| Previous changeset 0:26d7ec4af119 (2019-09-06) Next changeset 2:214874e24cd6 (2021-08-26) |
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Commit message:
"planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit 6a45aa4c34b4f3b73ab0c6c3d9e7a315b62bf761" |
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modified:
macros.xml moabs.xml |
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added:
test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt |
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removed:
test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr |
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| diff -r 26d7ec4af119 -r 8c8cc81b34cd macros.xml --- a/macros.xml Fri Sep 06 09:54:27 2019 -0400 +++ b/macros.xml Sat Apr 11 04:14:34 2020 -0400 |
| b |
| @@ -8,16 +8,32 @@ <token name="@VERSION@">1.3.4.6</token> + <token name="@DMCExample@"> + +Example:: + + chr11 87 89 6 1 0.652,1 10 0.2 0,0.47 -0.8 -0.327 -0.857,-0.327 0.000318 0.00699 strongHypo + chr11 152 154 4 1 0.549,1 9 0.333 0.0575,0.609 -0.667 -0.113 -0.761,-0.113 0.0035 0.0699 hypo + chr11 258 260 3 1 0.473,1 13 0.231 0,0.466 -0.769 -0.165 -0.809,-0.165 0.00236 0.0357 hypo + chr11 331 333 6 0.667 0.341,0.992 22 0.227 0.0499,0.405 -0.439 -0.058 -0.66,-0.058 0.00636 0.0638 hypo + chr11 630 632 3 1 0.473,1 5 0 0,0.393 -1 -0.271 -1,-0.271 0.000954 0.0179 strongHypo + chr11 638 640 3 0.667 0.249,1 5 0.6 0.264,0.936 -0.0667 -0 -0.461,0.418 0.0286 1 hypo + chr11 641 643 4 1 0.549,1 5 0.4 0.064,0.736 -0.6 -0.0122 -0.748,-0.0122 0.00715 0.167 hypo + chr11 645 647 4 1 0.549,1 8 1 0.717,1 0 0 -0.183,0.374 0.067 1 hypo + chr11 666 668 4 1 0.549,1 9 0.667 0.391,0.942 -0.333 -0 -0.506,0.15 0.021 0.497 hypo + chr11 685 687 3 1 0.473,1 8 0 0,0.283 -1 -0.342 -1,-0.342 0.000364 0.00606 strongHypo + + </token> + <token name="@DMRExample@"> Example:: - chr11 316 1705 - 35 30 5 -1 - chr11 3052 3674 - 17 16 1 -1 - chr11 18599 19013 - 9 7 3 -1 - chr11 19120 19931 - 39 39 0 -1 - chr11 22138 22618 - 14 12 3 -1 - chr11 28140 28356 - 4 4 0 -1 + chr11 2529 2582 0.787 77 8 0.226 123 8 -0.204 3.79e-17 strongHypo + chr11 2976 3065 0.833 222 3 0.241 116 3 -0.339 1.69e-22 strongHypo + chr11 4327 5335 0.722 286 29 0.143 563 29 -0.201 2.3e-48 strongHypo + chr11 6544 7008 0.955 86 17 0.126 97 17 -0.223 6.5e-34 strongHypo + </token> <xml name="citations"> |
| b |
| diff -r 26d7ec4af119 -r 8c8cc81b34cd moabs.xml --- a/moabs.xml Fri Sep 06 09:54:27 2019 -0400 +++ b/moabs.xml Sat Apr 11 04:14:34 2020 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@">\n+<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@+galaxy1">\n <description>MOdel based Analysis of Bisulfite Sequencing data</description>\n <macros>\n <import>macros.xml</import>\n@@ -11,10 +11,13 @@\n #end if\n moabs -v 1 --def MMAP.p="\\${GALAXY_SLOTS:-4}" --def MCALL.p="\\${GALAXY_SLOTS:-4}" --def MCOMP.p="\\${GALAXY_SLOTS:-4}" --cf \'$cfg_file\' &&\n #if "1" in $output_selector:\n- cp -f dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr \'$output1\' &&\n+ cp -f dmc_M2_g1.G.bed_vs_g2.G.bed.txt \'$output1\' &&\n #end if\n #if "2" in $output_selector:\n- cp -f comp.g1.vs.g2.txt \'$output2\' &&\n+ cp -f dmr_M2_g1.G.bed_vs_g2.G.bed.txt \'$output2\' &&\n+ #end if\n+ #if "3" in $output_selector:\n+ cp -f comp.g1.vs.g2.txt \'$output3\' &&\n #end if\n echo Done\n ]]>\n@@ -62,18 +65,54 @@\n #if str( $bsmap_advanced.bsmap_mismatch.bsmap_mismatch_selector ) != "0":\n v=$bsmap_advanced.bsmap_mismatch.v\n #end if\n+ s=$bsmap_advanced.s\n+ w=$bsmap_advanced.w\n+ #if $bsmap_advanced.D:\n+ D=$bsmap_advanced.D\n+ #end if\n+ S=$bsmap_advanced.S\n n=$bsmap_advanced.n\n+ q=$bsmap_advanced.q\n+ z=$bsmap_advanced.z\n+ f=$bsmap_advanced.f\n+ #if $bsmap_advanced.A:\n+ A=$bsmap_advanced.A\n+ #end if\n r=$bsmap_advanced.r\n- R=\'\'\n+ #if str( $bsmap_advanced.R ) == "1":\n+ R=\'\'\n+ #end if\n+ #if str( $bsmap_advanced.u ) == "1":\n+ u=\'\'\n+ #end if\n+ m=$bsmap_advanced.m\n+ x=$bsmap_advanced.x\n \n [MCALL]\n Path=mcall\n r=\'${reference_fasta_filename}\'\n+ cytosineMinScore=$mcall_advanced.cytosineMinScore\n+ nextBaseMinScore=$mcall_advanced.nextBaseMinScore\n+ qualityScoreBase=$mcall_advanced.qualityScoreBase\n+ trimWGBSEndRepairPE2Seq=$mcall_advanced.trimWGBSEndRepairPE2Seq\n+ trimWGBSEndRepairPE1Seq=$mcall_advanced.trimWGBSEndRepairPE1Seq\n+ processPEOverlapSeq=$mcall_advanced.processPEOverlapSeq\n+ trimRRBSEndRepairSeq=$mcall_advanced.trimRRBSEndRepairSeq\n+ minFragSize=$mcall_advanced.minFragSize\n+ minMMFragSize=$mcall_advanced.minMMFragSize\n+ reportCpX=$mcall_advanced.reportCpX\n \n [MCOMP]\n Path=mcomp\n- reference=\'${reference_fasta_filename}\'\n doComp=$mcomp_advanced.doComp.compare_selector\n+ d=$mcomp_advanced.d\n+ filterCredibleDif=$mcomp_advanced.filterCredibleDif\n+ pFetDmc=$mcomp_advanced.pFetDmc\n+ pFetDmr=$mcomp_advanced.pFetDmr\n+ minNominalDif=$mcomp_advanced.minNominalDif\n+ minCredibleDif=$mcomp_advanced.minCredibleDif\n+ minDmcsInDmr=$mcomp_advanced.minDmcsInDmr\n+ maxDistConsDmcs=$mcomp_advanced.maxDistConsDmcs\n </configfile>\n </configfiles>\n \n@@ -134,9 +173,10 @@\n </conditional>\n </repeat>\n <section name="bsmap_advanced" title="Advanced options for BSMAP" expanded="False">\n+ <param argument="-s" type="integer" value="16" min="8" max="16" label="Seed size" help="The seed size for the HASH table. BSMAP implements a seeding algorithm by indexing reference for all possible k-mers, i.e. seeds. As for the seed size, i.e. the length of k-mers, 16 is suggested for the WGBS mode, and 12 is suggested for the RRBS mode. Min=8, max=16."/>\n <conditional name="bsmap_mismatch">\n- <param name="bsmap_mismatch_selector" type="select" label="Set the mismatch rate or number?" help="">\n- <option value="0">Do not set</option>\n+ '..b'n result\n+ 4. **BAM files** - intermediate BAM files\n+ 5. **Methylation BED files** - intermediate methylation BED files\n \n -----\n \n-MOABS will detect differential methylated regions (DMRs) using the input BS-Seq\n-reads. The output file is a tab-delimited text file (not strictly a BED\n-format), representing DMRs. It has 8 columns as below.\n+MOABS detects differentially methylated cytosines (DMCs) and differentially\n+methylated regions (DMRs) using the input BS-Seq reads. The output DMC and DMR\n+file are tab-delimited text files (not strictly a BED format), representing\n+DMCs and DMRs.\n+\n+A DMC site file has 15 columns as below.