| Previous changeset 2:601ad3ea888b (2019-05-08) Next changeset 4:142310a198c2 (2019-05-08) |
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Commit message:
Deleted selected files |
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removed:
epic2/.shed.yml epic2/epic2_wrapper.xml epic2/macros.xml epic2/test-data/control.bam epic2/test-data/control.bed.gz epic2/test-data/epic2_results.txt epic2/test-data/epic2_results1.txt epic2/test-data/epic2_results2.txt epic2/test-data/epic2_results3.bed epic2/test-data/epic2_results3.txt epic2/test-data/test.bam epic2/test-data/test.bed.gz epic2/test-data/test_ChIP.bam epic2/test-data/test_Input.bam epic2/test-data/test_chromsizes.txt epic2/test-data/test_fasta.fasta |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/.shed.yml --- a/epic2/.shed.yml Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -categories: [ChIP-seq] -description: Peak calling of broad ChIP-Seq marks -homepage_url: https://github.com/biocore-ntnu/epic2 -name: epic2 -owner: mpaya -remote_repository_url: https://github.com/wilkinsonlab/galaxy_tools/epic2/ \ No newline at end of file |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/epic2_wrapper.xml --- a/epic2/epic2_wrapper.xml Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,372 +0,0 @@\n-<tool id="epic2" name="epic2" version="@VERSION@.0">\n- <description>peak calling of broad ChIP-Seq marks</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements" />\n- \n- <stdio>\n- <exit_code range="1:125" level="fatal" description="Unknown error occurred" />\n- <exit_code range="130:" level="fatal" description="Unknown error occurred" />\n- <regex match="epic2: (command ){0,1}not found" source="stderr" level="fatal" description="The epic2 python package is not properly installed, contact Galaxy administrators" />\n- </stdio>\n- \n- <command><![CDATA[\n-\n- ##set up treatment files, extension must be bed, bedpe, bam, sam\n- #set $t_file_list = list()\n- #if str($treatment.t_multi_select) == "No":\n- #if $treatment.input_treatment_file.is_of_type(\'bed\')\n- #set $t_file = \'ChIP_file.bed\'\n- ln -s \'$treatment.input_treatment_file\' $t_file &&\n- #elif $treatment.input_treatment_file.is_of_type(\'bam\')\n- #set $t_file = \'ChIP_file.bam\'\n- ln -s \'$treatment.input_treatment_file\' $t_file &&\n- ln -s \'$treatment.input_treatment_file.metadata.bam_index\' ${t_file}.bai &&\n- #elif $treatment.input_treatment_file.is_of_type(\'sam\')\n- #set $t_file = \'ChIP_file.sam\'\n- ln -s \'$treatment.input_treatment_file\' $t_file &&\n- #end if\n- $t_file_list.append($t_file)\n- #else\n- #set $inputs = $treatment.input_treatment_file\n- #for $i, $f in enumerate($inputs)\n- #if $f.is_of_type(\'bed\')\n- #set $t_file = \'\'.join([\'ChIP_file_\',str($i),\'.bed\'])\n- ln -s \'$f\' $t_file &&\n- #elif $f.is_of_type(\'bam\')\n- #set $t_file = \'\'.join([\'ChIP_file_\',str($i),\'.bam\'])\n- ln -s \'$f\' $t_file &&\n- ln -s \'$f.metadata.bam_index\' ${t_file}.bai &&\n- #elif $f.is_of_type(\'sam\')\n- #set $t_file = \'\'.join([\'ChIP_file_\',str($i),\'.sam\'])\n- ln -s \'$f\' $t_file &&\n- #end if\n- $t_file_list.append($t_file)\n- #end for\n- #end if\n-\n- ##set up control files, extension must be bed, bedpe, bam, sam\n- #if str($control.c_select) == "Yes":\n- #set $c_file_list = list()\n- #if str($control.c_multiple.c_multi_select) == "No":\n- #set $f = $control.c_multiple.input_control_file\n- #if $f.is_of_type(\'bed\')\n- #set $c_file = \'control_file.bed\'\n- ln -s \'$f\' $c_file &&\n- #elif $f.is_of_type(\'bam\')\n- #set $c_file = \'control_file.bam\'\n- ln -s \'$f\' $c_file &&\n- ln -s \'$f.metadata.bam_index\' ${c_file}.bai &&\n- #elif $f.is_of_type(\'sam\')\n- #set $c_file = \'control_file.sam\'\n- ln -s \'$f\' $c_file &&\n- #end if\n- $c_file_list.append($c_file)\n- #else\n- #set $inputs = $control.c_multiple.input_control_file\n- #for $i, $f in enumerate($inputs)\n- #if $f.is_of_type(\'bed\')\n- #set $c_file = \'\'.join([\'control_file\',str($i),\'.bed\'])\n- ln -s \'$f\' $c_file &&\n- #elif $f.is_of_type(\'bam\')\n- #set $c_file = \'\'.join([\'control_file\',str($i),\'.bam\'])\n- ln -s \'$f\' $c_file &&\n- ln -s \'$f.metadata.bam_index\' ${c_file}.bai &&\n- #elif $f.is_of_type(\'sam\')\n- #set $c_file = \'\'.join([\'control_file\',str($i),\'.sam\'])\n- ln -s \'$f\' $c_file &&\n- #end if\n- $c_file_list.append($c_file)\n- '..b'" type="integer" optional="True" label="Fragment size" \n- help="(Single end reads only) Size of the sequenced fragment. Each read is extended half the fragment size from the 5\' end. \n- Default 150 (i.e. extend by 75). (--fragment-size)" />\n- <param name="original_algorithm" type="boolean" checked="false" truevalue="--original-algorithm" falsevalue="" \n- label="Compute p-values with SICER original algorithm?" \n- help="Use the original SICER algorithm, without the epic2 fix. This will use all reads in your files to compute\n- the p-values, including those falling outside the genome boundaries. (--original-algorithm)" />\n- </section>\n- </inputs>\n-\n- <outputs>\n- <data format="tabular" name="peaks" label="${tool.name} on ${on_string}"/>\n- <data format=\'bed\' name=\'bed_peaks\' label="${tool.name} on ${on_string}: BED">\n- <filter>to_bed</filter>\n- </data>\n-\n- </outputs>\n-\n- <tests>\n- <test>\n- <param name="input_treatment_file" value="test.bam" ftype="bam" />\n- <param name="c_select" value="Yes" />\n- <param name="input_control_file" value="control.bam" ftype="bam"/>\n- <output name="peaks" file="epic2_results.txt"/>\n- </test>\n- <test>\n- <param name="input_treatment_file" value="test.bed.gz" ftype="bed" />\n- <param name="c_select" value="Yes" />\n- <param name="input_control_file" value="control.bed.gz" ftype="bed"/>\n- <output name="peaks" file="epic2_results1.txt"/>\n- </test>\n- <test>\n- <param name="input_treatment_file" value="test_ChIP.bam" ftype="bam" />\n- <param name="c_select" value="Yes" />\n- <param name="input_control_file" value="test_Input.bam" ftype="bam"/>\n- <param name="g_select" value="No" />\n- <param name="chr_select" value="No" />\n- <param name="cs_file" value="test_chromsizes.txt" />\n- <param name="egf" value="0.99" />\n- <param name="original_algorithm" value="Yes" />\n- <output name="peaks" file="epic2_results2.txt"/>\n- </test>\n- <test>\n- <param name="input_treatment_file" value="test_ChIP.bam" ftype="bam" />\n- <param name="c_select" value="Yes" />\n- <param name="input_control_file" value="test_Input.bam" ftype="bam"/>\n- <param name="g_select" value="No" />\n- <param name="chr_select" value="No" />\n- <param name="cs_file" value="test_fasta.fasta" />\n- <param name="egf" value="0.99" />\n- <param name="to_bed" value="Yes" />\n- <param name="mapq" value="10" />\n- <param name="bin_size" value="100" />\n- <param name="gaps_allowed" value="0" />\n- <output name="peaks" file="epic2_results3.txt"/>\n- <output name="bed_peaks" file="epic2_results3.bed"/>\n- </test>\n- </tests>\n-\n- <help>\n-Chip-Seq broad peak/domain finder based on SICER.\n-\n-**Accepted input formats**\n-\n-Input file extension must be bed, bedpe, bam or sam.\n-\n-**Broad peaks format**\n- \n-Original epic2 output does not follow any standard format, then broad peaks bed format is offered. This format follows the standard from ENCODE, BED 6 + 3, and contains the following columns:\n- \n- * **1.** Chrom \n- * **2.** Start \n- * **3.** End \n- * **4.** Name \n- * **5.** Score \n- * **6.** Strand \n- * **7.** log2FoldChange \n- * **8.** -log10PValue \n- * **9.** -log10FDR\n- \n-.. class:: warningmark\n-\n- On columns 8 and 9, the max value is set to 50 when Pvalue == 0.0.\n-\n-Tool adapted to Galaxy by Miriam Pay\xc3\xa1 Milans. Original documentation on https://github.com/biocore-ntnu/epic2.\n- \n- \n- </help>\n- <expand macro="citations" />\n-</tool> \n' |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/macros.xml --- a/epic2/macros.xml Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,117 +0,0 @@ -<macros> - - <token name="@VERSION@">1.0</token> - <xml name="requirements"> - <requirements> - <requirement type="package" version="0.0.26">epic2</requirement> - <requirement type="package">htslib</requirement> - </requirements> - </xml> - - <xml name="effectiveGenomeSize"> - <param name="builtin_genome" argument="--genome" type="select" label="Genome" help="Default hg19 (--genome)" > - <option value="ailMel1">ailMel1</option> - <option value="anoCar2">anoCar2</option> - <option value="apiMel1">apiMel1</option> - <option value="aplCal1">aplCal1</option> - <option value="aquChr2">aquChr2</option> - <option value="balAcu1">balAcu1</option> - <option value="braFlo1">braFlo1</option> - <option