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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq commit 8b472e8680bb0ae5d11ee48b642ab305f9333a48 |
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added:
nastiseq.xml test-data/input_TAIR10_annotation.gtf test-data/input_positive_pair.tsv test-data/input_read_count_asmt.tsv test-data/input_read_count_smt.tsv test-data/output_neworphan.tsv test-data/output_newpairs.tsv test-data/test.r |
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| diff -r 000000000000 -r 0a0bba8e1823 nastiseq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nastiseq.xml Wed Feb 22 07:32:08 2017 -0500 |
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| @@ -0,0 +1,175 @@ +<tool id="nastiseq" name="NASTIseq" version="1.0"> + <description>Identify cis-NATs using ssRNA-seq</description> + + <requirements> + <requirement type="package" version="1.0">r-nastiseq</requirement> + </requirements> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> + <command> +<![CDATA[ + Rscript '$script_file' +]]> + </command> + <configfiles> + <configfile name="script_file"> + library(NASTIseq) + + genepos = read.delim("${annotation}", header=FALSE, comment.char="#") + colnames(genepos) = c("seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes") + genepos = subset(genepos, feature=="gene") + + get_id = function(attri){ + gene_info = strsplit(attri, ";")[[1]][1] + gene_id = strsplit(gene_info, " ")[[1]][2] + gene_id = gsub('\"', '', gene_id) + return(gene_id) + } + + genepos\$attributes = as.character(lapply(as.character(genepos\$attributes), get_id)) + + pospairs = read.table("${positive_pair}", sep = "\t", as.is = TRUE) + + smat = as.matrix(read.table("${count_smt}", sep = "\t", row.names = 1)) + + asmat = as.matrix(read.table("${count_asmt}", sep = "\t", row.names = 1)) + + WRscore = getNASTIscore(smat, asmat) + + negpairs = getnegativepairs(genepos) + + WRpred = NASTIpredict(smat,asmat, pospairs, negpairs) + + WRpred_rocr = prediction(WRpred\$predictions,WRpred\$labels) + + thr = defineFDR(WRpred_rocr,0.05) + + WR_names = FindNATs(WRscore, thr, pospairs, genepos) + + write.table(WR_names\$newpairs, file = "output_newpairs.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) + + write.table(WR_names\$neworphan, file = "output_neworphan.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) + + </configfile> + </configfiles> + <inputs> + <param name="annotation" type="data" format="gtf" label="Annotation file" + help="The gene ids should be in agreement in the files of annotation, known pairs and read count."> + </param> + <param name="positive_pair" type="data" format="tabular" label="Known pairs" + help="A known pair of cis-natural antisense transcripts"> + </param> + <param name="count_smt" type="data" format="tabular" label="Read count of sense strand" + help=""> + </param> + <param name="count_asmt" type="data" format="tabular" label="Read count of antisense strand" + help=""> + </param> + </inputs> + <outputs> + <data name="newpairs" format="tabular" + from_work_dir="output_newpairs.tsv" + label="${tool.name} on ${on_string}: New pairs"> + </data> + <data name="neworphan" format="tabular" + from_work_dir="output_neworphan.tsv" + label="${tool.name} on ${on_string}: New orphans"> + </data> + </outputs> + <tests> + <test> + <param name="annotation" value="input_TAIR10_annotation.gtf" ftype="gtf" /> + <param