\n+\n+chrom<TAB>start<TAB>end<TAB>totalC_0<TAB>nominalRatio_0<TAB>ratioCI_0<TAB>totalC_1<TAB>nominalRatio_1<TAB>ratioCI_1<TAB>nominalDif_1-0<TAB>credibleDif_1-0<TAB>difCI_1-0<TAB>p_sim_1_v_0<TAB>p_fet_1_v_0<TAB>class\n \n-chrom<TAB>start<TAB>end<TAB>methylation_state<TAB>CpGsites<TAB>DMCcount<TAB>nonDMCcount<TAB>hidden_state\n+ 1. **chrom** - The chromosome of the CpG site.\n+ 2. **start** - The start genomic locus of the CpG site.\n+ 3. **end** - The end genomic locus of the CpG site.\n+ 4. **totalC_0** - The total number of CpG read coverage in group 0.\n+ 5. **nominalRatio_0** - The nominal methylation ratio of the CpG in group 0.\n+ 6. **ratioCI_0** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 0.\n+ 7. **totalC_1** - The total number of CpG read coverage in group 1.\n+ 8. **nominalRatio_1** - The nominal methylation ratio of the CpG in group 1.\n+ 9. **ratioCI_1** - The confidence interval (CI) of the nominal methylation ratio at the CpG site in group 1.\n+ 10. **nominalDif_1-0** - The nominal methylation difference between the group 1 and the group 0.\n+ 11. **credibleDif_1-0** - The credible methylation difference (CDIF) between the group 1 and the group 0.\n+ 12. **difCI_1-0** - The difference of ratio CIs between the group 1 and the group 0.\n+ 13. **p_sim_1_v_0** - P-value according to the similarity probablities.\n+ 14. **p_fet_1_v_0** - P-value according to the Fisher exact test.\n+ 15. **class** - 5-state class labels by methylation differences and p-values.\n+\n+For example, CpGs in the DMC file are recorded in the following format.\n+\n+@DMCExample@\n+\n+A DMR result file has 12 columns as below.\n+\n+chrom<TAB>start<TAB>end<TAB>meanRatio_0<TAB>totalC_0<TAB>cSites_0<TAB>meanRatio_1<TAB>totalC_1<TAB>cSites_1<TAB>methDif_1-0<TAB>p_1_v_0<TAB>class_1_v_0\n \n 1. **chrom** - The chromosome of the region.\n 2. **start** - The start genomic locus of the region.\n 3. **end** - The end genomic locus of the region.\n- 4. **methylation_state** - The methylation state of the region, "+"/"-" representing hyper- or hypo-methylation regions.\n- 5. **CpGsites** - Total number of CpG sites in the region.\n- 6. **DMCcount** - The number of differential methylated CpG sites (DMCs) in the region.\n- 7. **nonDMCcount** - The number of non-DMCs in the region.\n- 8. **hidden_state** - The hidden state prediced by Hidden Markov Model (HMM), "1"/"-1" representing hyper- or hypo-methylation states.\n+ 4. **meanRatio_0** - Mean methylation ratio of the region in group 0.\n+ 5. **totalC_0** - Total cytosine coverage of the region in group 0.\n+ 6. **cSites_0** - The number of CpG sites of the region in group 0.\n+ 7. **meanRatio_1** - Mean methylation ratio of the region in group 1.\n+ 8. **totalC_1** - Total cytosine coverage of the region in group 1.\n+ 9. **cSites_1** - The number of CpG sites of the region in group 1.\n+ 10. **methDif_1-0** - Average methylation difference of the region between group 1 and group 0.\n+ 11. **p_1_v_0** - P-value from Fisher exact test of the region between group 1 and group 0.\n+ 12. **class_1_v_0** - 5-state class labels for the DMR.\n \n-For example, six DMRs are identified in the following format.\n+For example, four DMRs are identified in the following format.\n \n @DMRExample@\n \n' |
