chrII\tnucleR\tTSS classification\t237471\t237729\t.\t-\t.\tid=YBL001C (ECM15);TSS_position=237512;nucleosome_plus1=237471;nucleosome_minus1=237729;distance=258;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t235927\t236547\t.\t+\t.\tid=YBL002W (HTB2);TSS_position=236439;nucleosome_plus1=236547;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t235732\t235927\t.\t-\t.\tid=YBL003C (HTA2 H2A2);TSS_position=235827;nucleosome_plus1=235732;nucleosome_minus1=235927;distance=195;classification=W-close-W\n+chrII\tnucleR\tTSS classification\t227275\t227593\t.\t+\t.\tid=YBL004W (UTP20);TSS_position=227535;nucleosome_plus1=227593;nucleosome_minus1=227275;distance=318;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t217109\t217419\t.\t+\t.\tid=YBL005W (PDR3 AMY2 TPE2);TSS_position=217408;nucleosome_plus1=217419;nucleosome_minus1=217109;distance=310;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t217109\t217419\t.\t-\t.\tid=YBL006C (LDB7 RSC14);TSS_position=217150;nucleosome_plus1=217109;nucleosome_minus1=217419;distance=310;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t216367\t216652\t.\t-\t.\tid=YBL007C (SLA1);TSS_position=216418;nucleosome_plus1=216367;nucleosome_minus1=216652;distance=285;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t209402\t209623\t.\t+\t.\tid=YBL008W (HIR1);TSS_position=209588;nucleosome_plus1=209623;nucleosome_minus1=209402;distance=221;classification=W-open-F\n+chrII\tnucleR\tTSS classification\t206905\t207212\t.\t+\t.\tid=YBL009W (ALK2);TSS_position=207160;nucleosome_plus1=207212;nucleosome_minus1=206905;distance=307;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t206905\t207212\t.\t-\t.\tid=YBL010C;TSS_position=206969;nucleosome_plus1=206905;nucleosome_minus1=207212;distance=307;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t203078\t203428\t.\t+\t.\tid=YBL011W (SCT1 GAT2);TSS_position=203445;nucleosome_plus1=203428;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t201728\t202045\t.\t-\t.\tid=YBL014C (RRN6);TSS_position=201777;nucleosome_plus1=201728;nucleosome_minus1=202045;distance=317;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t193915\t194110\t.\t+\t.\tid=YBL015W (ACH1);TSS_position=194037;nucleosome_plus1=194110;nucleosome_minus1=193915;distance=195;classification=F-close-F\n+chrII\tnucleR\tTSS classification\t192400\t192558\t.\t+\t.\tid=YBL016W (FUS3 DAC2);TSS_position=192430;nucleosome_plus1=192558;nucleosome_minus1=192400;distance=158;classification=W-close-W\n+chrII\tnucleR\tTSS classification\t191720\t191996\t.\t-\t.\tid=YBL017C (PEP1 VPS10 VPT1);TSS_position=191767;nucleosome_plus1=191720;nucleosome_minus1=191996;distance=276;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t186470\t186747\t.\t-\t.\tid=YBL018C (POP8);TSS_position=186515;nucleosome_plus1=186470;nucleosome_minus1=186747;distance=277;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t183983\t184356\t.\t+\t.\tid=YBL019W (APN2 ETH1);TSS_position=184307;nucleosome_plus1=184356;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t182064\t182353\t.\t+\t.\tid=YBL020W (RFT1);TSS_position=182342;nucleosome_plus1=182353;nucleosome_minus1=182064;distance=289;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t182064\t182353\t.\t-\t.\tid=YBL021C (HAP3);TSS_position=182126;nucleosome_plus1=182064;nucleosome_minus1=182353;distance=289;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t181363\t181623\t.\t-\t.\tid=YBL022C (PIM1 LON1);TSS_position=181394;nucleosome_plus1=181363;nucleosome_minus1=181623;distance=260;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t177564\t177830\t.\t-\t.