name="positive_pair" value="input_positive_pair.tsv" ftype="tabular" /> + <param name="count_smt" value="input_read_count_smt.tsv" ftype="tabular" /> + <param name="count_asmt" value="input_read_count_asmt.tsv" ftype="tabular" /> + <output name="newpairs" file="output_newpairs.tsv" ftype="tabular"/> + <output name="neworphan" file="output_neworphan.tsv" ftype="tabular"/> + </test> + </tests> +<help> +<![CDATA[ +.. class:: infomark + +**What it does** + + Pairs of RNA molecules transcribed from partially or entirely complementary loci + are called cis-natural antisense transcripts (cis-NATs), + and they play key roles in the regulation of gene expression in many organisms. + A promising experimental tool for profiling sense and antisense transcription + is strand-specific RNA sequencing (ssRNA-seq). `NASTIseq`_ is to identify + cis-NATs using ssRNA-seq. `NASTIseq`_ is based on model comparison that incorporates + the inherent variable efficiency of generating perfectly strand-specific libraries. + Applying the method to the ssRNA-seq data from whole root and + cell-type specific Arabidopsis libraries confirmed most of + the known cis-NAT pairs and identified hundreds of additional cis-NAT pairs. + +.. _NASTIseq: https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/ + +.. class:: infomark + +**Inputs** + + ``Annotation file``: the annotation in `gtf`_ format + + .. _gtf: http://www.ensembl.org/info/website/upload/gff.html + + ``Known pairs``: a table of two column matrix, with each row contains the + names of a known pair of cis-natural antisense transcripts. Example as following:: + + AT2G46910 AT2G46915 + AT3G12250 AT3G12260 + AT5G50315 AT5G50320 + + ``Read count of sense strand``: a table of N by M matrix of read count for reads that mapped + to the sense strand. N is the number of gene loci. M is the + number of biological replicates in the sample. Each + rowname must be a unique locus name. Example as following:: + + AT1G38440 0 2 0 + AT1G43171 2 8 1 + AT1G67670 3 7 0 + + ``Read count of antisense strand``: a table of N by M matrix of read count for reads that mapped + to the antisense strand. N is the number of gene loci. M is the + number of biological replicates in the sample. Each + rowname must be a unique locus name. Example as following:: + + AT1G38440 0 0 0 + AT1G43171 0 0 0 + AT1G67670 0 0 2 + + Read counts can be obtained using popular software such as `RSamtools`_. + +.. _RSamtools: http://bioconductor.org/packages/release/bioc/html/Rsamtools.html + +.. class:: infomark + +**Outputs** + + ``New pairs``: a table of two column matrix, with each row contains the + names of a new pair of cis-natural antisense transcripts. Example as following:: + + AT1G76630 AT1G76640 + AT2G06045 AT2G06050 + AT4G30100 AT4G30110 + + + ``New orphans``: a list of new orphan transcripts. Example as following:: + + ATMG00030 + AT5G49440 + AT2G11240 +]]> +</help> +<citations> + <citation type="doi">10.1101/gr.149310.112</citation> +</citations> +</tool> |
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| diff -r 000000000000 -r 0a0bba8e1823 test-data/input_TAIR10_annotation.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_TAIR10_annotation.gtf Wed Feb 22 07:32:08 2017 -0500 |