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| diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 |
| b |
| b'@@ -0,0 +1,122 @@\n+#chrom\tstart\tend\ttotalC_0\tnominalRatio_0\tratioCI_0\ttotalC_1\tnominalRatio_1\tratioCI_1\tnominalDif_1-0\tcredibleDif_1-0\tdifCI_1-0\tp_sim_1_v_0\tp_fet_1_v_0\tclass\n+seg\t87\t89\t6\t1\t0.652,1\t10\t0.2\t0,0.47\t-0.8\t-0.327\t-0.857,-0.327\t0.000318\t0.00699\tstrongHypo\n+seg\t152\t154\t4\t1\t0.549,1\t9\t0.333\t0.0575,0.609\t-0.667\t-0.113\t-0.761,-0.113\t0.0035\t0.0699\thypo\n+seg\t258\t260\t3\t1\t0.473,1\t13\t0.231\t0,0.466\t-0.769\t-0.165\t-0.809,-0.165\t0.00236\t0.0357\thypo\n+seg\t331\t333\t6\t0.667\t0.341,0.992\t22\t0.227\t0.0499,0.405\t-0.439\t-0.058\t-0.66,-0.058\t0.00636\t0.0638\thypo\n+seg\t630\t632\t3\t1\t0.473,1\t5\t0\t0,0.393\t-1\t-0.271\t-1,-0.271\t0.000954\t0.0179\tstrongHypo\n+seg\t638\t640\t3\t0.667\t0.249,1\t5\t0.6\t0.264,0.936\t-0.0667\t-0\t-0.461,0.418\t0.0286\t1\thypo\n+seg\t641\t643\t4\t1\t0.549,1\t5\t0.4\t0.064,0.736\t-0.6\t-0.0122\t-0.748,-0.0122\t0.00715\t0.167\thypo\n+seg\t645\t647\t4\t1\t0.549,1\t8\t1\t0.717,1\t0\t0\t-0.183,0.374\t0.067\t1\thypo\n+seg\t666\t668\t4\t1\t0.549,1\t9\t0.667\t0.391,0.942\t-0.333\t-0\t-0.506,0.15\t0.021\t0.497\thypo\n+seg\t685\t687\t3\t1\t0.473,1\t8\t0\t0,0.283\t-1\t-0.342\t-1,-0.342\t0.000364\t0.00606\tstrongHypo\n+seg\t689\t691\t4\t1\t0.549,1\t9\t0.667\t0.391,0.942\t-0.333\t-0\t-0.506,0.15\t0.021\t0.497\thypo\n+seg\t697\t699\t3\t1\t0.473,1\t7\t0.571\t0.27,0.872\t-0.429\t-0\t-0.595,0.156\t0.017\t0.475\thypo\n+seg\t699\t701\t3\t1\t0.473,1\t9\t1\t0.741,1\t0\t0\t-0.149,0.454\t0.0596\t1\thypo\n+seg\t820\t822\t7\t0.857\t0.529,1\t20\t0.4\t0.2,0.6\t-0.457\t-0.0729\t-0.62,-0.0729\t0.00528\t0.0768\thypo\n+seg\t830\t832\t7\t0.857\t0.529,1\t18\t0.222\t0.0252,0.419\t-0.635\t-0.236\t-0.766,-0.236\t0.000768\t0.0068\tstrongHypo\n+seg\t842\t844\t4\t0.75\t0.343,1\t10\t0.3\t0.035,0.565\t-0.45\t-0\t-0.672,0.0536\t0.0117\t0.245\thypo\n+seg\t1172\t1174\t3\t1\t0.473,1\t12\t0.333\t0.0889,0.578\t-0.667\t-0.0658\t-0.738,-0.0658\t0.005\t0.0769\thypo\n+seg\t1180\t1182\t3\t1\t0.473,1\t11\t0.0909\t0,0.339\t-0.909\t-0.286\t-0.909,-0.286\t0.000705\t0.011\tstrongHypo\n+seg\t1201\t1203\t3\t0.667\t0.249,1\t14\t0.214\t0,0.44\t-0.452\t-0\t-0.7,0.0401\t0.0118\t0.191\thypo\n+seg\t1203\t1205\t3\t0.667\t0.249,1\t13\t0.308\t0.0724,0.543\t-0.359\t-0\t-0.629,0.133\t0.0176\t0.518\thypo\n+seg\t1303\t1305\t3\t1\t0.473,1\t4\t0\t0,0.451\t-1\t-0.229\t-1,-0.229\t0.00143\t0.0286\tstrongHypo\n+seg\t1333\t1335\t4\t0.25\t0,0.657\t6\t0.167\t0,0.521\t-0.0833\t-0\t-0.47,0.291\t0.0339\t1\thypo\n+seg\t1343\t1345\t3\t0\t0,0.527\t10\t0.2\t0,0.47\t0.2\t0\t-0.318,0.357\t0.0363\t1\thypo\n+seg\t2310\t2312\t8\t1\t0.717,1\t11\t0.455\t0.198,0.711\t-0.545\t-0.162\t-0.69,-0.162\t0.00184\t0.0181\thypo\n+seg\t2336\t2338\t8\t1\t0.717,1\t5\t0.6\t0.264,0.936\t-0.4\t-0.0115\t-0.656,-0.0115\t0.0099\t0.128\thypo\n+seg\t2396\t2398\t8\t1\t0.717,1\t12\t0.333\t0.0889,0.578\t-0.667\t-0.273\t-0.774,-0.273\t0.000439\t0.0047\tstrongHypo\n+seg\t2488\t2490\t3\t0.333\t0,0.751\t7\t0\t0,0.312\t-0.333\t-0\t-0.669,0.0603\t0.0175\t0.3\thypo\n+seg\t2516\t2518\t7\t0.571\t0.27,0.872\t16\t