value="calJac1">calJac1</option> - <option value="calJac3">calJac3</option> - <option value="cavPor3">cavPor3</option> - <option value="ce10">ce10</option> - <option value="ce11">ce11</option> - <option value="cerSim1">cerSim1</option> - <option value="chlSab2">chlSab2</option> - <option value="chrPic1">chrPic1</option> - <option value="danRer10">danRer10</option> - <option value="danRer3">danRer3</option> - <option value="danRer4">danRer4</option> - <option value="danRer5">danRer5</option> - <option value="danRer6">danRer6</option> - <option value="danRer7">danRer7</option> - <option value="dm3">dm3</option> - <option value="dm6">dm6</option> - <option value="echTel2">echTel2</option> - <option value="equCab1">equCab1</option> - <option value="equCab2">equCab2</option> - <option value="eriEur1">eriEur1</option> - <option value="eriEur2">eriEur2</option> - <option value="fr1">fr1</option> - <option value="fr2">fr2</option> - <option value="galVar1">galVar1</option> - <option value="gasAcu1">gasAcu1</option> - <option value="geoFor1">geoFor1</option> - <option value="gorGor3">gorGor3</option> - <option value="gorGor4">gorGor4</option> - <option value="gorGor5">gorGor5</option> - <option value="hetGla1">hetGla1</option> - <option value="hetGla2">hetGla2</option> - <option value="hg18">hg18</option> - <option value="hg19" selected="true">hg19</option> - <option value="hg38">hg38</option> - <option value="loxAfr3">loxAfr3</option> - <option value="macEug2">macEug2</option> - <option value="melGal1">melGal1</option> - <option value="melGal5">melGal5</option> - <option value="micMur2">micMur2</option> - <option value="mm10">mm10</option> - <option value="mm9">mm9</option> - <option value="monDom4">monDom4</option> - <option value="monDom5">monDom5</option> - <option value="myoLuc2">myoLuc2</option> - <option value="nanPar1">nanPar1</option> - <option value="nasLar1">nasLar1</option> - <option value="nomLeu1">nomLeu1</option> - <option value="nomLeu2">nomLeu2</option> - <option value="nomLeu3">nomLeu3</option> - <option value="ochPri3">ochPri3</option> - <option value="oreNil2">oreNil2</option> - <option value="ornAna1">ornAna1</option> - <option value="ornAna2">ornAna2</option> - <option value="oryCun2">oryCun2</option> - <option value="oryLat2">oryLat2</option> - <option value="oviAri1">oviAri1</option> - <option value="oviAri3">oviAri3</option> - <option value="papAnu2">papAnu2</option> - <option value="petMar1">petMar1</option> - <option value="petMar2">petMar2</option> - <option value="ponAbe2">ponAbe2</option> - <option value="priPac1">priPac1</option> - <option value="rheMac2">rheMac2</option> - <option value="rheMac3">rheMac3</option> - <option value="rheMac8">rheMac8</option> - <option value="rhiRox1">rhiRox1</option> - <option value="rn4">rn4</option> - <option value="rn5">rn5</option> - <option value="rn6">rn6</option> - <option value="sacCer1">sacCer1</option> - <option value="sacCer2">sacCer2</option> - <option value="sacCer3">sacCer3</option> - <option value="saiBol1">saiBol1</option> - <option value="sorAra2">sorAra2</option> - <option value="speTri2">speTri2</option> - <option value="strPur1">strPur1</option> - <option value="strPur2">strPur2</option> - <option value="susScr2">susScr2</option> - <option value="susScr3">susScr3</option> - <option value="taeGut1">taeGut1</option> - <option value="taeGut2">taeGut2</option> - <option value="tarSyr2">tarSyr2</option> - <option value="tetNig1">tetNig1</option> - <option value="tetNig2">tetNig2</option> - <option value="triMan1">triMan1</option> - <option value="xenTro3">xenTro3</option> - <option value="xenTro7">xenTro7</option> - </param> - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">0.1093/bioinformatics/btz232</citation> - <yield /> - </citations> - </xml> - -</macros> |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/control.bam |
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| Binary file epic2/test-data/control.bam has changed |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/control.bed.gz |