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| b'@@ -0,0 +1,33598 @@\n+#!genome-build TAIR10 gene\n+Chr1\tprotein_coding\tgene\t3631\t5899\t.\t+\t.\tgene_id "AT1G01010";\n+Chr1\tprotein_coding\tgene\t5928\t8737\t.\t-\t.\tgene_id "AT1G01020";\n+Chr1\tprotein_coding\tgene\t11649\t13714\t.\t-\t.\tgene_id "AT1G01030";\n+Chr1\tprotein_coding\tgene\t23146\t31227\t.\t+\t.\tgene_id "AT1G01040";\n+Chr1\tmiRNA\tgene\t28500\t28706\t.\t+\t.\tgene_id "AT1G01046";\n+Chr1\tprotein_coding\tgene\t31170\t33153\t.\t-\t.\tgene_id "AT1G01050";\n+Chr1\tprotein_coding\tgene\t33379\t37871\t.\t-\t.\tgene_id "AT1G01060";\n+Chr1\tprotein_coding\tgene\t38752\t40944\t.\t-\t.\tgene_id "AT1G01070";\n+Chr1\tprotein_coding\tgene\t44677\t44787\t.\t+\t.\tgene_id "AT1G01073";\n+Chr1\tprotein_coding\tgene\t45296\t47019\t.\t-\t.\tgene_id "AT1G01080";\n+Chr1\tprotein_coding\tgene\t47485\t49286\t.\t-\t.\tgene_id "AT1G01090";\n+Chr1\tprotein_coding\tgene\t50075\t51199\t.\t-\t.\tgene_id "AT1G01100";\n+Chr1\tprotein_coding\tgene\t52239\t54692\t.\t+\t.\tgene_id "AT1G01110";\n+Chr1\tprotein_coding\tgene\t56624\t56740\t.\t+\t.\tgene_id "AT1G01115";\n+Chr1\tprotein_coding\tgene\t57269\t59167\t.\t-\t.\tgene_id "AT1G01120";\n+Chr1\tprotein_coding\tgene\t61905\t63811\t.\t-\t.\tgene_id "AT1G01130";\n+Chr1\tprotein_coding\tgene\t64166\t67625\t.\t-\t.\tgene_id "AT1G01140";\n+Chr1\tprotein_coding\tgene\t70115\t72138\t.\t-\t.\tgene_id "AT1G01150";\n+Chr1\tprotein_coding\tgene\t72339\t74096\t.\t+\t.\tgene_id "AT1G01160";\n+Chr1\tprotein_coding\tgene\t73931\t74737\t.\t-\t.\tgene_id "AT1G01170";\n+Chr1\tprotein_coding\tgene\t75583\t76758\t.\t+\t.\tgene_id "AT1G01180";\n+Chr1\tmiRNA\tgene\t78932\t79032\t.\t-\t.\tgene_id "AT1G01183";\n+Chr1\tprotein_coding\tgene\t83045\t84864\t.\t-\t.\tgene_id "AT1G01190";\n+Chr1\tprotein_coding\tgene\t86515\t88213\t.\t-\t.\tgene_id "AT1G01200";\n+Chr1\tprotein_coding\tgene\t88898\t89745\t.\t+\t.\tgene_id "AT1G01210";\n+Chr1\tprotein_coding\tgene\t91376\t95651\t.\t+\t.\tgene_id "AT1G01220";\n+Chr1\tprotein_coding\tgene\t95987\t97407\t.\t+\t.\tgene_id "AT1G01225";\n+Chr1\tprotein_coding\tgene\t97456\t99240\t.\t+\t.\tgene_id "AT1G01230";\n+Chr1\tprotein_coding\tgene\t99894\t101834\t.\t+\t.\tgene_id "AT1G01240";\n+Chr1\tprotein_coding\tgene\t104491\t105330\t.\t-\t.\tgene_id "AT1G01250";\n+Chr1\tprotein_coding\tgene\t108946\t111609\t.\t+\t.\tgene_id "AT1G01260";\n+Chr1\ttRNA\tgene\t111890\t111961\t.\t-\t.\tgene_id "AT1G01270";\n+Chr1\tprotein_coding\tgene\t112263\t113947\t.\t+\t.\tgene_id "AT1G01280";\n+Chr1\tprotein_coding\tgene\t114286\t116108\t.\t+\t.\tgene_id "AT1G01290";\n+Chr1\tprotein_coding\tgene\t116943\t118764\t.\t+\t.\tgene_id "AT1G01300";\n+Chr1\tprotein_coding\tgene\t119397\t119997\t.\t+\t.\tgene_id "AT1G01305";\n+Chr1\tprotein_coding\tgene\t120154\t121130\t.\t+\t.\tgene_id "AT1G01310";\n+Chr1\tprotein_coding\tgene\t121067\t130577\t.\t-\t.\tgene_id "AT1G01320";\n+Chr1\tprotein_coding\tgene\t132328\t135831\t.\t-\t.\tgene_id "AT1G01340";\n+Chr1\tprotein_coding\tgene\t136124\t138162\t.\t+\t.\tgene_id "AT1G01350";\n+Chr1\tprotein_coding\tgene\t138513\t139568\t.\t+\t.\tgene_id "AT1G01355";\n+Chr1\tprotein_coding\tgene\t141971\t143183\t.\t+\t.\tgene_id "AT1G01360";\n+Chr1\tprotein_coding\tgene\t143564\t145684\t.\t+\t.\tgene_id "AT1G01370";\n+Chr1\tprotein_coding\tgene\t147153\t147942\t.\t+\t.\tgene_id "AT1G01380";\n+Chr1\tprotein_coding\tgene\t148120\t149806\t.\t-\t.\tgene_id "AT1G01390";\n+Chr1\tprotein_coding\tgene\t150689\t152210\t.\t-\t.\tgene_id "AT1G01400";\n+Chr1\tprotein_coding\tgene\t153113\t154198\t.\t+\t.\tgene_id "AT1G01410";\n+Chr1\tprotein_coding\tgene\t154492\t156011\t.\t-\t.