0.5\t0.278,0.722\t-0.0714\t-0\t-0.372,0.269\t0.0377\t1\thypo\n+seg\t2529\t2531\t7\t0.571\t0.27,0.872\t25\t0.04\t0,0.17\t-0.531\t-0.203\t-0.745,-0.203\t0.000552\t0.00445\tstrongHypo\n+seg\t2548\t2550\t10\t0.7\t0.435,0.965\t17\t0.0588\t0,0.238\t-0.641\t-0.303\t-0.787,-0.303\t0.000131\t0.000939\tstrongHypo\n+seg\t2550\t2552\t10\t0.8\t0.53,1\t20\t0.4\t0.2,0.6\t-0.4\t-0.0665\t-0.586,-0.0665\t0.00582\t0.0577\thypo\n+seg\t2556\t2558\t11\t0.636\t0.382,0.891\t19\t0.0526\t0,0.216\t-0.584\t-0.271\t-0.746,-0.271\t0.000167\t0.0011\tstrongHypo\n+seg\t2567\t2569\t9\t0.889\t0.606,1\t11\t0.364\t0.109,0.618\t-0.525\t-0.135\t-0.697,-0.135\t0.0027\t0.0281\thypo\n+seg\t2573\t2575\t10\t0.9\t0.636,1\t12\t0.167\t0,0.41\t-0.733\t-0.352\t-0.835,-0.352\t0.000117\t0.00191\tstrongHypo\n+seg\t2578\t2580\t9\t0.889\t0.606,1\t10\t0.5\t0.234,0.766\t-0.389\t-0.0151\t-0.6,-0.0151\t0.0092\t0.141\thypo\n+seg\t2580\t2582\t11\t0.909\t0.661,1\t9\t0.222\t0,0.507\t-0.687\t-0.287\t-0.812,-0.287\t0.00036\t0.00452\tstrongHypo\n+seg\t2603\t2605\t8\t1\t0.717,1\t3\t0.333\t0,0.751\t-0.667\t-0.119\t-0.834,-0.119\t0.00328\t0.0545\thypo\n+seg\t2625\t2627\t8\t1\t0.717,1\t5\t0.6\t0.264,0.936\t-0.4\t-0.0115\t-0.656,-0.0115\t0.0099\t0.128\thypo\n+seg\t2641\t2643\t10\t0.9\t0.636,1\t10\t0.2\t0,0.47\t-0.7\t-0.299\t-0.817,-0.299\t0.00031\t0.00548\tstrongHypo\n+seg\t2645\t2647\t9\t0.667\t0.391,0.942\t8\t0.25\t0,0.55\t-0.417\t-0\t-0.642,0.00262\t0.00968\t0.153\thypo\n+seg\t2659\t2661\t11\t0.727\t0.473,0.982\t7\t0.429\t0.128,0.73\t-0.299\t-0\t-0.567,0.0906\t0.0183\t0.332\thypo\n+seg\t2684\t2686\t9\t0.778\t0.493,1\t10\t0.5\t0.234,0.766\t-0.278\t-0\t-0.'..b'\t0.00203\tstrongHypo\n+seg\t4982\t4984\t15\t0.6\t0.374,0.826\t11\t0.455\t0.198,0.711\t-0.145\t-0\t-0.414,0.169\t0.034\t0.692\thypo\n+seg\t4984\t4986\t14\t0.571\t0.338,0.804\t11\t0.455\t0.198,0.711\t-0.117\t-0\t-0.393,0.198\t0.0369\t0.695\thypo\n+seg\t5011\t5013\t16\t0.375\t0.157,0.593\t12\t0.25\t0.00535,0.495\t-0.125\t-0\t-0.364,0.168\t0.0389\t0.687\thypo\n+seg\t501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|
| b |
| diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +#chrom start end meanRatio_0 totalC_0 cSites_0 meanRatio_1 totalC_1 cSites_1 methDif_1-0 p_1_v_0 class_1_v_0 +seg 2529 2582 0.787 77 8 0.226 123 8 -0.204 3.79e-17 strongHypo +seg 2976 3065 0.833 222 3 0.241 116 3 -0.339 1.69e-22 strongHypo +seg 4327 5335 0.722 286 29 0.143 563 29 -0.201 2.3e-48 strongHypo +seg 6544 7008 0.955 86 17 0.126 97 17 -0.223 6.5e-34 strongHypo |
| b |
| diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr --- a/test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr Fri Sep 06 09:54:27 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -seg 152 1305 - 20 15 5 1 -seg 2310 7008 - 95 77 18 1 -seg 8052 8091 - 3 3 0 1 |
| b |
| diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_dmc_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 |
| b |