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| Binary file epic2/test-data/control.bed.gz has changed |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/epic2_results.txt --- a/epic2/test-data/epic2_results.txt Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,166 +0,0 @@\n-#Chromosome\tStart\tEnd\tPValue\tScore\tStrand\tChIPCount\tInputCount\tFDR\tlog2FoldChange\n-chr1\t23568400\t23568599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t26401200\t26401399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t33054800\t33055399\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr1\t33365200\t33365399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t39422200\t39422799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr1\t51473600\t51474399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr1\t58785200\t58786199\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr1\t59430000\t59430199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t65065600\t65066199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr1\t91625400\t91625799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr1\t100589600\t100589799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t103840400\t103841199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr1\t113416400\t113416799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr1\t113486600\t113487199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr1\t115014800\t115014999\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t144181600\t144181999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr1\t171053400\t171054599\t2.0859275044291852e-11\t930.748585550573\t.\t3\t0\t6.925279314704895e-10\t9.30748585550573\n-chr1\t181707400\t181707999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr1\t203357400\t203357799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr1\t210178400\t210178999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr1\t210471400\t210471599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t219659800\t219660199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr1\t220704400\t220705199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t32400\t33399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr2\t15618800\t15619599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t39208000\t39208799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t48521000\t48521199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr2\t61986000\t61986599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr2\t73314400\t73315199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t101681600\t101682399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t136216000\t136216799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t175474200\t175474599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr2\t181811200\t181811799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr2\t201039600\t201040199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.83670952162628e-09\t9.722523354784574\n-chr2\t202215400\t202215799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr2\t207865600\t207866599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr2\t224033800\t224034799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.98555776'..b'.30748585550573\n-chr13\t113095600\t113095999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr14\t30160600\t30161599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr14\t44201400\t44201799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr14\t54727600\t54727799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr14\t67356600\t67356999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8411683763634284e-09\t10.30748585550573\n-chr14\t75051400\t75051799\t6.543911699123029e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|
| b |
| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/epic2_results1.txt --- a/epic2/test-data/epic2_results1.txt Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,166 +0,0 @@\n-#Chromosome\tStart\tEnd\tPValue\tScore\tStrand\tChIPCount\tInputCount\tFDR\tlog2FoldChange\n-chr1\t23568400\t23568599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t26401200\t26401399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t33054800\t33055399\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t33365200\t33365399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t39422200\t39422799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t51473600\t51474399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr1\t58785200\t58786199\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr1\t59430000\t59430199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t65065600\t65066199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t91625400\t91625799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr1\t100589600\t100589799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t103840400\t103841199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr1\t113416400\t113416799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr1\t113486600\t113487199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t115014800\t115014999\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t144181400\t144181999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t171053400\t171054599\t2.0859275044291852e-11\t930.748585550573\t.\t3\t0\t6.925279314704895e-10\t9.30748585550573\n-chr1\t181707400\t181707999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t203357400\t203357799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr1\t210178400\t210178999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr1\t210471400\t210471599\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr1\t219659800\t219660199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr1\t220704400\t220705199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t32400\t33399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr2\t15618800\t15619599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t39208000\t39208799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t48521000\t48521199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr2\t61986000\t61986599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr2\t73314400\t73315199\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t101681600\t101682399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t136216000\t136216799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr2\t175474200\t175474599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr2\t181811200\t181811799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr2\t201039600\t201040199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr2\t202215400\t202215799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr2\t207865600\t207866599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr2\t224033800\t224034799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8'..b'.30748585550573\n-chr13\t113095600\t113095999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr14\t30160600\t30161599\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr14\t44201400\t44201799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr14\t54727600\t54727799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr14\t67356600\t67356999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr14\t75051400\t75051799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr14\t76404200\t76404399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr14\t76912200\t76912799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr15\t38781800\t38782599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr15\t57638400\t57638999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr15\t76517200\t76517399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr16\t9080000\t9080599\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr16\t20683000\t20683799\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr16\t20724800\t20725799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr16\t22216800\t22217199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr16\t28892800\t28893599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr16\t30612600\t30612999\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr16\t52910600\t52911399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr16\t65955600\t65956399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr16\t67987600\t67988199\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr16\t83646600\t83647399\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr16\t83749000\t83749599\t1.306175776413088e-12\t1000.0\t.\t3\t0\t7.227505962819087e-11\t10.30748585550573\n-chr17\t6340000\t6340199\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr17\t8036400\t8036799\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr17\t16496800\t16497799\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr17\t30567400\t30568399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr17\t34235000\t34235399\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr17\t35277000\t35277399\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chr17\t71748600\t71748799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr18\t9324200\t9324399\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr18\t14914400\t14915399\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chr19\t17239200\t17239799\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr19\t45288400\t45288999\t2.207263610333191e-09\t972.2523354784574\t.\t2\t0\t3.85690272963484e-09\t9.722523354784574\n-chr20\t43477600\t43477799\t8.184731894908448e-11\t1000.0\t.\t2\t0\t6.319374393278151e-10\t11.30748585550573\n-chr22\t16398800\t16399599\t5.228937118152232e-09\t930.748585550573\t.\t2\t0\t6.861688234097e-09\t9.30748585550573\n-chr22\t35502000\t35502999\t1.0206726421638307e-08\t898.5557760618368\t.\t2\t0\t1.1002055753194539e-08\t8.985557760618368\n-chrX\t37591800\t37592199\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n-chrX\t76940200\t76940599\t6.543911699123029e-10\t1000.0\t.\t2\t0\t1.8569048582126885e-09\t10.30748585550573\n' |
| b |
| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/epic2_results2.txt --- a/epic2/test-data/epic2_results2.txt Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -#Chromosome Start End PValue Score Strand ChIPCount InputCount FDR log2FoldChange -chr4 17800 18799 3.111675555106485e-25 129.5809069871083 . 172 59 4.445250793009265e-25 1.2958090698710831 -chr4 32000 33799 7.8685062790203735e-115 197.92562730767474 . 412 88 1.5737012558040745e-114 1.9792562730767476 -chr4 41600 46999 7.479314004730516e-245 168.2151595038671 . 1166 306 7.479314004730516e-244 1.6821515950386712 -chr4 61800 66399 1.4988860864785783e-165 152.4906706437191 . 926 271 7.494430432392892e-165 1.524906706437191 -chr4 72800 77799 4.26634983112049e-134 146.53062167426648 . 800 244 1.0665874577801224e-133 1.465306216742665 -chr4 78600 78999 5.6625739181345514e-05 103.22952837235616 . 34 14 6.29174879792728e-05 1.0322952837235615 -chr4 80600 81599 2.777975572732711e-17 103.59803305314176 . 168 69 3.472469465915889e-17 1.0359803305314177 -chr4 85600 87399 2.6091166307239775e-59 143.26724762962738 . 359 112 4.348527717873296e-59 1.4326724762962737 -chr4 89600 92199 3.3232371576770455e-142 174.76146347410025 . 630 158 1.1077457192256818e-141 1.7476146347410024 |
| b |
| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/epic2_results3.bed --- a/epic2/test-data/epic2_results3.bed Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -chr4 17800 18699 island_1 136 . 1.367561922471873 25.8998 25.6309 -chr4 32100 33699 island_2 232 . 2.32156573905299 142.531 141.894 -chr4 41500 46999 island_3 167 . 1.6743920068364044 244.104 242.99 -chr4 55500 55599 island_4 74 . 0.7474099932884168 1.38871 1.31616 -chr4 60900 60999 island_5 74 . 0.7474099932884168 1.50708 1.39314 -chr4 61900 66399 island_6 155 . 1.550841347409922 168.128 167.315 -chr4 72700 77899 island_7 143 . 1.43860868673979 131.985 131.57 -chr4 78600 78899 island_8 127 . 1.2779247099871966 4.67152 4.51182 -chr4 80600 81599 island_9 103 . 1.031202959289008 16.4299 16.2191 -chr4 85600 87299 island_10 146 . 1.4694673801584501 60.1299 59.7941 -chr4 89000 92299 island_11 163 . 1.6325895912865587 135.464 134.952 |
| b |
| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/epic2_results3.txt --- a/epic2/test-data/epic2_results3.txt Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -#Chromosome Start End PValue Score Strand ChIPCount InputCount FDR log2FoldChange -chr4 17800 18699 1.2596293166425706e-26 136.7561922471873 . 166 54 2.339311588050488e-26 1.367561922471873 -chr4 32100 33699 2.946445596867846e-143 232.156573905299 . 399 67 1.2767930919760667e-142 2.32156573905299 -chr4 41500 46999 7.868596428937404e-245 167.43920068364045 . 1175 309 1.0229175357618626e-243 1.6743920068364044 -chr4 55500 55599 0.0408590134545058 74.74099932884168 . 10 5 0.04828792499168868 0.7474099932884168 -chr4 60900 60999 0.031111272762994507 74.74099932884168 . 12 6 0.04044465459189286 0.7474099932884168 -chr4 61900 66399 7.454733262747862e-169 155.0841347409922 . 918 263 4.84557662078611e-168 1.550841347409922 -chr4 72700 77899 1.0341241230257782e-132 143.860868673979 . 817 253 2.6887227198670233e-132 1.43860868673979 -chr4 78600 78899 2.1304915144814984e-05 127.79247099871966 . 26 9 3.077376632028831e-05 1.2779247099871966 -chr4 80600 81599 3.715910533402511e-17 103.1202959289008 . 168 69 6.03835461677908e-17 1.031202959289008 -chr4 85600 87299 7.414135910777427e-61 146.946738015845 . 353 107 1.6063961140017758e-60 1.4694673801584501 -chr4 89000 92299 3.4369281602401456e-136 163.25895912865587 . 676 183 1.1170016520780473e-135 1.6325895912865587 |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/test.bam |