\tid=YBL023C (MCM2);TSS_position=177601;nucleosome_plus1=177564;nucleosome_minus1=177830;distance=266;classification=F-open-W\n+chrII\tnucleR\tTSS classification\t172239\t172550\t.\t+\t.\tid=YBL024W (NCL1 TRM4);TSS_position=172511;nucleosome_plus1=172550;nucleosome_minus1=172239;distance=311;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t171225\t1'..b'osome_minus1=760327;distance=251;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t760845\t761264\t.\t-\t.\tid=YBR277C;TSS_position=761048;nucleosome_plus1=760845;nucleosome_minus1=761264;distance=419;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t760076\t760327\t.\t+\t.\tid=YBR278W (DPB3);TSS_position=760269;nucleosome_plus1=760327;nucleosome_minus1=760076;distance=251;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t760845\t761264\t.\t+\t.\tid=YBR279W (PAF1);TSS_position=761219;nucleosome_plus1=761264;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t764675\t764975\t.\t-\t.\tid=YBR280C (SAF1);TSS_position=764720;nucleosome_plus1=764675;nucleosome_minus1=764975;distance=300;classification=F-open-W\n+chrII\tnucleR\tTSS classification\t767602\t767866\t.\t-\t.\tid=YBR281C (DUG2);TSS_position=767647;nucleosome_plus1=767602;nucleosome_minus1=767866;distance=264;classification=F-open-W\n+chrII\tnucleR\tTSS classification\t768013\t768242\t.\t+\t.\tid=YBR282W (MRPL27);TSS_position=768209;nucleosome_plus1=768242;nucleosome_minus1=768013;distance=229;classification=F-open-W\n+chrII\tnucleR\tTSS classification\t770545\t770893\t.\t-\t.\tid=YBR283C (SSH1);TSS_position=770559;nucleosome_plus1=770545;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t770545\t770893\t.\t+\t.\tid=YBR284W;TSS_position=770878;nucleosome_plus1=770893;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t773572\t773962\t.\t+\t.\tid=YBR285W;TSS_position=773867;nucleosome_plus1=773962;nucleosome_minus1=773572;distance=390;classification=W-open-F\n+chrII\tnucleR\tTSS classification\t774298\t774740\t.\t+\t.\tid=YBR286W (APE3 APY1);TSS_position=774680;nucleosome_plus1=774740;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t776256\t776557\t.\t+\t.\tid=YBR287W (ZSP1);TSS_position=776530;nucleosome_plus1=776557;nucleosome_minus1=776256;distance=301;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t779458\t779708\t.\t-\t.\tid=YBR288C (APM3 YKS6);TSS_position=779498;nucleosome_plus1=779458;nucleosome_minus1=779708;distance=250;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t779458\t779708\t.\t+\t.\tid=YBR289W (SNF5 HAF4 SWI10 TYE4);TSS_position=779645;nucleosome_plus1=779708;nucleosome_minus1=779458;distance=250;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t782328\t782629\t.\t+\t.\tid=YBR290W (BSD2);TSS_position=782576;nucleosome_plus1=782629;nucleosome_minus1=782328;distance=301;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t784604\t784878\t.\t-\t.\tid=YBR291C (CTP1);TSS_position=784608;nucleosome_plus1=784604;nucleosome_minus1=784878;distance=274;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t786463\t786639\t.\t+\t.\tid=YBR293W (VBA2);TSS_position=786653;nucleosome_plus1=786639;nucleosome_minus1=786463;distance=176;classification=W-close-F\n+chrII\tnucleR\tTSS classification\t788959\t789316\t.\t+\t.\tid=YBR294W (SUL1 SFP2);TSS_position=789128;nucleosome_plus1=789316;nucleosome_minus1=788959;distance=357;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t792570\t792851\t.\t+\t.\tid=YBR295W (PCA1 CAD2 PAY2);TSS_position=792812;nucleosome_plus1=792851;nucleosome_minus1=792570;distance=281;classification=W-open-W\n+chrII\tnucleR\tTSS classification\t798550\t798731\t.\t-\t.