| Next changeset 1:8c8cc81b34cd (2020-04-11) |
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Commit message:
"planemo upload for repository https://github.com/sunnyisgalaxy/moabs commit fca680a439f168971afc9944ccbbdd9b3b65c845" |
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added:
all_fasta.loc.sample macros.xml moabs.xml test-data/6_all_1.fq.gz test-data/6_all_2.fq.gz test-data/8_all_1.fq.gz test-data/8_all_2.fq.gz test-data/PE_comp.g1.vs.g2.txt test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr test-data/SE_comp.g1.vs.g2.txt test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr test-data/SE_g1.G.bed test-data/SE_g1_r1.bam test-data/SE_g1_r2.bam test-data/SE_g2.G.bed test-data/SE_g2_r1.bam test-data/SE_g2_r2.bam test-data/TKO2PE1.fastq.gz test-data/TKO2PE2.fastq.gz test-data/WTPE1.fastq.gz test-data/WTPE2.fastq.gz test-data/all_fasta.loc test-data/chr11.fa test-data/seg.fa tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 26d7ec4af119 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Fri Sep 06 09:54:27 2019 -0400 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
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| diff -r 000000000000 -r 26d7ec4af119 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 06 09:54:27 2019 -0400 |
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| @@ -0,0 +1,29 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">moabs</requirement> + </requirements> + </xml> + + <token name="@VERSION@">1.3.4.6</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 + </token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1186/gb-2014-15-2-r38</citation> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r 26d7ec4af119 moabs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/moabs.xml Fri Sep 06 09:54:27 2019 -0400 |
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| b'@@ -0,0 +1,465 @@\n+<tool id="moabs" name="MOABS" profile="16.04" version="@VERSION@">\n+ <description>MOdel based Analysis of Bisulfite Sequencing data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ #if str( $mcomp_advanced.doComp.compare_selector ) == "0":\n+ cp -f \'$mcomp_advanced.doComp.compFile\' comp.g1.vs.g2.txt &&\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+ #end if\n+ #if "2" in $output_selector:\n+ cp -f comp.g1.vs.g2.txt \'$output2\' &&\n+ #end if\n+ echo Done\n+ ]]>\n+ </command>\n+ <configfiles>\n+ <configfile name="cfg_file">\n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ #set $reference_fasta_filename = $reference_source.ref_file\n+ #else:\n+ #set $reference_fasta_filename = $reference_source.ref_file.fields.path\n+ #end if\n+ [INPUT]\n+ #for $i, $s in enumerate( $g1_fastq )\n+ #if str( $s.fastq_input.fastq_input_selector ) == "paired":\n+ s1_r${i+1}_1=\'$s.fastq_input.fastq_input1\'\n+ s1_r${i+1}_2=\'$s.fastq_input.fastq_input2\'\n+ #elif str( $s.fastq_input.fastq_input_selector ) == "paired_collection":\n+ s1_r${i+1}_1=\'$s.fastq_input.fastq_input1.forward\'\n+ s1_r${i+1}_2=\'$s.fastq_input.fastq_input1.reverse\'\n+ #else:\n+ s1_r${i+1}=\'$s.fastq_input.fastq_input1\'\n+ #end if\n+ #end for\n+\n+ #for $i, $s in enumerate( $g2_fastq )\n+ #if str( $s.fastq_input.fastq_input_selector ) == "paired":\n+ s2_r${i+1}_1=\'$s.fastq_input.fastq_input1\'\n+ s2_r${i+1}_2=\'$s.fastq_input.fastq_input2\'\n+ #elif str( $s.fastq_input.fastq_input_selector ) == "paired_collection":\n+ s2_r${i+1}_1=\'$s.fastq_input.fastq_input1.forward\'\n+ s2_r${i+1}_2=\'$s.fastq_input.fastq_input1.reverse\'\n+ #else:\n+ s2_r${i+1}=\'$s.fastq_input.fastq_input1\'\n+ #end if\n+ #end for\n+\n+ [TASK]\n+ Program=MMAP\n+ Label=g1,g2\n+ Parallel=NONE\n+\n+ [MMAP]\n+ Path=bsmap\n+ d=\'${reference_fasta_filename}\'\n+ #if str( $bsmap_advanced.bsmap_mismatch.bsmap_mismatch_selector ) != "0":\n+ v=$bsmap_advanced.bsmap_mismatch.v\n+ #end if\n+ n=$bsmap_advanced.n\n+ r=$bsmap_advanced.r\n+ R=\'\'\n+\n+ [MCALL]\n+ Path=mcall\n+ r=\'${reference_fasta_filename}\'\n+\n+ [MCOMP]\n+ Path=mcomp\n+ reference=\'${reference_fasta_filename}\'\n+ doComp=$mcomp_advanced.doComp.compare_selector\n+ </configfile>\n+ </configfiles>\n+\n+ <inputs>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a cache FASTA?" help="Cached FASTA">\n+ <option value="cached">Use a cached genome FASTA</option>\n+ <option value="history">Use a genome FASTA from history</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">\n+ <options from_data_table="all_fasta">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_optio'..b'rion result\n+ 3. **BAM files** - intermediate BAM files\n+ 4. **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+\n+chrom<TAB>start<TAB>end<TAB>methylation_state<TAB>CpGsites<TAB>DMCcount<TAB>nonDMCcount<TAB>hidden_state\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+\n+For example, six DMRs are identified in the following format.