\tgene_id "AT1G01420";\n+Chr1\tprotein_coding\tgene\t156801\t158655\t.\t-\t.\tgene_id "AT1G01430";\n+Chr1\tprotein_coding\tgene\t159856\t162572\t.\t-\t.\tgene_id "AT1G01440";\n+Chr1\tncRNA\tgene\t163419\t166239\t.\t+\t.\tgene_id "AT1G01448";\n+Chr1\tprotein_coding\tgene\t164105\t165517\t.\t-\t.\tgene_id "AT1G01450";\n+Chr1\tprotein_coding\tgene\t166589\t167842\t.\t-\t.\tgene_id "AT1G01453";\n+Chr1\tprotein_coding\tgene\t168723\t171165\t.\t+\t.\tgene_id "AT1G01460";\n+Chr1\tprotein_coding\tgene\t172146\t172948\t.\t-\t.\tgene_id "AT1G01470";\n+Chr1\tprotein_coding\tgene\t173251\t173466\t.\t+\t.\tgene_id "AT1G01471";\n+Chr1\tprotein_coding\tgene\t175782\t178400\t.\t+\t.\tgene_id "AT1G01480";\n+Chr1\tprotein_coding\tgene\t180059\t182358\t.\t-\t.\tgene_id "AT1G01490";\n+Chr1\tprotein_coding\tgene\t185133\t186923\t.\t+\t.\tgene_id "AT1G01500";\n+Chr1\tprotein_coding\tgene\t187211\t190056\t.\t+\t.\tgene_id "AT1G01510";\n+Chr1\tprotein_coding\tgene\t190'..b'ng\tgene\t228573\t229085\t.\t-\t.\tgene_id "ATMG00820";\n+ChrM\tprotein_coding\tgene\t231894\t233042\t.\t-\t.\tgene_id "ATMG00830";\n+ChrM\tprotein_coding\tgene\t234538\t234903\t.\t-\t.\tgene_id "ATMG00840";\n+ChrM\tprotein_coding\tgene\t235338\t235661\t.\t+\t.\tgene_id "ATMG00850";\n+ChrM\tprotein_coding\tgene\t235916\t236392\t.\t+\t.\tgene_id "ATMG00860";\n+ChrM\tprotein_coding\tgene\t236927\t237481\t.\t-\t.\tgene_id "ATMG00870";\n+ChrM\tprotein_coding\tgene\t237053\t237616\t.\t+\t.\tgene_id "ATMG00880";\n+ChrM\tprotein_coding\tgene\t239636\t239956\t.\t-\t.\tgene_id "ATMG00890";\n+ChrM\tprotein_coding\tgene\t239988\t240758\t.\t-\t.\tgene_id "ATMG00900";\n+ChrM\tprotein_coding\tgene\t241306\t241953\t.\t-\t.\tgene_id "ATMG00910";\n+ChrM\tprotein_coding\tgene\t249272\t249919\t.\t-\t.\tgene_id "ATMG00920";\n+ChrM\ttRNA\tgene\t250080\t250153\t.\t-\t.\tgene_id "ATMG00930";\n+ChrM\tprotein_coding\tgene\t251403\t251897\t.\t-\t.\tgene_id "ATMG00940";\n+ChrM\ttRNA\tgene\t254505\t254571\t.\t-\t.\tgene_id "ATMG00950";\n+ChrM\tprotein_coding\tgene\t256865\t257476\t.\t-\t.\tgene_id "ATMG00960";\n+ChrM\tprotein_coding\tgene\t258045\t258398\t.\t-\t.\tgene_id "ATMG00970";\n+ChrM\tprotein_coding\tgene\t260224\t260601\t.\t-\t.\tgene_id "ATMG00980";\n+ChrM\tprotein_coding\tgene\t260647\t261006\t.\t-\t.\tgene_id "ATMG00990";\n+ChrM\tprotein_coding\tgene\t260963\t261307\t.\t-\t.\tgene_id "ATMG01000";\n+ChrM\tprotein_coding\tgene\t261105\t261461\t.\t-\t.\tgene_id "ATMG01010";\n+ChrM\tprotein_coding\tgene\t261617\t262078\t.\t-\t.\tgene_id "ATMG01020";\n+ChrM\tprotein_coding\tgene\t264113\t264433\t.\t-\t.\tgene_id "ATMG01030";\n+ChrM\tprotein_coding\tgene\t270238\t270561\t.\t-\t.\tgene_id "ATMG01040";\n+ChrM\tprotein_coding\tgene\t272944\t273423\t.\t-\t.\tgene_id "ATMG01050";\n+ChrM\tprotein_coding\tgene\t274899\t275222\t.\t+\t.\tgene_id "ATMG01060";\n+ChrM\ttRNA\tgene\t275103\t275176\t.\t+\t.\tgene_id "ATMG01070";\n+ChrM\tprotein_coding\tgene\t278649\t279152\t.\t+\t.\tgene_id "ATMG01080";\n+ChrM\tprotein_coding\tgene\t279463\t280251\t.\t+\t.\tgene_id "ATMG01090";\n+ChrM\tprotein_coding\tgene\t281614\t281931\t.\t+\t.\tgene_id "ATMG01100";\n+ChrM\tprotein_coding\tgene\t283034\t283789\t.\t-\t.\tgene_id "ATMG01110";\n+ChrM\tprotein_coding\tgene\t287917\t289083\t.\t-\t.\tgene_id "ATMG01120";\n+ChrM\tprotein_coding\tgene\t289197\t289517\t.\t-\t.\tgene_id "ATMG01130";\n+ChrM\tprotein_coding\tgene\t292973\t293431\t.\t-\t.\tgene_id "ATMG01140";\n+ChrM\tprotein_coding\tgene\t293976\t294296\t.\t-\t.\tgene_id "ATMG01150";\n+ChrM\ttRNA\tgene\t296688\t296784\t.\t-\t.\tgene_id "ATMG01160";\n+ChrM\tprotein_coding\tgene\t296820\t298204\t.\t-\t.\tgene_id "ATMG01170";\n+ChrM\tprotein_coding\tgene\t300966\t301301\t.\t-\t.\tgene_id "ATMG01180";\n+ChrM\tprotein_coding\tgene\t302166\t303689\t.\t-\t.\tgene_id "ATMG01190";\n+ChrM\tprotein_coding\tgene\t303836\t304720\t.\t-\t.\tgene_id "ATMG01200";\n+ChrM\tprotein_coding\tgene\t304779\t305084\t.\t-\t.\tgene_id "ATMG01210";\n+ChrM\tprotein_coding\tgene\t305221\t305562\t.\t-\t.\tgene_id "ATMG01220";\n+ChrM\tprotein_coding\tgene\t308932\t309369\t.\t+\t.\tgene_id "ATMG01230";\n+ChrM\tprotein_coding\tgene\t309338\t309640\t.\t-\t.\tgene_id "ATMG01240";\n+ChrM\tprotein_coding\tgene\t310514\t310882\t.\t+\t.\tgene_id "ATMG01250";\n+ChrM\tprotein_coding\tgene\t312545\t313162\t.\t-\t.\tgene_id "ATMG01260";\n+ChrM\tprotein_coding\tgene\t314627\t315073\t.\t+\t.\tgene_id "ATMG01270";\n+ChrM\tprotein_coding\tgene\t318004\t318390\t.\t-\t.\tgene_id "ATMG01275";\n+ChrM\tprotein_coding\tgene\t318588\t319463\t.\t-\t.\tgene_id "ATMG01280";\n+ChrM\tprotein_coding\tgene\t324259\t324594\t.\t+\t.\tgene_id "ATMG01290";\n+ChrM\tprotein_coding\tgene\t325300\t325710\t.\t+\t.\tgene_id "ATMG01300";\n+ChrM\tprotein_coding\tgene\t326099\t326509\t.\t+\t.\tgene_id "ATMG01310";\n+ChrM\tprotein_coding\tgene\t327890\t333105\t.\t-\t.\tgene_id "ATMG01320";\n+ChrM\tprotein_coding\tgene\t329082\t329465\t.\t-\t.\tgene_id "ATMG01330";\n+ChrM\ttRNA\tgene\t337669\t337741\t.\t+\t.\tgene_id "ATMG01340";\n+ChrM\tprotein_coding\tgene\t346757\t347194\t.\t+\t.\tgene_id "ATMG01350";\n+ChrM\tprotein_coding\tgene\t349830\t351413\t.\t-\t.\tgene_id "ATMG01360";\n+ChrM\tprotein_coding\tgene\t360717\t361052\t.\t-\t.\tgene_id "ATMG01370";\n+ChrM\trRNA\tgene\t361062\t361179\t.\t-\t.\tgene_id "ATMG01380";\n+ChrM\trRNA\tgene\t361350\t363284\t.\t-\t.\tgene_id "ATMG01390";\n+ChrM\tprotein_coding\tgene\t363725\t364042\t.\t+\t.\tgene_id "ATMG01400";\n+ChrM\tprotein_coding\tgene\t366086\t366700\t.\t-\t.\tgene_id "ATMG01410";\n' |
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| diff -r 000000000000 -r 0a0bba8e1823 test-data/input_positive_pair.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_positive_pair.tsv Wed Feb 22 07:32:08 2017 -0500 |
| b |
| b'@@ -0,0 +1,874 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+AT3G18680\tAT3G18690\n+AT4G22730\tAT4G22740\n+AT4G36370\tAT4G36380\n+AT4G15820\tAT4G15830\n+AT1G11090\tAT1G11100\n+AT5G25170\tAT5G25180\n+AT5G63010\tAT5G63020\n+AT5G01960\tAT5G01970\n+AT1G62240\tAT1G62250\n+AT1G03970\tAT1G03980\n+AT3G02840\tAT3G02850\n+AT1G52087\tAT1G52090\n+AT5G13690\tAT5G13700\n+AT5G17410\tAT5G17420\n+AT2G36010\tAT2G36020\n+AT3G01460\tAT3G01470\n+AT4G35850\tAT4G35860\n+AT5G40640\tAT5G40645\n+AT5G62810\tAT5G62820\n+AT2G29410\tAT2G29420\n+AT1G18630\tAT1G18640\n+AT5G06310\tAT5G06320\n+AT2G31880\tAT2G31890\n+AT5G08390\tAT5G08400\n+AT4G19100\tAT4G19095\n+AT2G41950\tAT2G41960\n+AT3G62580\tAT3G62590\n+AT3G24020\tAT3G24030\n+AT1G70330\tAT1G70340\n+AT4G20300\tAT4G20290\n+AT5G13390\tAT5G13400\n+AT1G79560\tAT1G79570\n+AT3G47950\tAT3G47960\n+AT5G58300\tAT5G58310\n+AT1G31220\tAT1G31230\n+AT2G26170\tAT2G26180\n+AT5G64750\tAT5G64760\n+AT5G02120\tAT5G02130\n+AT1G18880\tAT1G18890\n+AT2G01860\tAT2G01870\n+AT4G21470\tAT4G21480\n+AT1G11770\tAT1G11780\n+AT5G38600\tAT5G38610\n+AT5G15440\tAT5G15450\n+AT2G41670\tAT2G41680\n+AT1G27300\tAT1G27310\n+AT3G45970\tAT3G45980\n+AT2G28290\tAT2G28280\n+AT4G26680\tAT4G26690\n+AT4G29250\tAT4G29260\n+AT5G47435\tAT5G47440\n+AT1G21270\tAT1G21280\n+AT1G48300\tAT1G48310\n+AT3G58710\tAT3G58720\n+AT3G29320\tAT3G29330\n+AT5G16060\tAT5G16070\n+AT5G11810\tAT5G11820\n+AT1G48100\tAT1G48110\n+AT3G14270\tAT3G14280\n+AT5G16300\tAT5G16310\n+AT1G16560\tAT1G16570\n+AT1G15410\tAT1G15415\n+AT2G31035\tAT2G31040\n+AT5G26030\tAT5G26040\n+AT2G41760\tAT2G41770\n+AT5G38630\tAT5G38640\n+AT3G48320\tAT3G48330\n+AT3G27750\tAT3G27770\n+AT5G02710\tAT5G02720\n+AT1G63980\tAT1G63990\n+AT1G71180\tAT1G71190\n+AT1G17130\tAT1G17140\n+AT4G24010\tAT4G24015\n+AT1G15810\tAT1G15820\n+AT2G36580\tAT2G36590\n+AT4G34410\tAT4G34412\n+AT4G18570\tAT4G18580\n+AT1G56000\tAT1G56010\n+AT5G51010\tAT5G51020\n+AT3G61560\tAT3G61570\n+AT1G31190\tAT1G31200\n+AT1G78050\tAT1G78060\n+AT1G16810\tAT1G16820\n+AT4G36760\tAT4G36770\n+AT5G41980\tAT5G41990\n+AT5G63880\tAT5G63890\n+AT2G20260\tAT2G20270\n+AT4G04860\tAT4G04870\n+AT3G62010\tAT3G62020\n+AT5G24800\tAT5G24810\n+AT5G63480\tAT5G63490\n+AT4G33666\tAT4G33670\n+AT1G54830\tAT1G54840\n+AT5G49910\tAT5G49920\n+AT5G66180\tAT5G66190\n+AT1G27650\tAT1G27640\n+AT4G29830\tAT4G29840\n+AT3G19700\tAT3G19710\n+AT5G42180\tAT5G42190\n+AT4G28760\tAT4G28770\n+AT1G05450\tAT1G05460\n+AT2G45990\tAT2G46000\n+AT3G13670\tAT3G13672\n+AT3G54780\tAT3G54790\n+AT2G46225\tAT2G46230\n+AT4G34850\tAT4G34860\n+AT1G04210\tAT1G04220\n+AT1G77230\tAT1G77240\n+AT5G58960\tAT5G58970\n+AT4G11970\tAT4G11980\n+AT1G14000\tAT1G14010\n+AT3G15870\tAT3G15880\n+AT2G40765\tAT2G40770\n+AT1G29320\tAT1G29330\n+AT2G27080\tAT2G27090\n+AT2G39340\tAT2G39350\n+AT5G02820\tAT5G02830\n+AT1G55265\tAT1G55270\n+AT5G60510\tAT5G60520\n+AT5G41320\tAT5G41330\n+AT2G16910\tAT2G16920\n+AT1G71300\tAT1G71310\n+AT1G09000\tAT1G09010\n+AT5G40155\tAT5G40160\n+AT3G61540\tAT3G61530\n+AT2G14680\tAT2G14690\n+AT4G28040\tAT4G28050\n+AT5G06420\tAT5G06410\n+AT1G43890\tAT1G43895\n+AT1G73220\tAT1G73230\n+AT5G17630\tAT5G17640\n+AT1G65960\tAT1G65970\n+AT3G13770\tAT3G13772\n+AT4G26970\tAT4G26980\n+AT3G22620\tAT3G22630\n+AT3G55030\tAT3G55040\n+AT5G55820\tAT5G55810\n+AT4G10470\tAT4G10480\n+AT1G10110\tAT1G10120\n+AT5G47640\tAT5G47650\n+AT5G49600\tAT5G49610\n+AT3G15060\tAT3G15070\n+AT5G19840\tAT5G19850\n+AT1G76350\tAT1G76360\n+AT1G79660\tAT1G79670\n+AT1G50520\tAT1G50530\n+AT1G60420\tAT1G60430\n+AT3G25550\tAT3G25560\n+AT5G65480\tAT5G65490\n+AT3G27110\tAT3G27120\n+AT1G23730\tAT1G23740\n+AT5G13720\tAT5G13730\n+AT5G47455\tAT5G47460\n+AT4G33100\tAT4G33110\n+AT3G61220\tAT3G61230\n+AT4G10020\tAT4G10030\n+AT3G15605\tAT3G15610\n+AT1G53440\tAT1G53450\n+AT5G52560\tAT5G52570\n+AT1G74550\tAT1G74560\n+AT5G43770\tAT5G43780\n+AT5G06220\tAT5G06230\n+AT5G02280\tAT5G02290\n' |
| b |
| diff -r 000000000000 -r 0a0bba8e1823 test-data/input_read_count_asmt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_read_count_asmt.tsv Wed Feb 22 07:32:08 2017 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 0a0bba8e1823 test-data/input_read_count_smt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_read_count_smt.tsv Wed Feb 22 07:32:08 2017 -0500 |
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|
| b |
| diff -r 000000000000 -r 0a0bba8e1823 test-data/output_neworphan.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_neworphan.tsv Wed Feb 22 07:32:08 2017 -0500 |
| b |