| b'@@ -0,0 +1,308 @@\n+#chrom\tstart\tend\ttotalC_0\tnominalRatio_0\tratioCI_0\ttotalC_1\tnominalRatio_1\tratioCI_1\tnominalDif_1-0\tcredibleDif_1-0\tdifCI_1-0\tp_sim_1_v_0\tp_fet_1_v_0\tclass\n+chr11\t41\t43\t3\t0\t0,0.527\t3\t0\t0,0.527\t0\t0\t-0.391,0.391\t0.0449\t1\thypo\n+chr11\t48\t50\t5\t0\t0,0.393\t3\t0\t0,0.527\t0\t0\t-0.267,0.422\t0.0521\t1\thypo\n+chr11\t56\t58\t6\t0\t0,0.348\t4\t0\t0,0.451\t0\t0\t-0.241,0.359\t0.0619\t1\thypo\n+chr11\t59\t61\t8\t0\t0,0.283\t5\t0.4\t0.064,0.736\t0.4\t0.0115\t0.0115,0.656\t0.0099\t0.128\thyper\n+chr11\t101\t103\t13\t0.0769\t0,0.297\t7\t0.143\t0,0.471\t0.0659\t0\t-0.152,0.364\t0.051\t1\thypo\n+chr11\t140\t142\t16\t0\t0,0.162\t9\t0\t0,0.259\t0\t0\t-0.107,0.216\t0.123\t1\thypo\n+chr11\t144\t146\t14\t0\t0,0.181\t10\t0.1\t0,0.364\t0.1\t0\t-0.0722,0.317\t0.0549\t0.417\thypo\n+chr11\t210\t212\t15\t0.133\t0,0.344\t12\t0.417\t0.169,0.664\t0.283\t0\t-0.00696,0.507\t0.0139\t0.185\thypo\n+chr11\t215\t217\t19\t0.263\t0.0688,0.458\t16\t0.25\t0.039,0.461\t-0.0132\t-0\t-0.238,0.226\t0.0566\t1\thypo\n+chr11\t316\t318\t24\t0.0833\t0,0.231\t26\t0.846\t0.692,1\t0.763\t0.538\t0.538,0.845\t9.21e-09\t3.52e-08\tstrongHyper\n+chr11\t331\t333\t27\t0.037\t0,0.159\t26\t0.808\t0.649,0.966\t0.771\t0.558\t0.558,0.85\t1.11e-09\t4.05e-09\tstrongHyper\n+chr11\t400\t402\t34\t0.0588\t0,0.169\t34\t0.412\t0.254,0.57\t0.353\t0.18\t0.18,0.486\t0.000192\t0.00115\thyper\n+chr11\t407\t409\t33\t0\t0,0.0843\t34\t0.588\t0.43,0.746\t0.588\t0.41\t0.41,0.692\t8.72e-09\t3.39e-08\tstrongHyper\n+chr11\t445\t447\t25\t0.08\t0,0.223\t33\t0.606\t0.447,0.766\t0.526\t0.316\t0.316,0.648\t9.32e-06\t3.59e-05\tstrongHyper\n+chr11\t469\t471\t26\t0.0385\t0,0.164\t34\t0.588\t0.43,0.746\t0.55\t0.352\t0.352,0.661\t1.43e-06\t5.87e-06\tstrongHyper\n+chr11\t546\t548\t20\t0.1\t0,0.271\t32\t0.812\t0.672,0.953\t0.713\t0.482\t0.482,0.806\t1.08e-07\t4.38e-07\tstrongHyper\n+chr11\t666\t668\t20\t0.05\t0,0.207\t38\t0.553\t0.401,0.704\t0.503\t0.29\t0.29,0.612\t2.88e-05\t0.000144\tstrongHyper\n+chr11\t694\t696\t22\t0.318\t0.132,0.504\t41\t0.902\t0.795,1\t0.584\t0.368\t0.368,0.716\t8.72e-07\t2.95e-06\tstrongHyper\n+chr11\t712\t714\t28\t0.0714\t0,0.202\t42\t0.881\t0.771,0.991\t0.81\t0.63\t0.63,0.873\t1.66e-12\t4.55e-12\tstrongHyper\n+chr11\t721\t723\t28\t0.0357\t0,0.153\t39\t0.923\t0.817,1\t0.887\t0.719\t0.719,0.926\t9.44e-15\t2.57e-14\tstrongHyper\n+chr11\t737\t739\t27\t0.037\t0,0.159\t37\t0.622\t0.471,0.772\t0.585\t0.393\t0.393,0.687\t2.21e-07\t9.15e-07\tstrongHyper\n+chr11\t753\t755\t23\t0.087\t0,0.24\t41\t0.78\t0.653,0.908\t0.694\t0.488\t0.488,0.783\t1.74e-08\t5.8e-08\tstrongHyper\n+chr11\t762\t764\t27\t0.037\t0,0.159\t42\t0.619\t0.477,0.761\t0.582\t0.397\t0.397,0.68\t1.42e-07\t5.56e-07\tstrongHyper\n+chr11\t792\t794\t37\t0.324\t0.178,0.471\t38\t0.842\t0.719,0.966\t0.518\t0.329\t0.329,0.642\t1.8e-06\t6.02e-06\tstrongHyper\n+chr11\t798\t800\t36\t0.306\t0.159,0.452\t40\t0.875\t0.761,0.989\t0.569\t0.384\t0.384,0.685\t1.25e-07\t3.94e-07\tstrongHyper\n+chr11\t816\t818\t33\t0.0303\t0,0.132\t34\t0.912\t0.793,1\t0.881\t0.714\t0.714,0.924\t5.66e-15\t1.61e-14\tstrongHyper\n+chr11\t830\t832\t37\t0.405\t0.254,0.557\t35\t0.914\t0.798,1\t0.509\t0.324\t0.324,0.629\t1.55e-06\t5.05e-06\tstrongHyper\n+chr11\t954\t956\t47\t0\t0,0.0605\t33\t0.485\t0.323,0.647\t0.485\t0.324\t0.324,0.606\t1.85e-08\t4.33e-08\tstrongHyper\n+chr11\t977\t979\t47\t0.255\t0.132,0.379\t37\t0.703\t0.559,0.847\t0.447\t0.264\t0.264,0.579\t1.7e-05\t5.98e-05\tstrongHyper\n+chr11\t1006\t1008\t38\t0\t0,0.0739\t38\t0.526\t0.374,0.678\t0.526\t0.364\