\n+\n+@DMRExample@\n+\n+-----\n+\n+The intermediate comparison file summarizes methylation ratio comparison\n+results on CpG sites. It has 19 columns as below.\n+\n+ 1. **chrom** - The chromosome of the GpG site.\n+ 2. **start** - The start position of the site.\n+ 3. **end** - The end position of the site.\n+ 4. **single** - The next two columns are attributes for the single position.\n+ 5. **totalC_0** - Total number of Cs in the first group.\n+ 6. **nominalRatio_0** - Nominal methylation ratio in the first group.\n+ 7. **ratioCI_0** - The confidence interval of the methylation ratio in the first group.\n+ 8. **single** - The next two columns are attributes for the single position.\n+ 9. **totalC_1** - Total number of Cs in the second group.\n+ 10. **nominalRatio_1** - Nominal methylation ratio in the second group.\n+ 11. **ratioCI_1** - The confidence interval of the methylation ratio in the second group.\n+ 12. **pair** - The next three columns are attributes for pairs of groups.\n+ 13. **nominalDif_1-0** - Nominal difference of methylation ratio between group 1 and group 0.\n+ 14. **credibleDif_1-0** - Credible methylation difference between group 1 and group 0.\n+ 15. **difCI_1-0** - Difference of confidence intervals between group 1 and group 0.\n+ 16. **p_sim** - The next column is the simulation p-value.\n+ 17. **p_sim_1_v_0** - Simulation p-value between group 1 and group 0.\n+ 18. **p_fet** - The next column is the FET p-value.\n+ 19. **p_fet_1_v_0** - FET p-value between group 1 and group 0.\n+\n+The comparison result file can be reused for DMR calling.\n+\n+-----\n+\n+BAM files are intermediate mapping results of input reads to the referene\n+genome. These BAM files can be reused in downstream methylation analysis.\n+\n+-----\n+\n+Methylation calling BED files are intermediate methylation calling results of\n+Cs in two groups of input reads. These methyation calling results can be easily\n+reused in downstream DMR calling and visualization. The BED file has 15 columns\n+as below.\n+\n+ 1. **chrom** - The chromosome of the site.\n+ 2. **start** - The start position of the site.\n+ 3. **end** - The end position of the site.\n+ 4. **ratio** - Methylation ratio in the site\n+ 5. **totalC** - Total number of reads in current Cs.\n+ 6. **methC** - Methylated Cs.\n+ 7. **strand** - The strand information for prevous three columns.\n+ 8. **next** - The next base.\n+ 9. **Plus** - Next two columns are for forward strand.\n+ 10. **totalC** - Total number of Cs.\n+ 11. **methC** - Methylated Cs.\n+ 12. **Minus** - Next two columns are for reverse strand.\n+ 13. **totalC** - Total number of Cs.\n+ 14. **methC** - Methylated Cs.\n+ 15. **localSeq** - Local sequences.\n+\n+]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 26d7ec4af119 test-data/PE_comp.g1.vs.g2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PE_comp.g1.vs.g2.txt Fri Sep 06 09:54:27 2019 -0400 |
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| b'@@ -0,0 +1,211 @@\n+#chrom\tstart\tend\tsingle:\ttotalC_0\tnominalRatio_0\tratioCI_0\tsingle:\ttotalC_1\tnominalRatio_1\tratioCI_1\tpair:\tnominalDif_1-0\tcredibleDif_1-0\tdifCI_1-0\tp_sim:\tp_sim_1_v_0\tp_fet:\tp_fet_1_v_0\n+seg\t87\t89\tsingle:\t6\t1\t0.652,1\tsingle:\t10\t0.2\t0,0.47\tpair:\t-0.8\t-0.327\t-0.857,-0.327\tp_acc:\t0.000318\tp_fet:\t0.00699\n+seg\t152\t154\tsingle:\t4\t1\t0.549,1\tsingle:\t9\t0.333\t0.0575,0.609\tpair:\t-0.667\t-0.113\t-0.761,-0.113\tp_acc:\t0.0035\tp_fet:\t0.0699\n+seg\t253\t255\tsingle:\tNA\tNA\tNA,NA\tsingle:\t9\t0\t0,0.259\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t255\t257\tsingle:\tNA\tNA\tNA,NA\tsingle:\t10\t0\t0,0.238\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t258\t260\tsingle:\t3\t1\t0.473,1\tsingle:\t13\t0.231\t0,0.466\tpair:\t-0.769\t-0.165\t-0.809,-0.165\tp_acc:\t0.00236\tp_fet:\t0.0357\n+seg\t331\t333\tsingle:\t6\t0.667\t0.341,0.992\tsingle:\t22\t0.227\t0.0499,0.405\tpair:\t-0.439\t-0.058\t-0.66,-0.058\tp_acc:\t0.00636\tp_fet:\t0.0638\n+seg\t468\t470\tsingle:\tNA\tNA\tNA,NA\tsingle:\t7\t0.143\t0,0.471\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t490\t492\tsingle:\tNA\tNA\