\tid=YBR296C (PHO89 ITN1);TSS_position=798588;nucleosome_plus1=798550;nucleosome_minus1=798731;distance=181;classification=F-close-F\n+chrII\tnucleR\tTSS classification\t800181\t800527\t.\t+\t.\tid=YBR297W (MAL33 MAL3R MALR);TSS_position=800477;nucleosome_plus1=800527;nucleosome_minus1=800181;distance=346;classification=F-open-W\n+chrII\tnucleR\tTSS classification\t804845\t805331\t.\t-\t.\tid=YBR298C (MAL31 MAL3T MALT);TSS_position=804872;nucleosome_plus1=804845;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n+chrII\tnucleR\tTSS classification\t804845\t805331\t.\t+\t.\tid=YBR299W (MAL32 MAL3S MALS);TSS_position=805323;nucleosome_plus1=805331;nucleosome_minus1=NA;distance=NA;classification=-1_missing\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/TSS__stats__cellcycleM_chrII.genes.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TSS__stats__cellcycleM_chrII.genes.csv Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,5681 @@\n+Name,TSS class,Distance from -1 to +1\n+Q0080 (ATP8 AAP1),NA,NA\n+Q0085 (ATP6 OLI2 OLI4 PHO1),NA,NA\n+Q0130 (OLI1 ATP9 OLI3),NA,NA\n+Q0275 (COX3 OXI2),NA,NA\n+YAL001C (TFC3 FUN24 TSV115),NA,NA\n+YAL002W (VPS8 FUN15 VPL8 VPT8),NA,NA\n+YAL003W (EFB1 TEF5),NA,NA\n+YAL004W,NA,NA\n+YAL005C (SSA1 YG100),NA,NA\n+YAL007C (ERP2),NA,NA\n+YAL008W (FUN14),NA,NA\n+YAL009W (SPO7),NA,NA\n+YAL010C (MDM10 FUN37),NA,NA\n+YAL011W (SWC3 SWC1),NA,NA\n+YAL012W (CYS3 CYI1 FUN35 STR1),NA,NA\n+YAL013W (DEP1 FUN54),NA,NA\n+YAL014C (SYN8 SLT2 UIP2),NA,NA\n+YAL015C (NTG1 FUN33 SCR1 ogg2),NA,NA\n+YAL016C-B,NA,NA\n+YAL016W (TPD3 FUN32),NA,NA\n+YAL017W (PSK1 FUN31),NA,NA\n+YAL018C,NA,NA\n+YAL019W (FUN30),NA,NA\n+YAL020C (ATS1 FUN28 KTI13),NA,NA\n+YAL021C (CCR4 FUN27 NUT21),NA,NA\n+YAL022C (FUN26),NA,NA\n+YAL023C (PMT2 FUN25),NA,NA\n+YAL024C (LTE1 MSI2),NA,NA\n+YAL025C (MAK16),NA,NA\n+YAL026C (DRS2 FUN38 SWA3),NA,NA\n+YAL027W (SAW1),NA,NA\n+YAL028W (FRT2 HPH2),NA,NA\n+YAL029C (MYO4 FUN22 SHE1),NA,NA\n+YAL030W (SNC1),NA,NA\n+YAL031C (GIP4 FUN21),NA,NA\n+YAL032C (PRP45 FUN20),NA,NA\n+YAL033W (POP5 FUN53),NA,NA\n+YAL034C (FUN19),NA,NA\n+YAL034C-B (YAL035C-A),NA,NA\n+YAL034W-A (MTW1 DSN3 NSL2),NA,NA\n+YAL035W (FUN12 yIF2),NA,NA\n+YAL036C (RBG1 FUN11),NA,NA\n+YAL037C-A,NA,NA\n+YAL037C-B,NA,NA\n+YAL037W,NA,NA\n+YAL038W (CDC19 PYK1),NA,NA\n+YAL039C (CYC3),NA,NA\n+YAL040C (CLN3 DAF1 FUN10 WHI1),NA,NA\n+YAL041W (CDC24 CLS4),NA,NA\n+YAL042W (ERV46 FUN9),NA,NA\n+YAL043C (PTA1 FUN39),NA,NA\n+YAL044C (GCV3),NA,NA\n+YAL044W-A,NA,NA\n+YAL045C,NA,NA\n+YAL046C (AIM1),NA,NA\n+YAL047C (SPC72 LDB4),NA,NA\n+YAL047W-A,NA,NA\n+YAL048C (GEM1 GON1),NA,NA\n+YAL049C (AIM2),NA,NA\n+YAL051W (OAF1 YAF1),NA,NA\n+YAL053W (FLC2 HUF2),NA,NA\n+YAL054C (ACS1 FUN44),NA,NA\n+YAL055W (PEX22 YAF5),NA,NA\n+YAL056W (GPB2 KRH1),NA,NA\n+YAL058W (CNE1 FUN48),NA,NA\n+YAL059W (ECM1),NA,NA\n+YAL060W (BDH1 BDH),NA,NA\n+YAL061W (BDH2),NA,NA\n+YAL062W (GDH3 FUN51),NA,NA\n+YAL064W-B,NA,NA\n+YAL067C (SEO1),NA,NA\n+YAR002C-A (ERP1),NA,NA\n+YAR002W (NUP60),NA,NA\n+YAR003W (SWD1 CPS50 FUN16 SAF49),NA,NA\n+YAR007C (RFA1 BUF2 FUN3 RPA1),NA,NA\n+YAR008W (SEN34 FUN4),NA,NA\n+YAR014C (BUD14),NA,NA\n+YAR015W (ADE1),NA,NA\n+YAR018C (KIN3 FUN52 NPK1),NA,NA\n+YAR019C (CDC15 LYT1),NA,NA\n+YAR023C,NA,NA\n+YAR027W (UIP3),NA,NA\n+YAR028W,NA,NA\n+YAR029W,NA,NA\n+YAR033W (MST28),NA,NA\n+YAR035W (YAT1),NA,NA\n+YAR042W (SWH1 OSH1 YAR044W),NA,NA\n+YAR066W,NA,NA\n+YBL001C (ECM15),W-open-W,258\n+YBL002W (HTB2),-1_missing,NA\n+YBL003C (HTA2 H2A2),W-close-W,195\n+YBL004W (UTP20),W-open-W,318\n+YBL005W (PDR3 AMY2 TPE2),W-open-W,310\n+YBL006C (LDB7 RSC14),W-open-W,310\n+YBL007C (SLA1),W-open-W,285\n+YBL008W (HIR1),W-open-F,221\n+YBL009W (ALK2),W-open-W,307\n+YBL010C,W-open-W,307\n+YBL011W (SCT1 GAT2),-1_missing,NA\n+YBL014C (RRN6),W-open-W,317\n+YBL015W (ACH1),F-close-F,195\n+YBL016W (FUS3 DAC2),W-close-W,158\n+YBL017C (PEP1 VPS10 VPT1),W-open-W,276\n+YBL018C (POP8),W-open-W,277\n+YBL019W (APN2 ETH1),-1_missing,NA\n+YBL020W (RFT1),W-open-W,289\n+YBL021C (HAP3),W-open-W,289\n+YBL022C (PIM1 LON1),W-open-W,260\n+YBL023C (MCM2),F-open-W,266\n+YBL024W (NCL1 TRM4),W-open-W,311\n+YBL025W (RRN10),W-open-F,238\n+YBL026W (LSM2 SMX5 SNP3),W-open-W,263\n+YBL027W (RPL19B),-1_missing,NA\n+YBL028C,-1_missing,NA\n+YBL029C-A,-1_missing,NA\n+YBL029W,W-close-F,148\n+YBL030C (PET9 AAC2 ANC2 OP1),-1_missing,NA\n+YBL031W (SHE1),F-open-W,333\n+YBL032W (HEK2 KHD1),-1_missing,NA\n+YBL033C (RIB1),-1_missing,NA\n+YBL034C (STU1),W-open-W,296\n+YBL035C (POL12),W-open-W,323\n+YBL036C,W-open-W,296\n+YBL037W (APL3),W-open-W,268\n+YBL038W (MRPL16),-1_missing,NA\n+YBL039C (URA7),-1_missing,NA\n+YBL039W-B (YBL039W-A),F-close-W,201\n+YBL040C (ERD2),F-open-W,266\n+YBL041W (PRE7 PRS3),F-open-W,309\n+YBL042C (FUI1),-1_missing,NA\n+YBL043W (ECM13),W-close-W,151\n+YBL045C (COR1 QCR1),-1_missing,NA\n+YBL046W (PSY4),W-open-W,307\n+YBL047C (EDE1 BUD15),W-open-W,307\n+YBL049W (MOH1),F-open-F,226\n+YBL050W (SEC17 RNS3),W-open-W,311\n+YBL051C (PIN4 MDT1),W-open-W,311\n+YBL052C (SAS3),F-open-W,250\n+YBL054W (TOD6 PBF1),-1_missing,NA\n+YBL055C (Tat-D),W-open-W,313\n+YBL056W (PTC3),W-open-W,281\n+YBL057C'..b'1),NA,NA\n+YPR019W (MCM4 CDC54 HCD21),NA,NA\n+YPR020W (ATP20),NA,NA\n+YPR021C (AGC1),NA,NA\n+YPR022C,NA,NA\n+YPR023C (EAF3),NA,NA\n+YPR024W (YME1 OSD1 YTA11),NA,NA\n+YPR025C (CCL1),NA,NA\n+YPR026W (ATH1),NA,NA\n+YPR027C,NA,NA\n+YPR028W (YOP1 YIP2),NA,NA\n+YPR029C (APL4),NA,NA\n+YPR030W (CSR2 ART8 MRG19),NA,NA\n+YPR031W (NTO1),NA,NA\n+YPR032W (SRO7 SNI1 SOP1),NA,NA\n+YPR033C (HTS1 TSM4572),NA,NA\n+YPR034W (ARP7 RSC11 SWP61),NA,NA\n+YPR035W (GLN1),NA,NA\n+YPR036W (VMA13 CLS11),NA,NA\n+YPR036W-A,NA,NA\n+YPR037C (ERV2),NA,NA\n+YPR040W (TIP41),NA,NA\n+YPR041W (TIF5 SUI5),NA,NA\n+YPR042C (PUF2),NA,NA\n+YPR043W (RPL43A),NA,NA\n+YPR044C (OPI11),NA,NA\n+YPR045C (THP3 MNI2),NA,NA\n+YPR046W (MCM16),NA,NA\n+YPR047W (MSF1),NA,NA\n+YPR048W (TAH18),NA,NA\n+YPR049C (ATG11 CVT9),NA,NA\n+YPR050C,NA,NA\n+YPR051W (MAK3 NAA30),NA,NA\n+YPR052C (NHP6A),NA,NA\n+YPR053C,NA,NA\n+YPR054W (SMK1),NA,NA\n+YPR055W (SEC8),NA,NA\n+YPR056W (TFB4),NA,NA\n+YPR057W (BRR1),NA,NA\n+YPR058W (YMC1),NA,NA\n+YPR059C,NA,NA\n+YPR060C (ARO7 HGS1 OSM2 TYR7),NA,NA\n+YPR061C (JID1),NA,NA\n+YPR062W (FCY1 yCD),NA,NA\n+YPR063C,NA,NA\n+YPR065W (ROX1 REO1),NA,NA\n+YPR067W (ISA2),NA,NA\n+YPR068C (HOS1),NA,NA\n+YPR069C (SPE3),NA,NA\n+YPR070W (MED1),NA,NA\n+YPR071W,NA,NA\n+YPR072W (NOT5),NA,NA\n+YPR073C (LTP1),NA,NA\n+YPR074C (TKL1),NA,NA\n+YPR075C (OPY2),NA,NA\n+YPR076W,NA,NA\n+YPR077C,NA,NA\n+YPR078C,NA,NA\n+YPR079W (MRL1),NA,NA\n+YPR080W (TEF1 EF-1%20alpha),NA,NA\n+YPR081C (GRS2),NA,NA\n+YPR082C (DIB1 SNU16),NA,NA\n+YPR083W (MDM36),NA,NA\n+YPR084W,NA,NA\n+YPR085C (ASA1),NA,NA\n+YPR086W (SUA7 SOH4),NA,NA\n+YPR088C (SRP54 SRH1),NA,NA\n+YPR089W (YPR090W),NA,NA\n+YPR091C,NA,NA\n+YPR093C (ASR1),NA,NA\n+YPR094W (RDS3),NA,NA\n+YPR095C (SYT1),NA,NA\n+YPR097W,NA,NA\n+YPR098C,NA,NA\n+YPR100W (MRPL51),NA,NA\n+YPR101W (SNT309 NTC25),NA,NA\n+YPR102C (RPL11A),NA,NA\n+YPR103W (PRE2 DOA3 PRG1 SRR2),NA,NA\n+YPR104C (FHL1 SPP42),NA,NA\n+YPR105C (COG4 COD1 SEC38 SGF1),NA,NA\n+YPR106W (ISR1),NA,NA\n+YPR107C (YTH1),NA,NA\n+YPR108W (RPN7),NA,NA\n+YPR109W,NA,NA\n+YPR110C (RPC40 RPC5),NA,NA\n+YPR111W (DBF20),NA,NA\n+YPR112C (MRD1),NA,NA\n+YPR113W (PIS1),NA,NA\n+YPR114W,NA,NA\n+YPR115W (RGC1 GCA1),NA,NA\n+YPR116W (RRG8),NA,NA\n+YPR117W,NA,NA\n+YPR118W (MRI1),NA,NA\n+YPR119W (CLB2),NA,NA\n+YPR120C (CLB5),NA,NA\n+YPR121W (THI22),NA,NA\n+YPR122W (AXL1 FUS5 STE22),NA,NA\n+YPR124W (CTR1),NA,NA\n+YPR125W (YLH47 MRS7),NA,NA\n+YPR126C,NA,NA\n+YPR127W,NA,NA\n+YPR128C (ANT1),NA,NA\n+YPR129W (SCD6 LSM13),NA,NA\n+YPR131C (NAT3 NAA20),NA,NA\n+YPR132W (RPS23B),NA,NA\n+YPR133C (SPN1 IWS1),NA,NA\n+YPR133W-A (TOM5 MOM8A),NA,NA\n+YPR134W (MSS18),NA,NA\n+YPR135W (CTF4 CHL15 POB1),NA,NA\n+YPR137W (RRP9),NA,NA\n+YPR138C (MEP3),NA,NA\n+YPR139C (VPS66),NA,NA\n+YPR140W (TAZ1),NA,NA\n+YPR141C (KAR3 OSR11),NA,NA\n+YPR143W (RRP15),NA,NA\n+YPR144C (NOC4 UTP19),NA,NA\n+YPR145C-A,NA,NA\n+YPR145W (ASN1),NA,NA\n+YPR147C,NA,NA\n+YPR148C,NA,NA\n+YPR149W (NCE102 NCE2),NA,NA\n+YPR150W,NA,NA\n+YPR151C (SUE1),NA,NA\n+YPR152C (URN1),NA,NA\n+YPR153W,NA,NA\n+YPR154W (PIN3 LSB2),NA,NA\n+YPR155C (NCA2),NA,NA\n+YPR156C (TPO3),NA,NA\n+YPR157W,NA,NA\n+YPR158W (CUR1),NA,NA\n+YPR159W (KRE6 CWH48),NA,NA\n+YPR160W (GPH1),NA,NA\n+YPR161C (SGV1 BUR1),NA,NA\n+YPR162C (ORC4),NA,NA\n+YPR163C (TIF3 RBL3 STM1),NA,NA\n+YPR164W (MMS1 RTT108 SLM6),NA,NA\n+YPR165W (RHO1),NA,NA\n+YPR166C (MRP2),NA,NA\n+YPR167C (MET16),NA,NA\n+YPR169W (JIP5),NA,NA\n+YPR169W-A,NA,NA\n+YPR170C,NA,NA\n+YPR170W-A,NA,NA\n+YPR170W-B,NA,NA\n+YPR171W (BSP1),NA,NA\n+YPR172W,NA,NA\n+YPR173C (VPS4 CSC1 DID6 END13 GRD13 VPL4 VPT10),NA,NA\n+YPR174C,NA,NA\n+YPR175W (DPB2),NA,NA\n+YPR176C (BET2),NA,NA\n+YPR178W (PRP4 RNA4),NA,NA\n+YPR179C (HDA3 PLO1),NA,NA\n+YPR180W (AOS1 RHC31),NA,NA\n+YPR181C (SEC23),NA,NA\n+YPR182W (SMX3),NA,NA\n+YPR183W (DPM1 SED3),NA,NA\n+YPR184W (GDB1),NA,NA\n+YPR185W (ATG13 APG13),NA,NA\n+YPR186C (PZF1 TFC2),NA,NA\n+YPR187W (RPO26 RPB6),NA,NA\n+YPR188C (MLC2),NA,NA\n+YPR189W (SKI3 SKI5),NA,NA\n+YPR190C (RPC82 RPC3),NA,NA\n+YPR191W (QCR2 COR2 UCR2),NA,NA\n+YPR192W (AQY1),NA,NA\n+YPR193C (HPA2),NA,NA\n+YPR194C (OPT2),NA,NA\n+YPR195C,NA,NA\n+YPR196W,NA,NA\n+YPR198W (SGE1 NOR1),NA,NA\n+YPR199C (ARR1 ACR1 YAP8),NA,NA\n+YPR201W (ARR3 ACR3),NA,NA\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/TSS__stats__cellcycleM_chrII.gw.png |
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| diff -r 707216744193 -r e88c806ddf3e test-data/cellcycleM_chrII.bam |
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| Binary file test-data/readBAM__cellcycleM_chrII.RData has changed |
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| diff -r 707216744193 -r e88c806ddf3e test-data/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes Fri Apr 12 05:28:43 2019 -0400 |
| b |
| @@ -0,0 +1,18 @@ +chrI 230218 +chrII 813184 +chrIII 316620 +chrIV 1531933 +chrV 576874 +chrVI 270161 +chrVII 1090940 +chrVIII 562643 +chrIX 439888 +chrX 745751 +chrXI 666816 +chrXII 1078177 +chrXIII 924431 +chrXIV 784333 +chrXV 1091291 +chrXVI 948066 +chrM 85779 +2-micron 6318 |
| b |
| diff -r 707216744193 -r e88c806ddf3e test-data/refGenomes/R64-1-1/genes.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refGenomes/R64-1-1/genes.gff Fri Apr 12 05:28:43 2019 -0400 |
| b |
| b'@@ -0,0 +1,5680 @@\n+chrM\t.\t.\t27645\t28106\t.\t+\t.\tname=Q0080 (ATP8 AAP1);bin=585;cdsStart=27665;cdsEnd=27812;proteinID=P00856;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=27645;Nagalakshmi_TTS=28106;tss=27645;tts=28106;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n+chrM\t.\t.\t27879\t29494\t.\t+\t.\tname=Q0085 (ATP6 OLI2 OLI4 PHO1);bin=585;cdsStart=28486;cdsEnd=29266;proteinID=P00854;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=27879;Nagalakshmi_TTS=29494;tss=27879;tts=29494;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n+chrM\t.\t.\t46675\t47014\t.\t+\t.