t0.364,0.633\t1.27e-08\t6.16e-08\tstrongHyper\n+chr11\t1066\t1068\t30\t0.367\t0.202,0.532\t45\t0.756\t0.63,0.881\t0.389\t0.192\t0.192,0.538\t0.00027\t0.00152\thyper\n+chr11\t1116\t1118\t22\t0.182\t0.0087,0.355\t35\t0.771\t0.632,0.911\t0.59\t0.362\t0.362,0.713\t4.09e-06\t2.32e-05\tstrongHyper\n+chr11\t1145\t1147\t18\t0.556\t0.345,0.766\t26\t0.538\t0.358,0.719\t-0.0171\t-0\t-0.248,0.222\t0.0547\t1\thypo\n+chr11\t1260\t1262\t18\t0.0556\t0,0.226\t24\t0.375\t0.192,0.558\t0.319\t0.0943\t0.0943,0.47\t0.00355\t0.0264\thyper\n+chr11\t1320\t1322\t17\t0.118\t0,0.31\t25\t0.64\t0.461,0.819\t0.522\t0.26\t0.26,0.661\t0.000172\t0.00122\tstrongHyper\n+chr11\t1559\t1561\t36\t0.194\t0.0615,0.327\t27\t0.852\t0.702,1\t0.657\t0.451\t0.451,0.762\t5.66e-08\t1.9e-07\tstrongHyper\n+chr11\t1574\t1576\t33\t0.152\t0.0184,0.285\t28\t0.607\t0.435,0.779\t0.456\t0.245\t0.245,0.601\t7.43e-05\t0.000388\tstrongHyper\n+chr11\t1592\t1594\t35\t0.343\t0.191,0.495\t33\t0.697\t0.544,0.85\t0.354\t0.149\t0.149,0.509\t0.001\t0.00421\thyper\n+chr11\t1609\t1611\t34\t0.0588\t0,0.169\t41\t0.244\t0.113,'..b'583\t7585\t26\t0.154\t6.6e-05,0.308\t34\t0.176\t0.0419,0.311\t0.0226\t0\t-0.145,0.172\t0.0825\t1\thypo\n+chr11\t7633\t7635\t21\t0.0952\t0,0.259\t26\t0.154\t6.6e-05,0.308\t0.0586\t0\t-0.116,0.209\t0.0723\t0.678\thypo\n+chr11\t7655\t7657\t15\t0\t0,0.171\t21\t0.143\t0,0.316\t0.143\t0\t-0.0375,0.275\t0.0356\t0.25\thypo\n+chr11\t7673\t7675\t16\t0\t0,0.162\t17\t0\t0,0.153\t0\t0\t-0.125,0.115\t0.165\t1\thypo\n+chr11\t7679\t7681\t17\t0\t0,0.153\t21\t0.0476\t0,0.198\t0.0476\t0\t-0.0895,0.162\t0.111\t1\thypo\n+chr11\t7688\t7690\t15\t0\t0,0.171\t18\t0.167\t0,0.359\t0.167\t0\t-0.0215,0.317\t0.0269\t0.233\thypo\n+chr11\t7695\t7697\t15\t0.0667\t0,0.264\t21\t0\t0,0.127\t-0.0667\t-0\t-0.23,0.0515\t0.079\t0.417\thypo\n+chr11\t7729\t7731\t14\t0\t0,0.181\t21\t0.19\t0.0119,0.369\t0.19\t0\t-0.0108,0.326\t0.021\t0.133\thypo\n+chr11\t7748\t7750\t15\t0\t0,0.171\t23\t0.0435\t0,0.183\t0.0435\t0\t-0.11,0.144\t0.118\t1\thypo\n+chr11\t7825\t7827\t18\t0\t0,0.146\t20\t0.05\t0,0.207\t0.05\t0\t-0.0806,0.171\t0.107\t1\thypo\n+chr11\t7866\t7868\t17\t0\t0,0.153\t22\t0.0455\t0,0.19\t0.0455\t0\t-0.0916,0.154\t0.116\t1\thypo\n+chr11\t7878\t7880\t15\t0.0667\t0,0.264\t21\t0.0952\t0,0.259\t0.0286\t0\t-0.161,0.177\t0.0837\t1\thypo\n+chr11\t7882\t7884\t13\t0.0769\t0,0.297\t20\t0.3\t0.107,0.493\t0.223\t0\t-0.0326,0.392\t0.0204\t0.202\thypo\n+chr11\t8027\t8029\t26\t0.0385\t0,0.164\t18\t0.167\t0,0.359\t0.128\t0\t-0.0241,0.302\t0.0357\t0.289\thypo\n+chr11\t8033\t8035\t27\t0.037\t0,0.159\t16\t0.0625\t0,0.25\t0.0255\t0\t-0.0862,0.195\t0.103\t1\thypo\n+chr11\t8303\t8305\t36\t0.0556\t0,0.161\t23\t0.0435\t0,0.183\t-0.0121\t-0\t-0.106,0.119\t0.131\t1\thypo\n+chr11\t8414\t8416\t16\t0.0625\t0,0.25\t27\t0.444\t0.268,0.621\t0.382\t0.14\t0.14,0.521\t0.00165\t0.0143\thyper\n+chr11\t8583\t8585\t24\t0.0833\t0,0.231\t27\t0.148\t0,0.298\t0.0648\t0\t-0.0948,0.209\t0.0723\t0.671\thypo\n+chr11\t8678\t8680\t19\t0\t0,0.139\t17\t0\t0,0.153\t0\t0\t-0.104,0.119\t0.178\t1\thypo\n+chr11\t8692\t8694\t23\t0.0435\t0,0.183\t19\t0.0526\t0,0.216\t0.00915\t0\t-0.116,0.155\t0.113\t1\thypo\n+chr11\t8755\t8757\t26\t0\t0,0.105\t24\t0.0417\t0,0.176\t0.0417\t0\t-0.0523,0.15\t0.126\t0.