tNA,NA\tsingle:\t3\t0.333\t0,0.751\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t630\t632\tsingle:\t3\t1\t0.473,1\tsingle:\t5\t0\t0,0.393\tpair:\t-1\t-0.271\t-1,-0.271\tp_acc:\t0.000954\tp_fet:\t0.0179\n+seg\t638\t640\tsingle:\t3\t0.667\t0.249,1\tsingle:\t5\t0.6\t0.264,0.936\tpair:\t-0.0667\t-0\t-0.461,0.418\tp_acc:\t0.0286\tp_fet:\t1\n+seg\t641\t643\tsingle:\t4\t1\t0.549,1\tsingle:\t5\t0.4\t0.064,0.736\tpair:\t-0.6\t-0.0122\t-0.748,-0.0122\tp_acc:\t0.00715\tp_fet:\t0.167\n+seg\t645\t647\tsingle:\t4\t1\t0.549,1\tsingle:\t8\t1\t0.717,1\tpair:\t0\t0\t-0.183,0.374\tp_acc:\t0.067\tp_fet:\t1\n+seg\t666\t668\tsingle:\t4\t1\t0.549,1\tsingle:\t9\t0.667\t0.391,0.942\tpair:\t-0.333\t-0\t-0.506,0.15\tp_acc:\t0.021\tp_fet:\t0.497\n+seg\t685\t687\tsingle:\t3\t1\t0.473,1\tsingle:\t8\t0\t0,0.283\tpair:\t-1\t-0.342\t-1,-0.342\tp_acc:\t0.000364\tp_fet:\t0.00606\n+seg\t689\t691\tsingle:\t4\t1\t0.549,1\tsingle:\t9\t0.667\t0.391,0.942\tpair:\t-0.333\t-0\t-0.506,0.15\tp_acc:\t0.021\tp_fet:\t0.497\n+seg\t697\t699\tsingle:\t3\t1\t0.473,1\tsingle:\t7\t0.571\t0.27,0.872\tpair:\t-0.429\t-0\t-0.595,0.156\tp_acc:\t0.017\tp_fet:\t0.475\n+seg\t699\t701\tsingle:\t3\t1\t0.473,1\tsingle:\t9\t1\t0.741,1\tpair:\t0\t0\t-0.149,0.454\tp_acc:\t0.0596\tp_fet:\t1\n+seg\t706\t708\tsingle:\tNA\tNA\tNA,NA\tsingle:\t4\t0.25\t0,0.657\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t708\t710\tsingle:\tNA\tNA\tNA,NA\tsingle:\t3\t0\t0,0.527\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t738\t740\tsingle:\tNA\tNA\tNA,NA\tsingle:\t5\t0\t0,0.393\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t749\t751\tsingle:\tNA\tNA\tNA,NA\tsingle:\t8\t0.25\t0,0.55\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t753\t755\tsingle:\tNA\tNA\tNA,NA\tsingle:\t12\t0.167\t0,0.41\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t820\t822\tsingle:\t7\t0.857\t0.529,1\tsingle:\t20\t0.4\t0.2,0.6\tpair:\t-0.457\t-0.0729\t-0.62,-0.0729\tp_acc:\t0.00528\tp_fet:\t0.0768\n+seg\t830\t832\tsingle:\t7\t0.857\t0.529,1\tsingle:\t18\t0.222\t0.0252,0.419\tpair:\t-0.635\t-0.236\t-0.766,-0.236\tp_acc:\t0.000768\tp_fet:\t0.0068\n+seg\t842\t844\tsingle:\t4\t0.75\t0.343,1\tsingle:\t10\t0.3\t0.035,0.565\tpair:\t-0.45\t-0\t-0.672,0.0536\tp_acc:\t0.0117\tp_fet:\t0.245\n+seg\t1149\t1151\tsingle:\tNA\tNA\tNA,NA\tsingle:\t7\t0\t0,0.312\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t1151\t1153\tsingle:\tNA\tNA\tNA,NA\tsingle:\t10\t0.1\t0,0.364\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t1172\t1174\tsingle:\t3\t1\t0.473,1\tsingle:\t12\t0.333\t0.0889,0.578\tpair:\t-0.667\t-0.0658\t-0.738,-0.0658\tp_acc:\t0.005\tp_fet:\t0.0769\n+seg\t1180\t1182\tsingle:\t3\t1\t0.473,1\tsingle:\t11\t0.0909\t0,0.339\tpair:\t-0.909\t-0.286\t-0.909,-0.286\tp_acc:\t0.000705\tp_fet:\t0.011\n+seg\t1201\t1203\tsingle:\t3\t0.667\t0.249,1\tsingle:\t14\t0.214\t0,0.44\tpair:\t-0.452\t-0\t-0.7,0.0401\tp_acc:\t0.0118\tp_fet:\t0.191\n+seg\t1203\t1205\tsingle:\t3\t0.667\t0.249,1\tsingle:\t13\t0.308\t0.0724,0.543\tpair:\t-0.359\t-0\t-0.629,0.133\tp_acc:\t0.0176\tp_fet:\t0.518\n+seg\t1303\t1305\tsingle:\t3\t1\t0.473,1\tsingle:\t4\t0\t0,0.451\tpair:\t-1\t-0.229\t-1,-0.229\tp_acc:\t0.00143\tp_fet:\t0.0286\n+seg\t1333\t1335\tsingle:\t4\t0.25\t0,0.657\tsingle:\t6\t0.167\t0,0.521\tpair:\t-0.0833\t-0\t-0.47,0.291\tp_acc:\t0.0339\tp_fet:\t1\n+seg\t1343\t1345\tsingle:\t3\t0\t0,0.527\tsingle:\t10\t0.2\t0,0.47\tpair:\t0.2\t0\t-0.318,0.357\tp_acc:\t0.0363\tp_fet:\t1\n+seg\t1407\t1409\tsingle:\tNA\tNA\tNA,NA\tsingle:\t4\t0\t0,0.451\tpair:\tNA\tNA\tNA,NA\tp_acc'..b'seg\t6420\t6422\tsingle:\t4\t1\t0.549,1\tsingle:\t3\t0.667\t0.249,1\tpair:\t-0.333\t-0\t-0.639,0.17\tp_acc:\t0.0214\tp_fet:\t0.429\n+seg\t6487\t6489\tsingle:\tNA\tNA\tNA,NA\tsingle:\t5\t0\t0,0.393\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n+seg\t6499\t6501\tsingle:\tNA\tNA\tNA,NA\tsingle:\t5\t0\t0,0.393\tpair:\tNA\tNA\tNA,NA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|