\tname=Q0130 (OLI1 ATP9 OLI3);bin=585;cdsStart=46722;cdsEnd=46953;proteinID=P61829;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=46675;Nagalakshmi_TTS=47014;tss=46675;tts=47014;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n+chrM\t.\t.\t79147\t80087\t.\t+\t.\tname=Q0275 (COX3 OXI2);bin=585;cdsStart=79212;cdsEnd=80022;proteinID=P00420;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=79147;Nagalakshmi_TTS=80087;tss=79147;tts=80087;tss_source=Nagalakshmi_2008;tts_source=Nagalakshmi_2008\n+chrI\t.\t.\t147536\t151218\t.\t-\t.\tname=YAL001C (TFC3 FUN24 TSV115);bin=586;cdsStart=151166;cdsEnd=147593;proteinID=P34111;Pelechano_UTR5=52;Pelechano_TSS=151218;Pelechano_UTR3=57;Pelechano_TTS=147536;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=151191;Yassour_TTS=147567;Nagalakshmi_TSS=151186;Nagalakshmi_TTS=147530;tss=151218;tts=147536;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrI\t.\t.\t143621\t147589\t.\t+\t.\tname=YAL002W (VPS8 FUN15 VPL8 VPT8);bin=586;cdsStart=143706;cdsEnd=147531;proteinID=P39702;Pelechano_UTR5=85;Pelechano_TSS=143621;Pelechano_UTR3=58;Pelechano_TTS=147589;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=143527;Yassour_TTS=147566;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=143621;tts=147589;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrI\t.\t.\t142141\t143381\t.\t+\t.\tname=YAL003W (EFB1 TEF5);bin=586;cdsStart=142173;cdsEnd=143160;proteinID=P32471;Pelechano_UTR5=32;Pelechano_TSS=142141;Pelechano_UTR3=221;Pelechano_TTS=143381;Miura_UTR5=32;Miura_TSS=142141;Miura_UTR3=66;Miura_TTS=143226;Yassour_TSS=142144;Yassour_TTS=143495;Nagalakshmi_TSS=142161;Nagalakshmi_TTS=143370;tss=142141;tts=143381;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrI\t.\t.\t140609\t141543\t.\t+\t.\tname=YAL004W;bin=586;cdsStart=140759;cdsEnd=141407;proteinID=n/a;Pelechano_UTR5=NA;Pelechano_TSS=NA;Pelechano_UTR3=NA;Pelechano_TTS=NA;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=140609;Yassour_TTS=141543;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=140609;tts=141543;tss_source=Yassour_2009;tts_source=Yassour_2009\n+chrI\t.\t.\t139357\t141493\t.\t-\t.\tname=YAL005C (SSA1 YG100);bin=586;cdsStart=141431;cdsEnd=139502;proteinID=P10591;Pelechano_UTR5=62;Pelechano_TSS=141493;Pelechano_UTR3=145;Pelechano_TTS=139357;Miura_UTR5=62;Miura_TSS=141493;Miura_UTR3=115;Miura_TTS=139387;Yassour_TSS=141543;Yassour_TTS=139226;Nagalakshmi_TSS=141495;Nagalakshmi_TTS=139376;tss=141493;tts=139357;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrI\t.\t.\t137552\t138414\t.\t-\t.\tname=YAL007C (ERP2);bin=586;cdsStart=138345;cdsEnd=137697;proteinID=P39704;Pelechano_UTR5=69;Pelechano_TSS=138414;Pelechano_UTR3=145;Pelechano_TTS=137552;Miura_UTR5=72;Miura_TSS=138417;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=138532;Yassour_TTS=137567;Nagalakshmi_TSS=138413;Nagalakshmi_TTS=137572;tss=138414;tts=137552;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrI\t.\t.\t136866\t137642\t.\t+\t.\tname=YAL008W (FUN14);bin=58'..b'_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t916983\t919071\t.\t-\t.\tname=YPR190C (RPC82 RPC3);bin=73;cdsStart=919041;cdsEnd=917076;proteinID=P32349;Pelechano_UTR5=30;Pelechano_TSS=919071;Pelechano_UTR3=93;Pelechano_TTS=916983;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=919130;Yassour_TTS=NA;Nagalakshmi_TSS=919084;Nagalakshmi_TTS=916984;tss=919071;tts=916983;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t919321\t920715\t.\t+\t.