| @@ -0,0 +1,414 @@ +ATMG00030 +AT5G49440 +AT2G11240 +AT5G49640 +AT2G33320 +AT2G24840 +AT4G17905 +AT1G72760 +AT1G21310 +AT3G23460 +AT3G53510 +AT3G04690 +AT5G13560 +AT3G22800 +AT4G15150 +AT5G59580 +AT1G55180 +AT1G19220 +AT3G41768 +AT1G68945 +AT5G01560 +AT4G08850 +AT5G19100 +AT1G29540 +AT3G19020 +AT2G34330 +ATMG00130 +AT5G51580 +AT5G62140 +AT1G25450 +ATMG00140 +AT5G16770 +AT2G15320 +AT3G44798 +AT1G23840 +AT4G14860 +AT4G19170 +AT1G79910 +AT3G06433 +AT2G38823 +AT2G07688 +AT2G38210 +AT1G22880 +AT2G21188 +AT5G60280 +AT3G56780 +AT3G32980 +AT3G54590 +AT3G28550 +AT4G21740 +AT3G57400 +AT2G46810 +AT1G04540 +AT2G39380 +AT1G35710 +AT5G66330 +AT5G09530 +AT2G42860 +AT5G37760 +AT3G25010 +AT3G53720 +AT2G35000 +AT1G03940 +AT5G25010 +AT1G49780 +AT3G04440 +AT5G01930 +AT5G24318 +AT1G73330 +AT2G38830 +AT1G63860 +AT3G14650 +AT1G65346 +AT1G66690 +AT5G67460 +AT5G26960 +AT4G08400 +AT5G52020 +AT4G37620 +AT2G05440 +AT5G53740 +AT4G02320 +AT1G03495 +ATMG00150 +AT5G22890 +AT5G01170 +AT1G41930 +AT1G14070 +AT5G55490 +AT3G14660 +AT4G03270 +AT4G26670 +AT2G37100 +AT3G60080 +AT5G57180 +AT3G28630 +AT2G30505 +ATCG00630 +AT3G25011 +AT5G58530 +AT2G02700 +AT4G31710 +AT1G29770 +AT3G09070 +AT3G49520 +AT3G14950 +AT5G40900 +AT1G63140 +AT5G27100 +AT3G46910 +AT3G14630 +AT5G49700 +AT1G35580 +AT5G58170 +AT2G35960 +AT3G17640 +AT5G15900 +AT4G29930 +AT5G22610 +AT2G47720 +AT1G78030 +AT1G73880 +AT1G06148 +AT3G53950 +AT1G10260 +AT5G58080 +ATCG01100 +AT3G26932 +AT4G02520 +AT1G66480 +AT1G68795 +AT4G15975 +AT4G08150 +AT3G27025 +AT5G09360 +AT2G37380 +AT4G34220 +AT3G11090 +AT1G07340 +AT2G17064 +ATMG00110 +AT4G01720 +AT4G38300 +AT1G28400 +AT5G44569 +AT3G13760 +AT5G42750 +AT1G49490 +AT4G23670 +ATCG01080 +AT1G23720 +AT5G42040 +AT2G31990 +ATCG00050 +ATCG00380 +AT1G73260 +AT5G57750 +AT5G36870 +AT1G77640 +AT1G75820 +AT4G33560 +AT2G01320 +AT1G73066 +AT1G21990 +AT3G56810 +ATCG00065 +AT3G05820 +AT2G23540 +AT5G25020 +AT3G01420 +AT1G26890 +AT1G13150 +AT4G33470 +AT4G38460 +AT3G46550 +AT3G25020 +AT3G50350 +AT2G01530 +AT5G65710 +AT1G28815 +AT3G27906 +AT5G04390 +AT4G08410 +AT1G67810 +AT3G54210 +AT5G09520 +AT5G25220 +AT1G33860 +AT5G53742 +AT3G57760 +AT3G57830 +AT5G03100 +AT2G07787 +AT2G03440 +AT2G15300 +AT2G23190 +AT1G64590 +AT5G49080 +AT1G67800 +AT1G27180 +AT3G62725 +ATCG00070 +AT5G45460 +AT4G37000 +AT5G25270 +AT4G28085 +AT5G10230 +AT2G01520 +AT4G12450 +AT3G19380 +AT2G26110 +AT1G77400 +AT1G33100 +AT5G14500 +AT5G40150 +AT2G35910 +AT5G17340 +AT4G14465 +AT1G12330 +AT2G08986 +AT1G72790 +AT1G12060 +AT3G13270 +AT5G26622 +AT2G36470 +AT5G61600 +AT5G06839 +AT2G48000 +AT3G04360 +AT3G52460 +AT4G18335 +AT5G61480 +AT5G24010 +AT5G01830 +AT5G44550 +AT5G55780 +ATCG00640 +AT1G70170 +AT4G12050 +AT5G12420 +AT1G08750 +AT5G14890 +AT5G15830 +AT5G62180 +AT1G69310 +AT2G41870 +AT2G45170 +AT5G28913 +AT1G13540 +AT5G65460 +AT1G19300 +AT5G14570 +AT2G07696 +AT2G07711 +AT3G61460 +AT4G19460 +AT3G55090 +AT5G12990 +AT5G10970 +AT3G54580 +AT1G29290 +AT5G64120 +AT3G57320 +AT5G58680 +AT3G62430 +ATMG00640 +AT2G46590 +AT1G21510 +AT1G05675 +AT5G06640 +AT1G09176 +AT3G18035 +AT3G44430 +ATMG01170 +AT5G07330 +AT5G11990 +AT5G37990 +AT5G22090 +AT3G25940 +AT1G68330 +AT3G49120 +AT3G50280 +AT3G62660 +AT2G44000 +AT5G65080 +AT3G44880 +AT4G24040 +AT1G62440 +AT5G66150 +AT3G11420 +AT3G51740 +AT1G73000 +AT3G01970 +AT4G26320 +AT2G27130 +AT2G17880 +AT1G77525 +AT4G19191 +AT1G49210 +AT2G24980 +AT1G07795 +AT5G19060 +AT2G31110 +AT1G80810 +AT3G14190 +AT5G14140 +AT4G25270 +AT2G30933 +ATMG01380 +AT5G15060 +ATCG00150 +AT5G50530 +AT3G62680 +ATCG00580 +AT5G65170 +AT3G43840 +AT2G47150 +AT4G34135 +AT1G50190 +AT3G11580 +AT1G07590 +AT4G28890 +AT4G09170 +AT5G12020 +AT2G39110 +AT1G08810 +AT4G18090 +AT5G41690 +AT2G07042 +AT2G30230 +AT2G28870 +AT3G01500 +ATCG01070 +AT5G35190 +AT5G51530 +AT3G09032 +AT1G12040 +AT5G64980 +AT5G13790 +AT4G29610 +AT3G45710 +AT1G48745 +AT5G06330 +AT5G61340 +ATCG00430 +AT3G30122 +AT3G28920 +AT4G37540 +AT3G44990 +AT5G65070 +AT5G62170 +AT3G54410 +AT1G43560 +AT4G35900 +AT2G24600 +AT3G14680 +AT4G33990 +AT5G37690 +AT2G35650 +AT3G03550 +AT4G36350 +AT4G03380 +AT3G26210 +AT5G50200 +AT4G39780 +AT5G03180 +AT1G17240 +AT1G03730 +AT3G54680 +AT5G64620 +AT5G38290 +AT5G03050 +AT5G13330 +AT2G35830 +AT1G76100 +AT4G30180 +AT1G80180 +AT2G28305 +AT1G14430 +AT5G25910 +AT5G17600 +AT2G02070 +AT1G12020 +AT1G67090 +AT4G12300 +AT5G38020 +AT4G00070 +AT4G37450 +AT1G80800 +AT5G01910 +AT5G47560 +AT3G12977 +AT2G25260 +AT4G36280 +AT1G69600 +ATCG00350 +AT1G11700 +AT5G49690 +AT3G56270 +AT1G17345 +AT5G17980 +AT3G20640 +AT1G07240 +AT2G40113 +AT2G38380 +AT1G49180 +AT3G43580 +AT2G35750 +AT1G65510 +AT5G28500 +AT5G04470 +AT2G41470 +AT1G63580 +AT5G66320 |
| b |
| diff -r 000000000000 -r 0a0bba8e1823 test-data/output_newpairs.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_newpairs.tsv Wed Feb 22 07:32:08 2017 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 0a0bba8e1823 test-data/test.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.r Wed Feb 22 07:32:08 2017 -0500 |
| [ |
| @@ -0,0 +1,53 @@ +library(NASTIseq) + +## generation of test set +# data(WholeRoot) +# WholeRoot$genepos$feature <- 'gene' +# +# set_attri <- function(attri){ +# attri = paste('gene_id ', '"', attri, '"', ';', sep = '') +# return(attri) +# } +# +# WholeRoot$genepos$attributes = as.character(lapply(as.character(WholeRoot$genepos$attributes), set_attri)) +# +# write.table(WholeRoot$genepos, file = "input_TAIR10_annotation.gtf", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) +# write.table(WholeRoot$smat, file = "input_read_count_smt.tsv", col.names = FALSE, sep = "\t", quote = FALSE) +# write.table(WholeRoot$asmat, file = "input_read_count_asmt.tsv", col.names = FALSE, sep = "\t", quote = FALSE) +# +# write.table(WholeRoot$pospairs, file = "input_positive_pair.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) + +genepos = read.delim("input_TAIR10_annotation.gtf", header=FALSE, comment.char="#") +colnames(genepos) = c("seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes") +genepos = subset(genepos, feature=="gene") + +get_id = function(attri){ + gene_info = strsplit(attri, ";")[[1]][1] + gene_id = strsplit(gene_info, " ")[[1]][2] + gene_id = gsub("\"", "", gene_id) + return(gene_id) +} + +genepos$attributes = as.character(lapply(as.character(genepos$attributes), get_id)) + +pospairs = read.table("input_positive_pair.tsv", sep = "\t", as.is = TRUE) + +smat = as.matrix(read.table("input_read_count_smt.tsv", sep = "\t", row.names = 1)) + +asmat = as.matrix(read.table("input_read_count_asmt.tsv", sep = "\t", row.names = 1)) + +WRscore = getNASTIscore(smat, asmat) + +negpairs = getnegativepairs(genepos) + +WRpred = NASTIpredict(smat,asmat, pospairs, negpairs) + +WRpred_rocr = prediction(WRpred$predictions,WRpred$labels) + +thr = defineFDR(WRpred_rocr,0.05) + +WR_names = FindNATs(WRscore, thr, pospairs, genepos) + +write.table(WR_names$newpairs, file = "output_newpairs.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) + +write.table(WR_names$neworphan, file = "output_neworphan.tsv", row.names = FALSE, col.names = FALSE, sep = "\t", quote = FALSE) |