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| Binary file epic2/test-data/test.bam has changed |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/test.bed.gz |
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| Binary file epic2/test-data/test.bed.gz has changed |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/test_ChIP.bam |
| b |
| Binary file epic2/test-data/test_ChIP.bam has changed |
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| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/test_Input.bam |
| b |
| Binary file epic2/test-data/test_Input.bam has changed |
| b |
| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/test_chromsizes.txt --- a/epic2/test-data/test_chromsizes.txt Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -chr4 99999 |
| b |
| diff -r 601ad3ea888b -r d3c28c4a2d16 epic2/test-data/test_fasta.fasta --- a/epic2/test-data/test_fasta.fasta Wed May 08 08:11:56 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1001 +0,0 @@\n->chr4\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNG\n-GACAGCGGAATCCTCGACCCGGTTGAGGAATGGTCGACGAAAATCTATCGGGTTCGAGGATTCGTCGACCAGGTGTTGGAATCGTCGACCGAGTCTGAGA\n-ATTCGTAGACCAGGACGGCGGAATCCTCGACAATGACGAGGTATGGTCGAGGAAAATCTATCGGGTTCGAGGATTCGTCTACCAGGTGATGGAATCCTCG\n-ACCAGGACAAAGAATTCGTCGACCAGGGGTGGAATTGTTGTTATTCCGATCATGAGAGCGGATATCAGTACAGATCCGACGCTGGTGAAAAAGATCACGG\n-CGATCGTGGATAGTATCAAGCCACCGAGAGTCTCGTATTCGGAGAAAGATCGGCCGATGAGGATAAGAGGTCGATCGGATGGACGGAAGAGGTAGAGGAA\n-GAGCCATGAAGCGGCGAGGCATAGGAGGAGGATGAGCGAGAATGGGTGGGCGGGAAGAGAGAAACTGATGATCAGAGCGATGATGCAGACGTAATTCACC\n-CTGAAATAAGAGGAGTTCTTCCAGAATCGCGTCATGGCCTCGAAGACAGAGTCAAGCTTGGTGAAAAGCAGATCGTTCGAGGAGCTCTGACCACGGCCGG\n-CTACGAGATAGACCACCACGAACCGTCTTGGTCACACTGTTGACAAATGCATGGACGGTTGGAGGTTGTGATTCCACCACATCAGTTACAATCGGAGGCT\n-GATCCGGACTTGGCTGTTGCGGTGGTGGAAATCGGAAGCACAGGGGGATTTGTGGACACCATTCGATTTTGTTCTTTAGGGATTTCAAGATTGGAAAATT\n-TTAGGAGACGATTGATTTGGAAGTCGGTGAAGTTTCGGTAGTGTTATGTATTTATTTTTTTTGTCATAAGCGGTAGCGTTATGTATTTGTAAGATCACAT\n-TAAGCGTCTTTCAACTTTGATTATACGCATTGCTTCATCTGATATCTAATCCATATTTTGATCAAAGTGACATTTGATAAAATAAAATAAAACTAACCTA\n-TTAATATTATAACTGAGGTTATTTTTTTAGAAAAAAGATAGCTAGCTACACGAATTATACGAGAATACATGGTCACATGCCAAGTATATTATTGTATCCT\n-TAACTACACGAAATTTATGTATTGCATGGCCACATATATGAACTATACTACGTCATGTGGCTAACATCATAGACATATAATTCCGGTATATCGACTGGTT\n-GACTCTGGCTTTGACTAACATTGACCGGCGTTGACCAACAAAAAATTTCAGAAAAAAACTTTAAAATAGTTTTTAATATTAAAAAATAAGAAACTGTTTT\n-TAGGTTTTGTATAAGAAAAAAAATTCTATTTTCAGCATAGATAGATTTGTATTTTTATCCATTAAATTTTATAATAATTAGTAAAAAGTCATTATTAAAT\n-TTTAAAATATTAAAATGGAAAAATATTATTTGAACAATTAAGTAGGAAATTGCTTAAATTTATATTGTCAATTAAAAAACCTTAATTTCTATACTATTTT\n-TATTATTATTTTGTATTTCTCAACCACAAAAATTATTAGAAGAAAACGTAATACGTATGAATTCTATTTTTATAAAAAAATTTGCTGAAATAAAAATGTT\n-AGATCAAACAACAAAATTTGTGCCTTTCTGGTTAATGTGGAGAATATGGAAGAGTAGGAATGATCTTGTATTCAACCGGAAAAGGACTGATTTCTATACT\n-ACAGTAGAATCCGCTCTCACTGACACGAAAGAATGGCTGGGTAATATACCAACGAAAGAAGATGATCAAGGAAATGCATTGTCGCCTACGAAGAGACACA\n-CTAAGTGGAGCCCCCCCCCCCCCCCCCCCCAAAAGTGATTGGCTAAAGTGCAATTATGATGCTTCTCACCATACGGGGAATACAATGTCTGGACTAGGGT\n-GGCTTATCCGCAACTCTCATGGCACGGTTTTGGAATGCGGTATGGGGTAGTTTCAAGGTCGAATGACTCCAGAAGAAGTTGAATGCTCGACACTTATCTG\n-GGCTATTCAAGCCGCTAGGGCCTATGGGTATACAAAGGTGATCTTTGAAGGTGATAACATAAATATTAATCGACTAATTAACCAGAAGTCTCCAAATCCC\n-CGACTACAACACTATCTTGATATCATATACAGTTGGATCCCAACTTTTACATCAGTAAAGTTCACCTTCAAGCATCGGGAACAAAATGCACGTGCGGATC\n-TTTTAGCTAAGAAAGCTATTTCAGCGGATACTCATTGGTCTCTGTTTCACTCATGTCCATATTTTCTTTATCATCTTGTAAACAACGATATCTCTTAAAG\n-TTCTAATAAAGTTTTTAGAAGGAAAAAAAAATGTTAGATTTTTTTTCTTTTTATAAAATAAAAGGAAAAATTGCAAGTTTTTTGTTTTATTATATTTTTA\n-ATTTAGTTTTGAAATTGAGAAAAATATATTTATATTGTATATAAAATATTTTTTTATTATACAGCAGGAAAAAATAATTCTTATTTTTTAATAATAAAAA\n-TAATTTTTAAGATTTTTTTGAATTTTTTGTTGGTCAAAGCCGGAATCAACTACTCAGTTTACCGAAATTGTATGTCTATGGTGTTAACCACATAACATCG\n-TATAGTTCATATATGTGGTCATGCAATACATCTACTTTGTGTAGCTGAAGATACAATAATATAGTTAGGCAAAGTGCATTTCACCATTACTGTTCCGGTC\n-ATAGGAAGTTTCCCTGATAGAAAAAAAAAATAACACAATGTTGCTCTTTCATAAGGAGTTGTAGACTTGACAATGTCAAATCCTTTTTTCTTTGATAACA\n-TTCATCTTCGAATTCTAAACATAATTATATCTAACGAGTAGACAAAAACTACATAACCATTGTTTCCCCTGATAAGTTGTAGCATCATATATAGCA'..b'ATCATTGTAAGTGATCAATAT\n-CTTGACAATGCTCAGATTTTCATGGCACCTGCCACCAGTGTTAATAGCTCCGTTGGCGATATTATCTACCGATATATCAACTCCACAAGGTCCTCTTTGA\n-TATTCTTGGGTATGATACTATACTACAAGTGTGTTCACAGCTAAGTAACTCTTTGTTTATGCTTTTCTCAGATCAGCGTCGGCTGTGATTCAGAAAACTC\n-GGCAAGTGACAATCCCTGCTCCATTTGTTGCTTCTTTTTCATCAAGAGGTCCCAATCCGGGATCAATACGTCTTCTCAAGGTATATATGACTTGATCAAT\n-GTCATCTGTTTATTGATAGATGATGATCTTATGTCTCTGCCATTTTTGCGGATTGTAGCCTGATATCGCTGCACCCGGGATTGATATATTGGCGGCCTTC\n-ACTCTAAAGAGATCACTGACTGGGTTAGATGGTGACACCCAGTTCTCAAAATTCACCATCCTGTCTGGCACCTCAATGGCCTGCCCTCATGTTGCTGGTG\n-TAGCTGCGTACGTCAAGTCTTTTCATCCGGATTGGACCCCTGCTGCCATCAAATCCGCCATCATTACCTCAGGTAACTCACGTCAAGTTCTCGTGAAACT\n-AAAAGCAGAGAAAGCAGTAATTATTTATCTGTTTGTTACGCAGCAAAACCGATAAGCCGGAGAGTGAACAAGGACGCAGAGTTTGCTTATGGAGGAGGCC\n-AAATAAACCCACGACGAGCCGCAAGCCCTGGCTTAGTCTACGACATGGACGACATCTCCTATGTTCAGTTCTTGTGCGGCGAAGGCTACAACGCAACCAC\n-TCTAGCTCCATTGGTGGGTACACGCTCCGTGAGCTGTTCCTCCATTGTCCCTGGACTCGGCCACGATTCCCTCAACTACCCAACAATCCAACTCACGTTG\n-AGATCCGCCAAAACGTCCACATTGGCTGTGTTCAGGCGGAGAGTCACCAACGTGGGACCACCGTCGTCGGTCTACACCGCCACCGTCCGAGCACCGAAAG\n-GAGTAGAAATCACGGTGGAGCCACAGAGTTTGTCATTTTCAAAGGCTTCACAAAAGAGAAGCTTCAAAGTGGTGGTGAAGGCCAAACAAATGACTCCTGG\n-GAAGATTGTGTCCGGCTTGCTCGTGTGGAAGAGCCCACGTCACTCTGTTCGTAGCCCCATTGTTATTTATAGTCCTACTTCGGATTGAAATTAATCACAT\n-CTCCAAAACAACATTTTACTTCAATGTAATCCTCTCACTTGTTCGTAAACTAACTCATTCCACTGCTTAATTTGAAAAAACCACTGTATTAAACTTATAG\n-GCCAATAAGCCCATATTAGAATATTTGGGCCTTTGGGCCCATTACACGAAACACTACTTACAGAATAACCTCTACCTCTCTCTCTATCGGAAAAGCCCTA\n-AAGCAAGCTTCTCTCCTTCGTCGTCAATGGAAGCTTCTCTACCGGAAGAGGTGCTTCAGCCGCTTCTACATGCTTCAGATTTATCATACTCTCTAGAAGA\n-TTGCTTGAAATTTCTTCTAGAGTCTTCCAAGACCGATTCAGGTCGTTCCGATCTCGCTTCCAAGTCTATACTTCCGTCGATCCTCCGTCTTCTTCAGCTT\n-CTTCCTTACCCATCTTCCCGCCATTATCTGAATCTCTCTCTGAAGGTCCTTCGAAACCTCTGCGCAGGTGAGGTTTCGAATCAGAACTCTTTCGTCGATC\n-ATGACGGCTCTGCTATCGTCTCCGACTTGCTTGATTCCGCCATTGCGGATTTCGAGACAGTTAGGTTCGGATTACAGGTTCTAGCGAACGTTGTATTGTT\n-CGGAGAGAAACGTCAGAGAGATGTGTGGCTCCGATTTTACCCGGAGAGGTTCTTATCAATCGCTAAGATTAGGAAACGTGAAACATTTGATCCTCTGTGT\n-ATGATTTTGTATACTTGCGTTGATGGAAGCTCAGAGATTGCTTCAGAGCTTTGTAGCTGTCAAGGGCTCACCATCATCGCTGAAACTCTACGGACTTCCT\n-CTTCCGGTAACACTCTTATTCCTGAAGCCAAAAATGCCATTTTGATCTTAAAGTCGTGATTTTTATCTGATTTGAGCCAATCTTGTTATAATTGTTTGTA\n-GTTGGGTCTGTGGAGGATTATTGGCTCAAGTTACTGGTTTCGAGAATCTGTGTTGAAGATGGTTACTTCCTCAAGCTCTTCTCTAAATTATACGAAGATG\n-CTGAAAATGAGATATTTTCATCAGAGCAAGCCTTTCTTGTGAGGATGGTGTCTGATATTGCTAATGAGCGGATAGGAAAAGTGTCAATCCCCAAGGATAC\n-AGCTTGTTCGATTCTCGGATTGTTTAGGCAATCAGTTGATGTTTTTGATTTTGTTTCGGGTGAAAGATCGGAGCTTCCAACGGGTTCAACTATAGTAGAT\n-GTGATGGGCTACTCTCTGGTGATAATAAGGGATGCTTGTGCTGGAGGACGTCTTGAAGAACTCAAGGAGGACAACAAGGATTCAGGTGATACTGTTGAAT\n-TGCTCTTGTCCTCTGGACTAATAGAACTTCTCCTTGATCTGCTTAGTAAACTTGATCCTCCAACAACAATAAAGAAGGCTTTAAACCAGAGTCCTAGTTC\n-TTCTTCTTCTTCATTAAAGCCGTGTCCTTACAGAGGATTCAGGAGAGATATTGTGTCGGTGATTGGGAACTGCGCGTACAGAAGAAAAGAGGTACAAGAT\n-GAGATCAGGGAGAGAGATGGGCTCTTTTTAATGCTGCAGCAGTGTGTGACCGATGATGAGAACCCGTTCTTGAGAGAATGGGGCTTGTGGTGTATAAGAA\n-ATTTACTGGAAGGGAACCCTGAAAACCAGGAAGTAGTGGCTGAGTTGGAGATTAAAGGCTCTGTGGATGTGCCTCAACTCCGTGAAATTGGTCTCAGGGT\n-TGAAATTGATCCTAAAACAGCCAGGCCAAAGCTTGTCAATGACACCTGAAGCTTCATTTGTCTCAGGGAAAAGAGGAGCTATACAATACACAACAAGAGG\n-TCCTTCTTGAGGCGGTGAAGATCATAAAGAAGCACGGTGTGTCGCTAGGTACCACCTGGGACAATTCTACATTGTGAGTGATCATTTTGTAGAGACAAGG\n-AATACTGATCCGGAAGCTATCTAGCTAGATGGATCCAAAACTCTGTGTTTTTGGGAAATTACAGAAAATCGTGATGACTTCTTAGGTTTCAAGAGAAAAA\n-TGTTTCATATTGGCCTTGCTTTTATTTGTTTCCTTCTTGGTATTTATAGGGTTCTAACAATTCCTATATACATGAAATGATCAATTCAATATGTTAAGCA\n-GAAAATGGCTCTCGTTTGATGTGGTTTGCAGTGCATGATCAATTAGTTCAGCTCAACTTTTGTGAAGCCTTTCATGTCTGTTGGTTTGTATTTAAGTTCC\n-TTGTTGTAAACCTTCTAAGCAGTTGTTGTGTTTCACTTTCTCTATAATAGAAAGGCAAGTTCTTCTCTATATTGTTCTGTTGACGATCAAACCAATTGTG\n-ATACAAAGTCTGATTCTCTTTCTCTGGTGTTCTGTTTCTAGAAGGAGATTCAGTTTCTAACAAGGTTCACTGCAGTCACAATTTACCGATATGCAGTCTT\n-TTCTCTGTTTTTAGATTGTTATGTTTGTTTGAGCAGAATCATGTTGAAGGTTTTCTCGAGATGTCAGCAAAAACTTACTTTACCACGGCTTGCAGACTTG\n-TACATGAAAGTTGATGATCAAACCAGGACTGATTGATTGATTGATTATACAAATGAAACCAAAAGTTCCGGAAAATACTCTGTGATAAGAATCTTATTGC\n-TCCCTGTTAACATATGGTTCAATATAACTCCAGAAAAAACCAGAGTCGTTGGCATTGAGCATTGTTGTGTGTATTCAGGAATTGTTTGATAGTCTGATT\n' 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