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr Fri Sep 06 09:54:27 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +seg 152 1305 - 20 15 5 1 +seg 2310 7008 - 95 77 18 1 +seg 8052 8091 - 3 3 0 1 |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/SE_comp.g1.vs.g2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_comp.g1.vs.g2.txt Fri Sep 06 09:54:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,310 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t0.131\tp_fet:\t1\n+chr11\t8414\t8416\tsingle:\t16\t0.0625\t0,0.25\tsingle:\t27\t0.444\t0.268,0.621\tpair:\t0.382\t0.14\t0.14,0.521\tp_acc:\t0.00165\tp_fet:\t0.0143\n+chr11\t8583\t8585\tsingle:\t24\t0.0833\t0,0.231\tsingle:\t27\t0.148\t0,0.298\tpair:\t0.0648\t0\t-0.0948,0.209\tp_acc:\t0.0723\tp_fet:\t0.671\n+chr11\t8678\t8680\tsingle:\t19\t0\t0,0.139\tsingle:\t17\t0\t0,0.153\tpair:\t0\t0\t-0.104,0.119\tp_acc:\t0.178\tp_fet:\t1\n+chr11\t8692\t8694\tsingle:\t23\t0.0435\t0,0.183\tsingle:\t19\t0.0526\t0,0.216\tpair:\t0.00915\t0\t-0.116,0.155\tp_acc:\t0.113\tp_fet:\t1\n+chr11\t8755\t8757\tsingle:\t26\t0\t0,0.105\tsingle:\t24\t0.0417\t0,0.176\tpair:\t0.0417\t0\t-0.0523,0.15\tp_acc:\t0.126\tp_fet:\t0.48\n+chr11\t8786\t8788\tsingle:\t25\t0\t0,0.109\tsingle:\t19\t0\t0,0.139\tpair:\t0\t0\t-0.0781,0.112\tp_acc:\t0.207\tp_fet:\t1\n+chr11\t8812\t8814\tsingle:\t22\t0.0909\t0,0.249\tsingle:\t21\t0\t0,0.127\tpair:\t-0.0909\t-0\t-0.217,0.038\tp_acc:\t0.0592\tp_fet:\t0.488\n+chr11\t8829\t8831\tsingle:\t20\t0\t0,0.133\tsingle:\t22\t0.136\t0,0.304\tpair:\t0.136\t0\t-0.0114,0.27\tp_acc:\t0.0304\tp_fet:\t0.233\n+chr11\t8836\t8838\tsingle:\t21\t0\t0,0.127\tsingle:\t21\t0.0476\t0,0.198\tpair:\t0.0476\t0\t-0.0664,0.167\tp_acc:\t0.112\tp_fet:\t1\n+chr11\t8855\t8857\tsingle:\t17\t0.0588\t0,0.238\tsingle:\t22\t0.0909\t0,0.249\tpair:\t0.0321\t0\t-0.14,0.174\tp_acc:\t0.0887\tp_fet:\t1\n+chr11\t8902\t8904\tsingle:\t17\t0\t0,0.153\tsingle:\t15\t0.333\t0.111,0.555\tpair:\t0.333\t0.104\t0.104,0.508\tp_acc:\t0.00262\tp_fet:\t0.0149\n+chr11\t8914\t8916\tsingle:\t20\t0.35\t0.153,0.547\tsingle:\t13\t0.308\t0.0724,0.543\tpair:\t-0.0423\t-0\t-0.281,0.229\tp_acc:\t0.0495\tp_fet:\t1\n+chr11\t8920\t8922\tsingle:\t22\t0\t0,0.122\tsingle:\t12\t0\t0,0.206\tpair:\t0\t0\t-0.0801,0.173\tp_acc:\t0.157\tp_fet:\t1\n+chr11\t8948\t8950\tsingle:\t33\t0\t0,0.0843\tsingle:\t17\t0.0588\t0,0.238\tpair:\t0.0588\t0\t-0.0234,0.214\tp_acc:\t0.0814\tp_fet:\t0.34\n+chr11\t8975\t8977\tsingle:\t42\t0.0476\t0,0.139\tsingle:\t19\t0\t0,0.139\tpair:\t-0.0476\t-0\t-0.11,0.0832\tp_acc:\t0.131\tp_fet:\t1\n+chr11\t9127\t9129\tsingle:\t41\t0.0244\t0,0.108\tsingle:\t31\t0.0968\t0,0.225\tpair:\t0.0724\t0\t-0.0228,0.187\tp_acc:\t0.0662\tp_fet:\t0.308\n+chr11\t9136\t9138\tsingle:\t42\t0.0476\t0,0.139\tsingle:\t33\t0.0606\t0,0.174\tpair:\t0.013\t0\t-0.0771,0.12\tp_acc:\t0.143\tp_fet:\t1\n+chr11\t9227\t9229\tsingle:\t45\t0.0444\t0,0.131\tsingle:\t38\t0.0526\t0,0.153\tpair:\t0.00819\t0\t-0.0754,0.103\tp_acc:\t0.16\tp_fet:\t1\n+chr11\t9270\t9272\tsingle:\t40\t0.025\t0,0.111\tsingle:\t33\t0.0909\t0,0.213\tpair:\t0.0659\t0\t-0.0287,0.175\tp_acc:\t0.0758\tp_fet:\t0.322\n+chr11\t9301\t9303\tsingle:\t40\t0.175\t0.0523,0.298\tsingle:\t33\t0.0303\t0,0.132\tpair:\t-0.145\t-0.0191\t-0.253,-0.0191\tp_acc:\t0.0174\tp_fet:\t0.0652\n+chr11\t9371\t9373\tsingle:\t25\t0\t0,0.109\tsingle:\t32\t0\t0,0.0868\tpair:\t0\t0\t-0.0872,0.0628\tp_acc:\t0.257\tp_fet:\t1\n+chr11\t9380\t9382\tsingle:\t25\t0.04\t0,0.17\tsingle:\t31\t0\t0,0.0894\tpair:\t-0.04\t-0\t-0.147,0.0405\tp_acc:\t0.129\tp_fet:\t0.446\n+chr11\t9447\t9449\tsingle:\t17\t0\t0,0.153\tsingle:\t30\t0\t0,0.0921\tpair:\t0\t0\t-0.129,0.0611\tp_acc:\t0.207\tp_fet:\t1\n+chr11\t9478\t9480\tsingle:\t16\t0\t0,0.162\tsingle:\t21\t0.0476\t0,0.198\tpair:\t0.0476\t0\t-0.097,0.16\tp_acc:\t0.111\tp_fet:\t1\n+chr11\t9510\t9512\tsingle:\t14\t0\t0,0.181\tsingle:\t23\t0.0435\t0,0.183\tpair:\t0.0435\t0\t-0.119,0.143\tp_acc:\t0.117\tp_fet:\t1\n+chr11\t9588\t9590\tsingle:\t20\t0\t0,0.133\tsingle:\t18\t0.111\t0,0.296\tpair:\t0.111\t0\t-0.0292,0.261\tp_acc:\t0.0448\tp_fet:\t0.218\n+chr11\t9677\t9679\tsingle:\t11\t0.0909\t0,0.339\tsingle:\t13\t0.231\t0,0.466\tpair:\t0.14\t0\t-0.131,0.354\tp_acc:\t0.0398\tp_fet:\t0.596\n+chr11\t9697\t9699\tsingle:\t14\t0\t0,0.181\tsingle:\t15\t0.2\t0,0.417\tpair:\t0.2\t0\t-0.00842,0.371\tp_acc:\t0.02\tp_fet:\t0.224\n+chr11\t9709\t9711\tsingle:\t11\t0\t0,0.221\tsingle:\t18\t0.111\t0,0.296\tpair:\t0.111\t0\t-0.104,0.245\tp_acc:\t0.0574\tp_fet:\t0.512\n+chr11\t9729\t9731\tsingle:\t6\t0.167\t0,0.521\tsingle:\t16\t0\t0,0.162\tpair:\t-0.167\t-0\t-0.475,0.0224\tp_acc:\t0.0282\tp_fet:\t0.273\n+chr11\t9799\t9801\tsingle:\tNA\tNA\tNA,NA\tsingle:\t7\t0\t0,0.312\tpair:\tNA\tNA\tNA,NA\tp_acc:\tNA\tp_fet:\tNA\n' |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_dmr_M3_g1.G.bed_vs_g2.G.bed.txt.dmr Fri Sep 06 09:54:27 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +chr11 316 1705 - 35 30 5 -1 +chr11 3052 3674 - 17 16 1 -1 |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/SE_g1.G.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_g1.G.bed Fri Sep 06 09:54:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,309 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| Binary file test-data/SE_g1_r2.bam has changed |