48\thypo\n+chr11\t8786\t8788\t25\t0\t0,0.109\t19\t0\t0,0.139\t0\t0\t-0.0781,0.112\t0.207\t1\thypo\n+chr11\t8812\t8814\t22\t0.0909\t0,0.249\t21\t0\t0,0.127\t-0.0909\t-0\t-0.217,0.038\t0.0592\t0.488\thypo\n+chr11\t8829\t8831\t20\t0\t0,0.133\t22\t0.136\t0,0.304\t0.136\t0\t-0.0114,0.27\t0.0304\t0.233\thypo\n+chr11\t8836\t8838\t21\t0\t0,0.127\t21\t0.0476\t0,0.198\t0.0476\t0\t-0.0664,0.167\t0.112\t1\thypo\n+chr11\t8855\t8857\t17\t0.0588\t0,0.238\t22\t0.0909\t0,0.249\t0.0321\t0\t-0.14,0.174\t0.0887\t1\thypo\n+chr11\t8902\t8904\t17\t0\t0,0.153\t15\t0.333\t0.111,0.555\t0.333\t0.104\t0.104,0.508\t0.00262\t0.0149\thyper\n+chr11\t8914\t8916\t20\t0.35\t0.153,0.547\t13\t0.308\t0.0724,0.543\t-0.0423\t-0\t-0.281,0.229\t0.0495\t1\thypo\n+chr11\t8920\t8922\t22\t0\t0,0.122\t12\t0\t0,0.206\t0\t0\t-0.0801,0.173\t0.157\t1\thypo\n+chr11\t8948\t8950\t33\t0\t0,0.0843\t17\t0.0588\t0,0.238\t0.0588\t0\t-0.0234,0.214\t0.0814\t0.34\thypo\n+chr11\t8975\t8977\t42\t0.0476\t0,0.139\t19\t0\t0,0.139\t-0.0476\t-0\t-0.11,0.0832\t0.131\t1\thypo\n+chr11\t9127\t9129\t41\t0.0244\t0,0.108\t31\t0.0968\t0,0.225\t0.0724\t0\t-0.0228,0.187\t0.0662\t0.308\thypo\n+chr11\t9136\t9138\t42\t0.0476\t0,0.139\t33\t0.0606\t0,0.174\t0.013\t0\t-0.0771,0.12\t0.143\t1\thypo\n+chr11\t9227\t9229\t45\t0.0444\t0,0.131\t38\t0.0526\t0,0.153\t0.00819\t0\t-0.0754,0.103\t0.16\t1\thypo\n+chr11\t9270\t9272\t40\t0.025\t0,0.111\t33\t0.0909\t0,0.213\t0.0659\t0\t-0.0287,0.175\t0.0758\t0.322\thypo\n+chr11\t9301\t9303\t40\t0.175\t0.0523,0.298\t33\t0.0303\t0,0.132\t-0.145\t-0.0191\t-0.253,-0.0191\t0.0174\t0.0652\thypo\n+chr11\t9371\t9373\t25\t0\t0,0.109\t32\t0\t0,0.0868\t0\t0\t-0.0872,0.0628\t0.257\t1\thypo\n+chr11\t9380\t9382\t25\t0.04\t0,0.17\t31\t0\t0,0.0894\t-0.04\t-0\t-0.147,0.0405\t0.129\t0.446\thypo\n+chr11\t9447\t9449\t17\t0\t0,0.153\t30\t0\t0,0.0921\t0\t0\t-0.129,0.0611\t0.207\t1\thypo\n+chr11\t9478\t9480\t16\t0\t0,0.162\t21\t0.0476\t0,0.198\t0.0476\t0\t-0.097,0.16\t0.111\t1\thypo\n+chr11\t9510\t9512\t14\t0\t0,0.181\t23\t0.0435\t0,0.183\t0.0435\t0\t-0.119,0.143\t0.117\t1\thypo\n+chr11\t9588\t9590\t20\t0\t0,0.133\t18\t0.111\t0,0.296\t0.111\t0\t-0.0292,0.261\t0.0448\t0.218\thypo\n+chr11\t9677\t9679\t11\t0.0909\t0,0.339\t13\t0.231\t0,0.466\t0.14\t0\t-0.131,0.354\t0.0398\t0.596\thypo\n+chr11\t9697\t9699\t14\t0\t0,0.181\t15\t0.2\t0,0.417\t0.2\t0\t-0.00842,0.371\t0.02\t0.224\thypo\n+chr11\t9709\t9711\t11\t0\t0,0.221\t18\t0.111\t0,0.296\t0.111\t0\t-0.104,0.245\t0.0574\t0.512\thypo\n+chr11\t9729\t9731\t6\t0.167\t0,0.521\t16\t0\t0,0.162\t-0.167\t-0\t-0.475,0.0224\t0.0282\t0.273\thypo\n' |
| b |
| diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_dmr_M2_g1.G.bed_vs_g2.G.bed.txt Sat Apr 11 04:14:34 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +#chrom start end meanRatio_0 totalC_0 cSites_0 meanRatio_1 totalC_1 cSites_1 methDif_1-0 p_1_v_0 class_1_v_0 +chr11 316 1705 0.148 1061 35 0.657 1278 35 0.326 3.11e-141 strongHyper |
| b |
| diff -r 26d7ec4af119 -r 8c8cc81b34cd test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr --- a/test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr Fri Sep 06 09:54:27 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -chr11 316 1705 - 35 30 5 -1 -chr11 3052 3674 - 17 16 1 -1 |