\tname=YPR191W (QCR2 COR2 UCR2);bin=592;cdsStart=919380;cdsEnd=920487;proteinID=P07257;Pelechano_UTR5=59;Pelechano_TSS=919321;Pelechano_UTR3=228;Pelechano_TTS=920715;Miura_UTR5=59;Miura_TSS=919321;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=919285;Yassour_TTS=920828;Nagalakshmi_TSS=919297;Nagalakshmi_TTS=920651;tss=919321;tts=920715;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t921845\t922917\t.\t+\t.\tname=YPR192W (AQY1);bin=592;cdsStart=921859;cdsEnd=922777;proteinID=D3W7A4;Pelechano_UTR5=14;Pelechano_TSS=921845;Pelechano_UTR3=140;Pelechano_TTS=922917;Miura_UTR5=28;Miura_TSS=921831;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=921493;Yassour_TTS=923376;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=921845;tts=922917;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t921059\t923831\t.\t-\t.\tname=YPR193C (HPA2);bin=592;cdsStart=923379;cdsEnd=922908;proteinID=Q06592;Pelechano_UTR5=452;Pelechano_TSS=923831;Pelechano_UTR3=1849;Pelechano_TTS=921059;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=922874;tss=923831;tts=921059;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t924143\t927232\t.\t-\t.\tname=YPR194C (OPT2);bin=592;cdsStart=926937;cdsEnd=924303;proteinID=Q06593;Pelechano_UTR5=295;Pelechano_TSS=927232;Pelechano_UTR3=160;Pelechano_TTS=924143;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=927355;Yassour_TTS=924135;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=927232;tts=924143;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t927456\t928316\t.\t-\t.\tname=YPR195C;bin=592;cdsStart=928294;cdsEnd=927964;proteinID=n/a;Pelechano_UTR5=22;Pelechano_TSS=928316;Pelechano_UTR3=508;Pelechano_TTS=927456;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=82;Miura_TTS=927882;Yassour_TSS=928631;Yassour_TTS=927360;Nagalakshmi_TSS=928305;Nagalakshmi_TTS=927801;tss=928316;tts=927456;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t931347\t933201\t.\t+\t.\tname=YPR196W;bin=592;cdsStart=931375;cdsEnd=932788;proteinID=Q06595;Pelechano_UTR5=28;Pelechano_TSS=931347;Pelechano_UTR3=413;Pelechano_TTS=933201;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=933239;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=931347;tts=933201;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t933979\t935825\t.\t+\t.\tname=YPR198W (SGE1 NOR1);bin=592;cdsStart=934033;cdsEnd=935665;proteinID=P33335;Pelechano_UTR5=54;Pelechano_TSS=933979;Pelechano_UTR3=160;Pelechano_TTS=935825;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=933993;Yassour_TTS=935838;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=935759;tss=933979;tts=935825;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t937969\t939042\t.\t-\t.\tname=YPR199C (ARR1 ACR1 YAP8);bin=592;cdsStart=939032;cdsEnd=938147;proteinID=Q06596;Pelechano_UTR5=10;Pelechano_TSS=939042;Pelechano_UTR3=178;Pelechano_TTS=937969;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=939041;Yassour_TTS=938062;Nagalakshmi_TSS=939058;Nagalakshmi_TTS=938044;tss=939042;tts=937969;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n+chrXVI\t.\t.\t939770\t942212\t.\t+\t.\tname=YPR201W (ARR3 ACR3);bin=592;cdsStart=939921;cdsEnd=941136;proteinID=Q06598;Pelechano_UTR5=151;Pelechano_TSS=939770;Pelechano_UTR3=1076;Pelechano_TTS=942212;Miura_UTR5=NA;Miura_TSS=NA;Miura_UTR3=NA;Miura_TTS=NA;Yassour_TSS=NA;Yassour_TTS=NA;Nagalakshmi_TSS=NA;Nagalakshmi_TTS=NA;tss=939770;tts=942212;tss_source=Pelechano_2013;tts_source=Pelechano_2013\n' |
| b |
| diff -r 707216744193 -r e88c806ddf3e txstart.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/txstart.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,75 @@ +<tool id="txstart" name="TSS classification" version="0.1"> + <description>: classify nucleosomes at Transcription Start Sites (TSS)</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> + <![CDATA[ + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics txstart --calls $gff_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if + --output $output_gff_file --window $window --open_thres $open_thres + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> + <param name="window" size="4" type="integer" value="300" label="Window" help="Number of nucleotides on each side of the TSS where -1 and +1 nucleosome are search for." /> + <param name="open_thres" size="4" type="integer" value="215" label="Open threshold" help="Distance between nucleosomes -1 and +1 to discriminate between 'open' and 'close' classes." /> +</inputs> + <outputs> + <data format="gff" name="output_gff_file" label="TSS__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" /> + </outputs> +<tests> + <test> + <param name="gff_file" value="NR__cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <param name="window" value="300" /> + <param name="open_thres" value="215" /> + <output name="output_gff_file" file="TSS__cellcycleM_chrII.gff" /> + </test> +</tests> +<help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics +</help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
| b |
| diff -r 707216744193 -r e88c806ddf3e txstart_stats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/txstart_stats.xml Fri Apr 12 05:28:43 2019 -0400 |
| [ |
| @@ -0,0 +1,79 @@ +<tool id="txstart_stats" name="TSS Statistics" version="0.1"> + <description>: gather gene and genome-wide statistics on nucleosomes at TSS</description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + ln -f -s $output_gw_png_file $output_gw_png_file\.png; + ln -f -s $output_gw2_png_file $output_gw2_png_file\.png; + docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics txstart_stats --input $gff_file + #if $assembly.source == "buildin": + --genome ${assembly.ref_genome_gff_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_genome_gff_history} + #end if + --out_genes $output_genes_csv_file --out_gw $output_gw_png_file\.png --out_gw2 $output_gw2_png_file\.png; + rm $output_gw_png_file\.png; + rm $output_gw2_png_file\.png + ]]> + </command> + <inputs> + <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Transcription Start Sites as annotated by TSS classification tool."/> + <conditional name="assembly"> + <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team."> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="4"/> + </options> + </param> + </when> + <when value="history"> + <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/> + </when> + </conditional> +</inputs> + <outputs> + <data format="csv" name="output_genes_csv_file" label="TSS__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.genes.csv" /> + <data format="png" name="output_gw_png_file" label="TSS__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.png" /> + <data format="png" name="output_gw2_png_file" label="TSS__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw2.png" /> + </outputs> + <tests> + <test> + <param name="gff_file" value="TSS__cellcycleM_chrII.gff" /> + <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" /> + <output name="output_genes_csv_file" file="TSS__stats__cellcycleM_chrII.genes.csv" /> + <output name="output_gw_png_file" file="TSS__stats__cellcycleM_chrII.gw.png" /> + <output name="output_gw2_png_file" file="TSS__stats__cellcycleM_chrII.gw2.png" /> + </test> + </tests> + <help> +.. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them. + +.. class:: infomark + +Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool> |