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| diff -r 000000000000 -r 26d7ec4af119 test-data/SE_g2.G.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SE_g2.G.bed Fri Sep 06 09:54:27 2019 -0400 |
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| b'@@ -0,0 +1,310 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| diff -r 000000000000 -r 26d7ec4af119 test-data/TKO2PE2.fastq.gz |
| b |
| Binary file test-data/TKO2PE2.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/WTPE1.fastq.gz |
| b |
| Binary file test-data/WTPE1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/WTPE2.fastq.gz |
| b |
| Binary file test-data/WTPE2.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Fri Sep 06 09:54:27 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chr11 chr11 chr11 ${__HERE__}/chr11.fa |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/chr11.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr11.fa Fri Sep 06 09:54:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,601 @@\n+>chr11\n+CCTGGGGTGTTTCAGGTCCCATCTCTCCTCCCAGACCAGAGCGGCTCCCG\n+GCATCCCGCCGTCCTGCTCACAGTATCTTCACCTCACCACTTCCACATAG\n+TCGCCACCCACAGAGAGTGAGAAAGTGGGACCCAGAGGGGCGAACGGGGG\n+AGGGGCAAGGATAGTGGGGTGGTTTTAGTTGGGAGACCACCACTTCCAAT\n+GCCCCATCCCCGACTCGCCCTGCATCTCCCTGCTCACCTTTTCATGTGCA\n+CCCTACTCATAGTCACATAATTTGTCAATTACAGCAAAAAGCAACAGGAT\n+ACAATTATGTTAACCTCGCAGTCTGTCAGTGCGTTATCTTGTCACACTTC\n+TACAAGGGGGCTCTCCCTGCATTCTAATGTCAAATTTGAATAGTGCACCA\n+CGCAGCTCGTTCTTATGCACACAGTGCTGCCCACAAACACACACACGCAC\n+CCACCAGCCACCTTCATACCGCTCCTGACATACACAACCCTCACATTCCC\n+AGGCCAACAAAATGGTTCAACAAACACCACCTACATACAATGTGGTCGAT\n+GTGTCCCAGGCCTTCAAATGCAGTCTCACCCATGACATTCCCCAAGCATG\n+GAAGCCCTGAGAGGAAATGGTTGGGAGAGTAGGGGACAGGCAAAGGGATG\n+CACATATGGAGAGCTGCGTGGATGGCTGCTTGGGTTTTACCTTGCGTAGG\n+TTGCCCTGGCACCGAAGTCCCCGGATACCAACCAGGGCGGGTGCCCCAGC\n+TTCCGGTCTGCCCGTTCAACATCCTTAGTTTATCATACATGCCGTCTGCG\n+CCCATCTGTTGCTTTTCGCTAGCCAGGTTGCGAAGAACTCTGTTTATTGA\n+TGACACCTGCAAATCAAACCAAAATCAAACCAAATGGTAGTGTCTCCTGA\n+AGACACAGTCACCCATCTCAGCTCACCCACAACCTTAAAAAGCAACTCTC\n+AACCCGTTAAAAAGCTCCCAGCCACCCCGGGACAGTGGGTGGATTTGCAG\n+ATACACCGTGGAAAAAATGATAGCTATCACTTTGGGCATGGAAATTTAGT\n+TGGATAGAGAATTGGGCGGAGGGGGTCCTTCACCATTGCTTGGTGTCTCT\n+GGTGACCTAACTCACACGGTTGCTTTGCTTTGTTAAAAGACTGCCCGAAA\n+ATAAAAACTATTTAGACTTGTTGTAAAGCTTTCTTTCATTATATTGTTTA\n+ATATTAGGATGGAAATGGATGTGTGACACCTGAAGGAAAGTTCTGGCAGG\n+TGGATTAGGACGAAGTTACAATCTGGTTCTCATTTTCCTTCTTCATTCAA\n+GTGCCTTTCCCTGGTGCCTCCGCCCTCTGTTTTGCAGCATGCAAATGAAG\n+TGAATGACTCCCCACACTTGACTCCCATTTTCCAGACAGTCAAAGAAAAG\n+TCAGGGCATTCCTCTCTGTTCCCCCAGGTACAAAGGAGACAAATGTGGAG\n+CAGGGAGAGGACACAGACTAAGAGACAGTGGAGAGAGAGGGTGGGAGGAG\n+GTAAAGAGGAGAGAGCATTGGGCTTAGGGCAGGGAGGGCAGATGTTCTCA\n+ATGAACTTACGCTTGGTATGTTATCGTTGGTACAGACCCCCTCGGACAGT\n+AATCTGTCTCGGATTTCCCAAGCAAAGATGGACGGGCACTCCCGCTTATA\n+CTGGGCTATTTTGCTTACAACTTCTGGAGTCGCTACTCTCGGTTTACTAC\n+CACCGATTGCCCTGGGTCTGATGGAGCCAGTCTCGTAATACCTGCCCAGA\n+ATTTTACTCACACATCCGTTGGACACCTGCATAGGGGAAGTGGACAGAAA\n+ACCACATTATTAATAATTTCAAGACAAAAATAAAATTGTTTAAGTATGCA\n+TTAAACAATGACAAGCTTACGTTTTGATTGTCCAGCACTTGGACTTTTGC\n+ATCTGCATGGGTCTATAACACAAAAATATACCTTCAATGGTATGAGAACT\n+TACTGTAGAGAGCTTTTTTTCTTAAAATTACATTTGTAGCCCTAAAAACT\n+ACAAATATGATGATACTTTCAAACAATTTGAACTAAAAAACGAATTTAAA\n+AGCTTTTTTTAAAAAAAAAACTTTTCTTAAACACTGCCTGAAGATGCATC\n+AAAACGAAGTAGATAAATTTATTTTTGTGCTGACCTTGCTTAAAGTGGCG\n+TTATGTTTTAAAGAACAAAGGTAAAAAATAAACTGATTTTTTTACTTCTT\n+CTTCTTTAAAAAATACTCAATTGAGTAAATGTGAGTTAGGGAGGAGTAAA\n+TAGCATTTGCCTTTTAAAATCAATATATATTATTCATAAACATGAAGAAT\n+AAACAAATACCTCAAAAGCTGAGGTAAGCATGGGCTGGGGAGAGCAGAAT\n+GAAATTATGCCGGTTTATATAACTCAGCTTATTACGGTTCATAAACTGTT\n+CCCACAATGAATGTCTTTACCAAATAAAAAGAGAAAGATTTTTTTAAAAA\n+AATCCGCACACAATATTTTTCTGAAGCAGATGAGTTATCTTATGTAACTG\n+ACCCAGGTTGAAAGAGATAGGGAAGGATGGTGGAAGGAGAGGGGAAAGTG\n+GGAAGGCAGGGGAGTGGGTGGGGGGACTGGGGACTGGGGTGGGTGAGGGT\n+GGGGGGGTCCATAATTAGCATCGTTTACAGTAAGAAATGAAGAGAGGGCG\n+TTGAGAGTGGAGGGCCGCGGGGGCGGCGAGTGGGGCGGCGCCGGGAGGAT\n+CACCTGCAGAATTCGGGAAATGTCGCACGGCCGGGCCCCGCTGTGAGCTA\n+GCTCTACAATCTTCTGCCGGGTGGAGTCCGGCAGTGGCCGCCCGTTGACA\n+AAGACACCACCGAGCTGATTCACTCCGCTGTGACCTGAGGAAAGGGAGAG\n+GAGAGGAAAGGGGAAAAGAAGAGAAGAGAGCAGAGTGAAGAGGAAGAAGA\n+GGGAGAAGAAGGAAGAGGAAGATGAGGGAGAACAAGAACAGAAAGGAGAG\n+GAGGAAGGGGAAGAGGAAGAAGGAGAGGAGGAGGAGACAACCACAATGCA\n+TCCTCATCCCCCTGCCAACCTGTGCCAACCTCGGCGGTCAGTTCCCTGCT\n+ATCGATCAAATAAAGGACAACAGGACCACCAGCCATGCCAGACATCGGGC\n+AGCCCAGTCCAAGCAACCGTGCCCCTGCCCACTGTACTGCAGCAGCAACA\n+CAGAGTCAGACACATGCCAAGGAACAAGTACACATGGACCTCACTACAGC\n+CATAACCCCAGCAGTGTCCCCAGCCCACTGCCCCTCTTCATAAACACTGC\n+AGCCAGCCTCTGAACCCACAAAGCGCTAAGAACCGGCTCTATAAATCTCC\n+CAAAGATCCCCTCTGAGTGTCACCGCAAACCATGGGTTCTACAGATCCCA\n+CACTGAACCTTCAAGGTCTCTGCAGTGTTGGGACAGTGATAGCAAACCTT\n+ACAGCCCTTGAGTGCTCCCTTAGACGCTAAAATCCAGAAATGTTTCCATC\n+ACCGTCCAAACTGGCCAAGGCCTGGCACAAGCATCGAGTTGGGTTTTGTT\n+TGGTTAGAATAGAAGAAGGAAGAGGAGAGAACAACCAGAGCAGCCAGTAT\n+GTGGCTGGTGAACCCCAGTCCAGGTTTCCGCACCTCCAGTGCAGACGTGA\n+GAGTCAGAGCCCGGGCTCGGCTTCAGCCACAGACAAGTCCGGCCACCGCA\n+AGTAAGGCTTAGAGCCGGGAGTCGGTTCGCACCAGCCACTGCTCGCTTTA\n+TTTCCGCCGCTGAACTCCGCCCTCCCCTTAGCCAAGGATAGATATTATCA\n+AAAAGAAAAAACAGAAAAGAAAAATACCACATCATAGTGTTCCCCATCCC\n+TCCTTTATCTTTGTATCTCA'..b'CCCGGGGAAAAGCGAAGAAAGCCAGAGTCTCTTTGCACGGCGGGGA\n+CGCTGGCGCTCACCTCTGGGCGCGGCCTCGGTGGAGCCTCAGGGCCAGGG\n+CGGGGTGTGGCGGGGTGTGGCCCGGTGGGGTGAGGGAGGGACCCGGGGTG\n+CAAGCCAGGCCAAGGCCTCCTCAGTGCGCAGGCGCCGTTCGGGCCCGCCG\n+CCCCCTCCCAAGGCGTGGGGTCCCGGGGACAGACCCCGAGCCCCTCTCTG\n+CGCAACTACCGCCTCTAAAAAAAAGACCATCTGGTAATTGTCTTTCTTTA\n+GATCTTCCCTTAATTATGCTTTTAATTAAAGATGGTTCAAGGCACCGGAC\n+CACATGAAGGGCAGTAATTACAAATTACATTACAAACCCGACAGACGTAG\n+CAGGATCTGCTGGGAAAAAGGTACCGGAATAAAAATTTGACTAAAGTTTG\n+GGATAAATTAATCGGTGGCTTGAAGAACAGTAGCACATTTCTGATTATGT\n+AGGCTCCAGCCAGGATTTAAGTTTTGTGTCATGATTGTTTTCATATTTCT\n+TTGACATCTATTGATTTGGAGGCAGCTGCAAGCCTTTGTCACAGGAGAGA\n+AGAGCAGTCACAATATATTAGCTTGATGGCATAACTCGAACCGGAGAAGC\n+GAGGGGAGCCTGAGTGACTGGGGCGCACATGACCCCCCTCCTGGGGCCTT\n+TGGGCTCAACCCTTACTTTTAACTTGTTCTAACAGGAATAATGGAGTAGT\n+ACTACTAATGCATGGTCAGAAGGGGCTTTTCTGTCTAGAACGCAGGCGGC\n+GGGAGTTGCACCGCCACAGCCCGGGAGACCAAAGAGTCTCCACTCCCCGC\n+TCCCGGCGCCTCCTCGCCGACCGGAGCCCCGAGCCCAGTGAGCCCAGCCG\n+GTCCCACGTCGAGAGGCGCTGGGTTGGGAGAAGTTCTGCTGGTCGTGGGC\n+TCGGCCCCCAGGCGCCAGGCCGAGTGCCCACCTCGGCTTCTTTAGGGGGC\n+CTACAGCGGGCAGCCGAGCGGCTGGCGGACCCGGAGCTTGGGAGGCGACC\n+GCCAGGCTGGTGCCCGGCCTGACCCGGCGTTCGCGGCCGCCCGCTCGCCC\n+GCCGCGGGCCGGGAGCGTACAGGAGTGTGACGCAGATTGTGAAAACAGAA\n+GGGAGGGAGTTGGGTCATTTCCTTCGCTAATCATCGCCCCCTCCTGCTCC\n+TCCTCCCCACCCCCATCCCATCCTCGCCGCCACCCAGCCTCGAACTCTCT\n+TCCTTGCCAGAGTCTGCCTCACTTTGAGCCAGTGGCTGCACTTTATGGAG\n+AAAATATATGTGCCCATCACTCACCCATCTATTTGCAGCGTCCATGGAGC\n+GCCTCGGGGAACACGCATGGACAATTAAACACACCCACTTACGGCGGGAT\n+GATGAGGCTTTCTGTTAACCACATGTGTTCAGAAATGGATACAGCCCTAA\n+TTTTGACACGGAATGCAGCTAATGCACCTTGCTATAGATGTACGTCCGTT\n+GGAAAAGTGTGTGATGGGCACCTGATCTACACCAAGAGAACAGGGCTGTC\n+TGCAGAAGACCCAGCGGCCTGACACCTTTTCTTGTTGCCGGGGAAGGAAA\n+GTTTTTCTTTTGATTTGTCCTCTCACGATTTTTCCCTTTTCCTTTGCATT\n+ACAGTTTCAGAGAGGAATGTAAATATTTTGACTAGACCTCTGCAGGGGCC\n+TTTTAAACACCAGGCACAATCATCTGTGGAATACTGTAGTTCATACTTTC\n+AAAACTTGGGTGTTAAAGAGTCTGTCTTGCTGAGGAAACCCATAGAACTA\n+GTGGCGACCTTTCAACTCCCTATTTGTGTGATGAAATGAAGTATGCCCTA\n+GTGATTGTCGAATTTTAAGGACTTGTTCTGTCACTGCTACTTTCCGATCG\n+TTTGCAGGGAAGAAAAATCAATCAAACAGACCTTTGATGGGGTTGTGGCA\n+AGGTCACATTTCACTGTGCTCCAGGCTTACCTCTTCTTAACGCCCCTCCC\n+TGCTGTGGAGCGTGTGCAGGTAGTATGCAAAACTCTAGAAATAATATTTG\n+AAAAAATTAACACCTTGTTTATCTCTTCTGTGTATTTGATATAGGGGTTT\n+CTTTCTTTTCCTGTTTTGGTGTTTAATACAAGGCTGATATATTGGAACAG\n+AATGCAGACTTCAAAGAAACTAAAATTAGGAGGCAAATAGCGTCAAGGTT\n+TCCTCGGTTTCTGTATGTAGTACAAATAGTATAGCGTCTTTTCATCCAAA\n+AAGAAGCAAAAATTGCCAGGAGGCATAAAGCATCTCTGAATATCCGTTTT\n+TTTTAAAGAAACAAACATTTCCCAAATATTGATGTACGCATGGTTTTATA\n+GTCTGAAAATATTTCTAGGCACAAATATGGCATACAAACATTCGTTTCAA\n+CTCTGTCGTTGTTGTTAAAATGACAGTAAATTATAGTTTATTTTAAGATA\n+CCTCCCTGTTAATGTCAGTTGAGGTTATTTTAGGGCCTGGATGCTCTAGG\n+AAGACCACCTAAAATGTGTTTATTTCTCTGCCCAATTCACCTATAGTGTA\n+AGGAGCATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTATACTT\n+TAAGTTTTAGGGTACATGTGCACAATGTGCAGGTTTGTTACATGTGTATA\n+CTTGTGCCATGTTGGTGTGATGCACCCATTAACTCGTCATTTAGCATTAG\n+GTATATCTCCTAATGCTATCCCTCCCCTCCCCCCATCCCACAACAGTCCC\n+CAGAGTGTCATGTAAGGAGCATTTTAAATAAAATATTTTGGGCATCCTTA\n+AGTCCTTTTTTAAAAATCCAACATTCTACAATTGTGACAAATAGGCTGAA\n+AAATTTTGTTTTGTTTATACCAAATTCATTTTAATAAAGCATTTGCTGAG\n+ATTTTAATACAACAAATGCCAACAAAATGCATCAGAGTAGAAAAAAGAAA\n+ATATTTTCAGAATTGCCTATAATATTGCTTGTGATCCTAAATTTTTTGAT\n+GCAAGGAACTTGAATTTTTCAGCTAATATTATTCTGTTTTCTTATTCTGT\n+GTTTCTATTAGAACACTCACCTATGCTCTGCTTCCCTTGCTGTCTTCCCA\n+TAGCTTATGTGTGCACTATGAATTTCAATAAATATAAATTACTGCTTAAA\n+AGAGTAAAGAATGGCTACTTTATGACTCACTGTTCTCTCCTTACAATCTG\n+CTCAAAAATCTTTTTTACAAATCCCATTGTAGCTACTTCCCCTCAATTCC\n+ACGATGAAAGTGAATGGCAAATGCCATTCAATTTAGAGGAACTCAAGCAC\n+AGAGAATATAAAGATGTTGTTCAAAGCCTCCCTCAAATCTATCTGTAGGC\n+TTACAAACAAAATGAGACTGGAGGCAACATCAGTACACATCTCCGACTCC\n+ATATGAGGTTACTTGAAGCTTTGGGGTTCACTCTGGAAACAGAAGACATG\n+CATCAAGGTATGTGTTCCTTAGAGACTGACAAGCAACAGTGGACCTCAGG\n+AGAAATAAAACAACTCATGCTCTCAACTGCCTCTGATTTGCAGACAAGGA\n+AGAGTTTTCTCTAATTTTTTTTTTTTTTTTTTTTTTTTGCCTGCATTACT\n+TTTTCTGTGCTTGGTGGCTAAACCAGAGAGCAGTCTGCAACATTTTGCTT\n+TTGGGGATTTCCTGTGGCTTTGCCACATTCCCTGGAGAAACTCATAAAGT\n+CCTGGAGTCTATGGAGGGATTACAGAGAGCCACAAACATCATTCTTCCTC\n+TAATCCATCTGGGGCAGATACAGTATTGATAACAACCTTTCTGTTACTTG\n+ACAGTTTCAGACCATTCAGATGAGAACAAATAATAGGAATTTGGTAGTGG\n' |
| b |
| diff -r 000000000000 -r 26d7ec4af119 test-data/seg.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seg.fa Fri Sep 06 09:54:27 2019 -0400 |
| b |
| b'@@ -0,0 +1,140 @@\n+>seg\n+CGAGGCTCTCTCAGGAAAGGAAACGCCACGCAGTGGTGAGGACAGGAAGTGCGCGGTTCT\n+GCTGCGGGCCTCTCTGTGGTCAGGACCCGGAAGCTCTCTGGGCCTCAGTTTCTTCAGCTA\n+CTCAGTGCCAATAATGCCAGCTCCCACTGCTCCGCGACCAGGGCCTCTGAGCCTCTGTCA\n+CGACCTGCACATTAGCTGAAAATTGGAAATTCCACAGCGTGGCCGCGCTGCCGCCTCCCC\n+TCGCCCACCTCGACGCGACGTCATCCATTGTCCCTCATTATTCATTATTGTTAGAGGGCT\n+CTTAAGTCATCCTTTCTCCTTCTGAACTAGCCGTTGCTCATCTGCTCATGTCTGTGGCTG\n+CAGCAATTAATGCCAGTTTCAGTCAGTACAAACCAATCATTCCCTCGGTTTGCTTCTTTG\n+GCTGCTATAAACAATTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTCTCGCTTTGTCACC\n+CAGGCTGGAGCGCAGTGGTTTGATCTCAGCTCACTGCAGCCTCGCGGTATGGGAGATGTC\n+CATTTAGTCACGCCCCCACCGGCGCCTGCCTGCCCCTGTCCCGCCTGGCCCCCACCGGCC\n+CCATTCGATGTTCACCGCGCGAAGAGCAGCCGCACCAGCGCCGGCCGTCCCTGGGCCACC\n+AGGGCCCGGGCCAGCCCCAACACCTCGTCCGTGTGCCCGCGCCACACGCGCTGCAGCTCC\n+TGGCGCAGGCGCGCGCCTCGGACACAAAGCGCCCGGCCTGGGGAATCTTTTCTACAGAAA\n+TAAAAGTACTACTTCAAAAGGATGTTTATTTTTATTGTTGCGCTATTTGTCGGGGCTGAG\n+AACGGAAAACAATCTAAACAATCTAAACTATTCAGGTGTCAAAAATACAAGTTATTGGTT\n+TTTTGTTTTTTTGTTTTTTTTGGTTTTTTTGAGACGCGTTGGTAGGGCTCCATGGTGCTC\n+GCTGCGCCAGGATGCAAGCCAGCTGCTGTTTCAGATCCTCGCGATGGACATTTATATCAC\n+GTCTGCTTTTTTGGCCGCTGAAACAAGCAGCCGCGGGGTACAGGTGGCTTCGTCCACCGA\n+GGTCCCCTCACCCACGCTGAGGCGTCGGAAGCTGCGGACACTGCTCGCGGCCCCTCCTGC\n+CGGACCCCTCGCGGCTCACCAGGCTTGCACTCCGGAATTACGGCCTGGTAATTGGTTCCA\n+ACGCGGATCATGCTGTCTGTGGAGCCAGGGGGAGGCAGTCAGGACTCCAGGGAGGGCGCG\n+CTCCGTTTCGCGCCGTTGTTCCTCCCAGATTTTATAACCCAGGCGTGTAACAGGCATATT\n+TACACTTGTGCCACGCACAGGATCGTGCACTTGAAGCAGCAAGGCTGTGGCAGAAATCTG\n+CACAGCTGTAGCCATCAGAAACAGGCTCGCGTCGGCTCTGGCCGCCCTCGAGGAGCCCTT\n+CAACCCGCCGCTGCGCTGTGGGGGCCCCTCTCTGGGGCTGGCTGAGGCCGAAGCCGGCTC\n+CCTCTGCTGGCGGGGAGGTGTGGAGTGGGAGGCGCGAGCGGGAGCCGGAGCTGCGCGCGG\n+AGATGTGAGTGCTAGGATGTCAGGGCTTCCCCAGCCCAGCAGTTGCGAGTCTGGAATCGC\n+GTGTTCCGCAAATTTACACAATCAAAGCCACCTCACTGGTTTCCGTTCACTTGCCGCGAT\n+GGGTACCACCAAGGGTTTGGTGAGGGAATTGGGGGATGGGGGCAGTGCCAGGCCAACAGG\n+TCCCCCATCCACTCTTCAGTCTGAGCAATGCCCATAAACTCGACTGACCTTTTTGGACAA\n+AAGCTTGCGCGGCGTGCCCGCGCGGCAGCGTGACAGTTGACGGCAGGGGGCGCTCATGCG\n+GTCGCGGCGAAAAGTCTCAGGGCACCCTCCGTTTCATTGGCCACAGCTGAGCCACGCGCG\n+CGCCGCGGGAACGTGGCCAGCAGGTAATGCGCGTACGCTTGGTGGTCGTGCACGCGCAGG\n+ATGGGCCGAGCCCCGCACGCCCCGAGGCAGCACCCCGCACGCAGTAGCCGGGCGTCGAGG\n+CGTTCCCAGCCCACACCAGGCGCGGGCTTGGTGCCAGCAAAGGGACCTGCGCGGTGCCCT\n+GGGGCCGGGGAGGCCCGCGCAATGTTTTTGAGGCTCATGGTGTGTGGTGGGGGTACCCGC\n+GCGCATCCTCCCTGGGCCCAAGATTCCTGGAGCTGGAGAACCCCCTTCCTCCCTGAGGCA\n+TGGAGACTGGGCTGGTCCTGAGCCCACTCCAGGCACAGGGGACACACCTGCTTCCTTCTT\n+AACTGAGTAGAGCAGAGTTATTTTGAAGATCGGTTTTCAGCAGGACAGTAAAAAGGCGAA\n+CTGGGAGATTGTTCATGCAGCAGCTTCTAAAACCAGTTTTTAGATAAATGCACCTTCGTC\n+TGTGGGGGGTGGCCGCACCCAGCCTCGCTTCAGGTGCCTGACGGGGTACGTGCTGCGCGT\n+TTTCTCATGTGGGAAAGATGCCGGCCCCCGCTGTTTGGGGTGGAAATCCTCTAACCCGCT\n+GGGCCTGTGCGCCAGGGCTGAGCAACAGCGCGGAGCCGTGCATCTGTCGGGGGCGGGACG\n+CGGCAGCAGGGCTGTGAGGGCTGCGTTTTCTCTGCCAGCCTGATCCGCATCCCCTGCCCC\n+TCGGTCGTCTGCCAGTGTCCGTGTATCTTTTGCCCCAGCTGGTGCGGGTTTAGGGATGTC\n+AGCCCCAGGAGTCACAGGTGAGCTGGTTCCAATGGGAACCTCGGCATCACCTGGGAACTG\n+AAATATGCATTGTCAGCCCCACGGCAGACCTCTGAATCAGAAACTCCGCGCCATGGGCCG\n+CTACCGCATCCGCGTGGCCACCGGGGCCTGGCTCTTCTCCGCGCCTGCGCACCTTTGACG\n+CGATGCATACACCACATGAAATATCCTATCATCTGTAGGCTCATTCATTTCCCTAACAGC\n+AGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCAAAGCGAAAAGTCCTAAT\n+AATAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCGCCCCACCCTACCACAC\n+ATTCGAAGAACCCGCGCCATCGGGTCCTCTGAAGTGCGCGGAAAACCAAGGTCGCGGGAG\n+ACGATCCAAAGAGGATGGGCTACGGTCAGACTTCGCGGGTTCAAGTGATTCTCCTGCCTC\n+AGCCTCCCCAGTAGCTGGGACTACAGGCGTGCACCACCACATCTGGCTAATTTTTGTACT\n+TTTAGTAAAGACATAGAGACGCGCCGGCCCGGGAGCGCCGCGCAGCCCGGGCTCCCGCCC\n+GTGCCTCCGCCTCCACACCTCCCCGCGAGCAGAGGGAGCCGCGCCTCCTGTCAGATCAGC\n+GGAGGCATTAGATTCTCATGCCAGAGAGAGCCCTATTCTGAACTGCGCATGCGAGGGATC\n+TAGGTAGCGCGCTCGTATGAGAATCTAATTCTTGATGATCTGAGGTGGAACAGTTTCATT\n+CTGAAACCATCTGCCCTTCCTCCCCCAAACGCCCCCCACCCCCACCCCACCACTGTCCGC\n+GCCCGCGCCCGGCAGCGAAGCAGTTAAGCGCGACTCCTCTACTTTGTAGGGGGGCTCCTT\n+GCACACTAAAAAGAAAAGGAAGAAACACACCCATCAGCCTCCTGCCTGTTTCAGGCCCAG\n+CTGCCAGCGGCAGTACCGCACCCCTCAACCCCACCACCTCCTCACAGGGGCTTGGCTGGC\n+CTCTCGGGGGTGGCTTTTCAGGAGGTTAAGCCCCCGACAGGATTGACTTCCACGCGGCCG\n+AGTGCACGAGGTCCAGCACCGCGGACGGCCGCGCCGCCTCCAGGCGCTTGAGCAGGTCCC\n+GGGCGT'..b'CGCGGCACAAATACCGCGCCGCCGCAGTGGCCCGCGCC\n+ACCAACGGCAGCGAGCCGAGCCATGCTGCTGCAGGCTTTCAAGCCTCCAGCGTGGGACAG\n+GTGACTCCTCCTCTAACCTGGGCATGGAGCAGATGGGCTGGCAGACGCAGAAGTGCCTGG\n+AATGGCAAGAACCCCTCCCCCCACAGACCGAGGTTATGCAAGTAAGGTTTCTGGACTACA\n+TGTTCAGATTGGATGAGAGAAAAACCTCTAGGTCTACTCTGATTGTGCTTTATTTTCACG\n+TTCTGACTGGATGACAGCAAGTCTTAGGATAACCAATCAGAACAAGATAACAAAGCCCGA\n+TCAGAGTAGGCCTAGAGGTTTCTCTCATCCGATCAGACTATGTAGTCGAGAAACTTCATT\n+TGCATTAAACTCAGTATATAAAGGATGCCAAGAGGGGTGGCTTGCCCTTCCAGGCTCATC\n+TGCGTCGGCCTGCGTAGCTGCTCTGTGCCCGGCTTAGAGGAGAAGGAGGAGGAGCCACTT\n+GCCGCGCATGCCAGAGGCTAGAGTCATCTACCGCGCATGCTGGAGGCTGGAGCCTACAGT\n+GGCTCACCTCGCTGCTGCGGTTGGTGGCCGCGAGGGTGACTACAGCGCGGAGTCTGATCT\n+GTACTATAAAGAGGTACAAAGTTCTGAGCGCTGTTTAGGAGCAGCTTTCCATTTGTGTAC\n+CGCGCCACATATTACATTTTTACGGATTTCTGCGGAACTCCCGCGCCTCTTCACGGGTAG\n+GTCAATTTCACTGGTTGAAAGTAAGAGACAGCTGAACCCTCGCGTAGGCATAGGAGATCA\n+TCCAAAAGGTGTGTGGATTTCAAACCAACCCAAAGAGAAGGTAAGATTTCTTCCGCTAAG\n+TGATGGCCACCAGATGGCTGTGCATCTCAAGGAATGGAGGGAGGACGTCTCTTCTGGACC\n+AGAACTGCCAAAGTCCACCATGAGCACTACCTCTCTGCTCTAAATCAAAGAGACAGGGAT\n+GAAGATCTGAAAGCGCGCCGGGCTTCATTACGGGCTCGTTGGCCACACCAGCGGCCCCGC\n+CTCTCGCCACAGCCTCGCGGTCCCCACAAGTATGAAATGGAGCCCCACAAAAATCTACTG\n+AAGCCTGCGTCCATTCTTGTTGCCTCTGACTTTGGTAGTGGAAAGGGTGTCCTGCAAAAG\n+CTGGGACCATTTATCACAGAGCTAAACGCGTCAGGTCAGCAGAGCTGAGCCACCCAAGGT\n+AGGAGAGAACTGCTCCCCACAGCTTTGACCACATGGGATTCTGAGGGTACTTTGTGGGAG\n+AAGCTGGTGGCAGGTTTCAAAGTGGTGGAAGTGGAGAATGCCTCAATCCAGGAAGCCCAG\n+GCAAAGCACAGGCTTCCTGGCTGAGTCTGGGGGTTGCCGGGCATTACTCCGCCAGACCCA\n+GTGGTACGGGTCTGGGCGCGCCTTGCAGAGCCCCACGGCCTCCTTCGGTGAGGACAAGAA\n+GTGGTAGTTGGTCGCGTTTTAGGGAAAATGACAATTAAGCTAAACTGCTAAAGCTGGAGA\n+TGATGGATAAGACAAGGATGAGAAAAAGAAGAAGACAGAAGAATTTCTAGGAAATTCAGA\n+TTCCTTCTGAGAAAAGTGAGGAGGCAGGGGACAGGACAATTTAAAGATGCCAAAGAATCC\n+TTTATTCTTCAAAATTTCAAAATCTTTCAATGCTACTTACTAAAGTAGAACCACTTTAAT\n+GGCGTTGGTGTTTACCTCATTTCCTCTTCACTCATTAACAGCAGTATTAGTGGGTCTTTT\n+TAGTCTATTTCATCTTCTGTGTCTATCACACCGCGACCTATGCAGCCTCTGCCCGAGGGA\n+GCCCCGCAGCCCAGAACACCTAACAAAAGCAACGCAGGCAGCCACCAGTGATTACAGGAG\n+GCTCCCCCAAGACCTAGGAGCTGGTAAAGGGCTATTGCTCTCCCGTCTCACCGCAAAGCA\n+CGCGCCCGGCCAGGGTGAACGCCGCGCGTGTCTGGAGTTTGTTCCTTCTGATGTTCGGAT\n+ATGTTCGCGCCCACCATCACGCCCAGCTAATTATTTTGTATTTTTAGTAGAGACGGGGTT\n+TCATCGTGTTAAGCAGGATGGTCTCCATCTCCTGACCTCGTGATCCGCCCGCGAGGGACG\n+TGGCTCAATTCATCCACGAATTTTCTTTCGCGGCGGCAGGCGGAGAGGAGTGCTCGGCTG\n+GCCTCTGCCTCCGGGAGCCAGGCCCCCTGCACAGCTGCCCTGGAGCTCCCCAGGGCCCAG\n+CTCATGGACAGCCGGGAGAGCCCCAGTGGGAGGAGGGAGTAGCAGAGAATAGGCCGTCAA\n+GAGAAAGTGCGCAGCGTGGAATTCAAAGATAGTGTGAAGCTGGCATGGGGCAGACAGGAC\n+GGAGGCGTTCTGGAACGCAGGCGTGTGCTCCCAACTGCCTAAATGGCTGTGTGGTGAGGT\n+GCGGAGGTGCGGCCACACCCCTAATGGCGGTGTGGTAAGGCGCGGAGGTGCGGCCGCAAC\n+ATCCTCATGTGTCCTTTGGTTTGCGTGTGCCATGCAGCCCTGCAGACGCAGACAGCACCC\n+CAGTGAGCTCCTCCCCAGGGGGAGCGCGTTAACATCGGTCCTGGGGAAACCCACTGTGCC\n+TGCTTCCAAATGGAAATCAGGGCGGCGCGCTCTTTTCCCCCAGTCTGGAGTGCAATGGTG\n+CAATCTCGGCTCGGTGCAATCTCGGCTCACTGCAAGCTCCGTCTCCCGCGCTGAGGAAAC\n+AAATCGTTGGCTCAATAGTTTTCCTTTTGTGTAATATACTGTCCCAGTGTGTTTAGGGAG\n+TTACGCGCCGCCGCCACCACCATCGCATAATTCACCGGCATTGATGAAGGCTGCCGCGGA\n+GGGGAAGAGGGCAGACCTCAGCGCTGCGGGGGCCGGCGGCGCGCTCGGGAAGCAGCGCGG\n+CCCCAGGAGGAAGGCGGCGCGGCCGAGGCCAGAGCCGGCGGCTACTGCGACCTTCCGGCT\n+GGCGCGCAGTGGCAGGCACCTGTAATCTCAGCTACTCGGGAGGCTGAGGGAGGAGATTCA\n+CCTGAACCTGGGAGGAAGAATTTGCAGTGATCAGAGATGTCGCCATCGTACTCCAGCCTG\n+GGCAACAAGAGTGAAACTCCATTTCAAAAAAAGAAAAAGGATGACCAGGAGCAAATTAAT\n+CACATGAATTCCATCTTGCTCAAAAGATATTACAATCAGGAAAAACATGAAAAAAAATCT\n+GAGCAAAAAGACAAAAAGGATAATTACATGTCTTTGCTATTTAGTTCTACTCCTCTTTTC\n+CTTGTATCTTTTTGTATATCCACCTCTGCAGTCTACTGGTACCTCTATGTTCAGATCCAA\n+TATCGCGTGAGGTAATAAGTGGAAAAGAGCTGATGAATTTTCAGGTGATTTTCATTTACA\n+CTGAGGAAATGTAACCAAGTTGGGAGGAAAAAAATCAATGATCTCTATGTCCTAATGATA\n+CTGAAAATTTTAAATTTTCAATATAGTATTATACACACCTAGAACTCAGGGAAAAAAGAA\n+GAGGCTTCGTCCAATTATGATATTCTTCTCTCCCTTTCTGTTTCAGTTCTGGCCCTAGAG\n+CAAAAATGTCTGCGAGGGCGTTCTGCCCTTTGTGATTTGTAAAAGGCACCGAGGCGCAGC\n+CCGGAGGAGACAGCGCGCCTGGCACTGGCGTCACTACAAAAAATCAGTTCCAAGATGACT\n+CACGCGCACAAAGAAGGCTAACGCCGAGGGTGCGCCCGGCTGGCGGAGGGCGCGGGTCTC\n+CAGAGACGCGGGAGGGCGGGCCGTGCGGCGGGTGAGGCCGCGGCCAAGGCTATAAATTCG\n+CAGGCCGCGGCCGGGCCCCACAGGAGCAGCCGCCCGGGGCACCGGAGCTGCG\n' |
| b |
| diff -r 000000000000 -r 26d7ec4af119 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Sep 06 09:54:27 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 26d7ec4af119 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Sep 06 09:54:27 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |