| Previous changeset 1:202a99525669 (2019-06-25) Next changeset 3:ecce0cbe659f (2019-10-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada" |
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modified:
macros.xml test-data/gff_to_prot-in1.gff3 test-data/gff_to_prot-out1.txt test-data/gumbel-sites1.txt test-data/hmm-genes1.txt test-data/hmm-sites1.txt test-data/resampling-sites1.txt test-data/transit-co1-rep1.wig test-data/transit-co1-rep2.wig test-data/transit-co1-rep3.wig test-data/transit-in1-rep1.wig test-data/transit-in1-rep2.wig test-data/transit-in1.prot transit_gumbel.xml |
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added:
test-data/tn5gaps-sites1.txt test-data/transit-in-tn5.wig test-data/transit-in2-tn5.wig test-data/transit_tn5.prot |
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removed:
test-data/transit-in1.gff3 |
| b |
| diff -r 202a99525669 -r c980be2c002c macros.xml --- a/macros.xml Tue Jun 25 17:43:58 2019 -0400 +++ b/macros.xml Tue Oct 08 08:24:12 2019 -0400 |
| [ |
| @@ -9,10 +9,11 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">transit</requirement> + <requirement type="package" version="3.7">python</requirement> <yield /> </requirements> </xml> - <token name="@VERSION@">2.5.2</token> + <token name="@VERSION@">3.0.1</token> <xml name="outputs"> <yield /> <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> @@ -43,10 +44,22 @@ <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." /> <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." /> </xml> + <xml name="normal"> + <param name="normalization" argument="-n" type="select" label="Normalization method" value="TTR"> + <option value="TTR">TTR</option> + <option value="nonorm">No Normalization</option> + <option value="nzmean">Non-Zero Mean</option> + <option value="totreads">Total read counts</option> + <option value="zinfnb">Zero inflated Negative Binomial model</option> + <option value="quantile">Quantile Normalization</option> + <option value="betageom">Beta-Geometric Correction</option> + </param> + </xml> <xml name="standard_inputs"> <expand macro="inputs" /> <yield /> <expand macro="ignore_tas" /> + <expand macro="normal" /> </xml> <token name="@LINK_INPUTS@"> <![CDATA[ @@ -64,5 +77,6 @@ <token name="@STANDARD_OPTIONS@"> -iN $nterm -tC $cterm + -n $normalization </token> </macros> |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/gff_to_prot-in1.gff3 --- a/test-data/gff_to_prot-in1.gff3 Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/gff_to_prot-in1.gff3 Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -498,5302 +498,3 @@\n NC_007795.1\tRefSeq\tgene\t287243\t287560\t.\t+\t.\tID=gene-SAOUHSC_00267;Dbxref=GeneID:3919208;Name=SAOUHSC_00267;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00267\n NC_007795.1\tRefSeq\tCDS\t287243\t287560\t.\t+\t0\tID=cds-YP_498860.1;Parent=gene-SAOUHSC_00267;Dbxref=Genbank:YP_498860.1,GeneID:3919208;Name=YP_498860.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498860.1;transl_table=11\n NC_007795.1\tRefSeq\tgene\t287570\t289414\t.\t+\t.\tID=gene-SAOUHSC_00268;Dbxref=GeneID:3919209;Name=SAOUHSC_00268;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00268\n-NC_007795.1\tRefSeq\tCDS\t287570\t289414\t.\t+\t0\tID=cds-YP_498861.1;Parent=gene-SAOUHSC_00268;Dbxref=Genbank:YP_498861.1,GeneID:3919209;Name=YP_498861.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498861.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t289425\t289916\t.\t+\t.\tID=gene-SAOUHSC_00269;Dbxref=GeneID:3919210;Name=SAOUHSC_00269;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00269\n-NC_007795.1\tRefSeq\tCDS\t289425\t289916\t.\t+\t0\tID=cds-YP_498862.1;Parent=gene-SAOUHSC_00269;Dbxref=Genbank:YP_498862.1,GeneID:3919210;Name=YP_498862.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498862.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t290124\t290807\t.\t+\t.\tID=gene-SAOUHSC_00270;Dbxref=GeneID:3919211;Name=SAOUHSC_00270;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00270\n-NC_007795.1\tRefSeq\tCDS\t290124\t290807\t.\t+\t0\tID=cds-YP_498863.1;Parent=gene-SAOUHSC_00270;Dbxref=Genbank:YP_498863.1,GeneID:3919211;Name=YP_498863.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498863.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t290954\t291565\t.\t+\t.\tID=gene-SAOUHSC_00271;Dbxref=GeneID:3919212;Name=SAOUHSC_00271;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00271\n-NC_007795.1\tRefSeq\tCDS\t290954\t291565\t.\t+\t0\tID=cds-YP_498864.1;Parent=gene-SAOUHSC_00271;Dbxref=Genbank:YP_498864.1,GeneID:3919212;Name=YP_498864.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498864.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t291701\t291919\t.\t+\t.\tID=gene-SAOUHSC_00272;Dbxref=GeneID:3919213;Name=SAOUHSC_00272;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00272\n-NC_007795.1\tRefSeq\tCDS\t291701\t291919\t.\t+\t0\tID=cds-YP_498865.1;Parent=gene-SAOUHSC_00272;Dbxref=Genbank:YP_498865.1,GeneID:3919213;Name=YP_498865.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498865.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t292051\t292551\t.\t+\t.\tID=gene-SAOUHSC_00274;Dbxref=GeneID:3919214;Name=SAOUHSC_00274;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00274\n-NC_007795.1\tRefSeq\tCDS\t292051\t292551\t.\t+\t0\tID=cds-YP_498866.1;Parent=gene-SAOUHSC_00274;Dbxref=Genbank:YP_498866.1,GeneID:3919214;Name=YP_498866.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498866.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t292562\t293062\t.\t+\t.\tID=gene-SAOUHSC_00275;Dbxref=GeneID:3919215;Name=SAOUHSC_00275;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00275\n-NC_007795.1\tRefSeq\tCDS\t292562\t293062\t.\t+\t0\tID=cds-YP_498867.2;Parent=gene-SAOUHSC_00275;Dbxref=Genbank:YP_498867.2,GeneID:3919215;Name=YP_498867.2;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498867.2;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t293073\t293573\t.\t+\t.\tID=gene-SAOUHSC_00276;Dbxref=GeneID:3918960;Name=SAOUHSC_00276;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00276\n-NC_007795.1\tRefSeq\tCDS\t293073\t293573\t.\t+\t0\tID=cds-YP_498868.1;Parent=gene-SAOUHSC_00276;Dbxref=Genbank:YP_498868.1,GeneID:3918960;Name=YP_498868.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498868.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t293584\t294084\t.\t+\t.\tID=gene-SAOUHSC_00277;Dbxref=GeneI'..b"NC_007795.1\tRefSeq\tgene\t2814666\t2815019\t.\t-\t.\tID=gene-SAOUHSC_03048;Dbxref=GeneID:3921312;Name=SAOUHSC_03048;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_03048\n-NC_007795.1\tRefSeq\tCDS\t2814666\t2815019\t.\t-\t0\tID=cds-YP_501494.1;Parent=gene-SAOUHSC_03048;Dbxref=Genbank:YP_501494.1,GeneID:3921312;Name=YP_501494.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_501494.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2815473\t2816312\t.\t-\t.\tID=gene-SAOUHSC_03049;Dbxref=GeneID:3921313;Name=SAOUHSC_03049;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_03049\n-NC_007795.1\tRefSeq\tCDS\t2815473\t2816312\t.\t-\t0\tID=cds-YP_501495.1;Parent=gene-SAOUHSC_03049;Dbxref=Genbank:YP_501495.1,GeneID:3921313;Name=YP_501495.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_501495.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2816355\t2817074\t.\t-\t.\tID=gene-SAOUHSC_03051;Dbxref=GeneID:3921314;Name=gidB;gbkey=Gene;gene=gidB;gene_biotype=protein_coding;locus_tag=SAOUHSC_03051\n-NC_007795.1\tRefSeq\tCDS\t2816355\t2817074\t.\t-\t0\tID=cds-YP_501496.1;Parent=gene-SAOUHSC_03051;Dbxref=Genbank:YP_501496.1,GeneID:3921314;Name=YP_501496.1;Note=glucose-inhibited division protein B%3B SAM-dependent methyltransferase%3B methylates the N7 position of guanosine in position 527 of 16S rRNA;gbkey=CDS;gene=gidB;product=16S rRNA methyltransferase GidB;protein_id=YP_501496.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2817074\t2818951\t.\t-\t.\tID=gene-SAOUHSC_03052;Dbxref=GeneID:3921315;Name=gidA;gbkey=Gene;gene=gidA;gene_biotype=protein_coding;gene_synonym=gidA;locus_tag=SAOUHSC_03052\n-NC_007795.1\tRefSeq\tCDS\t2817074\t2818951\t.\t-\t0\tID=cds-YP_501497.2;Parent=gene-SAOUHSC_03052;Dbxref=Genbank:YP_501497.2,GeneID:3921315;Name=YP_501497.2;Note=GidA%3B glucose-inhibited cell division protein A%3B involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs;gbkey=CDS;gene=gidA;product=tRNA uridine 5-carboxymethylaminomethyl modification protein GidA;protein_id=YP_501497.2;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2819018\t2820397\t.\t-\t.\tID=gene-SAOUHSC_03053;Dbxref=GeneID:3921316;Name=trmE;gbkey=Gene;gene=trmE;gene_biotype=protein_coding;gene_synonym=mnmE,thdF;locus_tag=SAOUHSC_03053\n-NC_007795.1\tRefSeq\tCDS\t2819018\t2820397\t.\t-\t0\tID=cds-YP_501498.1;Parent=gene-SAOUHSC_03053;Dbxref=Genbank:YP_501498.1,GeneID:3921316;Name=YP_501498.1;Note=in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine%2C which is found in the wobble position of some tRNAs and affects ribosomal frameshifting%3B shows potassium-dependent dimerization and GTP hydrolysis%3B also involved in regulation of glutamate-dependent acid resistance and activation of gadE;gbkey=CDS;gene=trmE;product=tRNA modification GTPase TrmE;protein_id=YP_501498.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2820536\t2820889\t.\t-\t.\tID=gene-SAOUHSC_03054;Dbxref=GeneID:3921317;Name=rnpA;gbkey=Gene;gene=rnpA;gene_biotype=protein_coding;locus_tag=SAOUHSC_03054\n-NC_007795.1\tRefSeq\tCDS\t2820536\t2820889\t.\t-\t0\tID=cds-YP_501499.1;Parent=gene-SAOUHSC_03054;Dbxref=Genbank:YP_501499.1,GeneID:3921317;Name=YP_501499.1;Note=protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus%3B this enzyme also cleaves other RNA substrates;gbkey=CDS;gene=rnpA;product=ribonuclease P;protein_id=YP_501499.1;transl_table=11\n-NC_007795.1\tRefSeq\tgene\t2821010\t2821147\t.\t-\t.\tID=gene-SAOUHSC_03055;Dbxref=GeneID:3921318;Name=rpmH;gbkey=Gene;gene=rpmH;gene_biotype=protein_coding;locus_tag=SAOUHSC_03055\n-NC_007795.1\tRefSeq\tCDS\t2821010\t2821147\t.\t-\t0\tID=cds-YP_501500.1;Parent=gene-SAOUHSC_03055;Dbxref=Genbank:YP_501500.1,GeneID:3921318;Name=YP_501500.1;Note=in Escherichia coli transcription of this gene is enhanced by polyamines;gbkey=CDS;gene=rpmH;product=50S ribosomal protein L34;protein_id=YP_501500.1;transl_table=11\n-\n" |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/gff_to_prot-out1.txt --- a/test-data/gff_to_prot-out1.txt Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/gff_to_prot-out1.txt Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b"@@ -244,2599 +244,4 @@\n conserved hypothetical protein\t286255\t286569\t+\t104\t-\t-\tSAOUHSC_00265\tSAOUHSC_00265\t-\r\n conserved hypothetical protein\t286569\t287243\t+\t224\t-\t-\tSAOUHSC_00266\tSAOUHSC_00266\t-\r\n conserved hypothetical protein\t287243\t287560\t+\t105\t-\t-\tSAOUHSC_00267\tSAOUHSC_00267\t-\r\n-conserved hypothetical protein\t287570\t289414\t+\t614\t-\t-\tSAOUHSC_00268\tSAOUHSC_00268\t-\r\n-conserved hypothetical protein\t289425\t289916\t+\t163\t-\t-\tSAOUHSC_00269\tSAOUHSC_00269\t-\r\n-conserved hypothetical protein\t290124\t290807\t+\t227\t-\t-\tSAOUHSC_00270\tSAOUHSC_00270\t-\r\n-conserved hypothetical protein\t290954\t291565\t+\t203\t-\t-\tSAOUHSC_00271\tSAOUHSC_00271\t-\r\n-conserved hypothetical protein\t291701\t291919\t+\t72\t-\t-\tSAOUHSC_00272\tSAOUHSC_00272\t-\r\n-conserved hypothetical protein\t292051\t292551\t+\t166\t-\t-\tSAOUHSC_00274\tSAOUHSC_00274\t-\r\n-conserved hypothetical protein\t292562\t293062\t+\t166\t-\t-\tSAOUHSC_00275\tSAOUHSC_00275\t-\r\n-conserved hypothetical protein\t293073\t293573\t+\t166\t-\t-\tSAOUHSC_00276\tSAOUHSC_00276\t-\r\n-conserved hypothetical protein\t293584\t294084\t+\t166\t-\t-\tSAOUHSC_00277\tSAOUHSC_00277\t-\r\n-conserved hypothetical protein\t294095\t294583\t+\t162\t-\t-\tSAOUHSC_00278\tSAOUHSC_00278\t-\r\n-conserved hypothetical protein\t295206\t295580\t+\t124\t-\t-\tSAOUHSC_00279\tSAOUHSC_00279\t-\r\n-conserved hypothetical protein\t295733\t296131\t+\t132\t-\t-\tSAOUHSC_00280\tSAOUHSC_00280\t-\r\n-conserved hypothetical protein\t296347\t297171\t-\t274\t-\t-\tSAOUHSC_00281\tSAOUHSC_00281\t-\r\n-branched-chain amino acid transport system II carrier protein\t297408\t298685\t-\t425\t-\t-\tSAOUHSC_00282\tSAOUHSC_00282\t-\r\n-5'-nucleotidase%2C lipoprotein e(P4) family\t299299\t300189\t+\t296\t-\t-\tSAOUHSC_00284\tSAOUHSC_00284\t-\r\n-conserved hypothetical protein\t300438\t301487\t+\t349\t-\t-\tSAOUHSC_00285\tSAOUHSC_00285\t-\r\n-ABC transporter%2C ATP-binding protein%2C putative\t301500\t302177\t+\t225\t-\t-\tSAOUHSC_00287\tSAOUHSC_00287\t-\r\n--\t302336\t302476\t-\t46\t-\t-\tSAOUHSC_00289\tSAOUHSC_00289\t-\r\n-conserved hypothetical protein\t302466\t303416\t+\t316\t-\t-\tSAOUHSC_00290\tSAOUHSC_00290\t-\r\n-pfkB family carbohydrate kinase family%2C putative\t303759\t304877\t+\t372\t-\t-\tSAOUHSC_00291\tSAOUHSC_00291\t-\r\n-conserved hypothetical protein\t304852\t305775\t+\t307\t-\t-\tSAOUHSC_00292\tSAOUHSC_00292\t-\r\n-conserved hypothetical protein\t305786\t307006\t+\t406\t-\t-\tSAOUHSC_00293\tSAOUHSC_00293\t-\r\n-conserved hypothetical protein\t307111\t308643\t-\t510\t-\t-\tSAOUHSC_00294\tSAOUHSC_00294\t-\r\n-catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid\t308683\t309564\t-\t293\t-\t-\tSAOUHSC_00295\tSAOUHSC_00295\t-\r\n-ROK family protein\t309722\t310582\t+\t286\t-\t-\tSAOUHSC_00296\tSAOUHSC_00296\t-\r\n-conserved hypothetical protein\t310860\t311660\t-\t266\t-\t-\tSAOUHSC_00297\tSAOUHSC_00297\t-\r\n-Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate\t311800\t312468\t+\t222\t-\t-\tSAOUHSC_00298\tSAOUHSC_00298\t-\r\n-conserved hypothetical protein\t312595\t313908\t-\t437\t-\t-\tSAOUHSC_00299\tSAOUHSC_00299\t-\r\n-lipase precursor\t314326\t316398\t+\t690\t-\t-\tSAOUHSC_00300\tSAOUHSC_00300\t-\r\n-conserved hypothetical protein\t316640\t317467\t-\t275\t-\t-\tSAOUHSC_00301\tSAOUHSC_00301\t-\r\n-conserved hypothetical protein\t317540\t318739\t-\t399\t-\t-\tSAOUHSC_00302\tSAOUHSC_00302\t-\r\n--\t318835\t318927\t+\t30\t-\t-\tSAOUHSC_00303\tSAOUHSC_00303\t-\r\n-conserved hypothetical protein\t319041\t320042\t+\t333\t-\t-\tSAOUHSC_00304\tSAOUHSC_00304\t-\r\n-conserved hypothetical protein\t320076\t320408\t+\t110\t-\t-\tSAOUHSC_00305\tSAOUHSC_00305\t-\r\n-conserved hypothetical protein\t320409\t321209\t+\t266\t-\t-\tSAOUHSC_00306\tSAOUHSC_00306\t-\r\n-conserved hypothetical protein\t321199\t322143\t+\t314\t-\t-\tSAOUHSC_00307\tSAOUHSC_00307\t-\r\n-conserved hypothetical protein\t322121\t323143\t+\t340\t-\t-\tSAOUHSC_00308\tSAOUHSC_00308\t-\r\n-conserved hypothetical protein\t323458\t324483\t+\t341\t-\t-\tSAOUHSC_00309\tSAOUHSC_00309\t-\r\n-membrane component%3B functions with enzymes IIB (sgaB%3B ulaB) and IIA (sgaA%3B ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate%3B sgaTBA are regulated by yifQ as well as Crp and Fnr\t324576\t325922\t-\t448\t-\t-\tulaA\tSAOUHSC_00310\t-\r\n-conserved hypothetical protein\t325937\t326221\t-\t94\t"..b"\t2790526\t-\t374\t-\t-\tSAOUHSC_03016\tSAOUHSC_03016\t-\r\n-conserved hypothetical protein\t2790644\t2791141\t-\t165\t-\t-\tSAOUHSC_03017\tSAOUHSC_03017\t-\r\n-conserved hypothetical protein\t2791188\t2792021\t-\t277\t-\t-\tSAOUHSC_03018\tSAOUHSC_03018\t-\r\n-ABC transporter%2C ATP-binding protein%2C putative\t2792018\t2793730\t-\t570\t-\t-\tSAOUHSC_03019\tSAOUHSC_03019\t-\r\n-conserved hypothetical protein\t2793783\t2794337\t-\t184\t-\t-\tSAOUHSC_03020\tSAOUHSC_03020\t-\r\n-conserved hypothetical protein\t2794366\t2795214\t-\t282\t-\t-\tSAOUHSC_03021\tSAOUHSC_03021\t-\r\n-conserved hypothetical protein\t2795594\t2796109\t+\t171\t-\t-\tSAOUHSC_03022\tSAOUHSC_03022\t-\r\n-Drp35\t2796258\t2797229\t-\t323\t-\t-\tSAOUHSC_03023\tSAOUHSC_03023\t-\r\n-conserved hypothetical protein\t2797473\t2798429\t+\t318\t-\t-\tSAOUHSC_03024\tSAOUHSC_03024\t-\r\n-catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline\t2798581\t2799219\t+\t212\t-\t-\tSAOUHSC_03025\tSAOUHSC_03025\t-\r\n-conserved hypothetical protein\t2799338\t2800105\t-\t255\t-\t-\tSAOUHSC_03026\tSAOUHSC_03026\t-\r\n-conserved hypothetical protein\t2800095\t2800433\t-\t112\t-\t-\tSAOUHSC_03027\tSAOUHSC_03027\t-\r\n-conserved hypothetical protein\t2800600\t2801064\t+\t154\t-\t-\tSAOUHSC_03028\tSAOUHSC_03028\t-\r\n-sodium%2C sulfate symporter%2C putative\t2801302\t2802720\t+\t472\t-\t-\tSAOUHSC_03030\tSAOUHSC_03030\t-\r\n-conserved hypothetical protein\t2803133\t2804041\t-\t302\t-\t-\tSAOUHSC_03031\tSAOUHSC_03031\t-\r\n-conserved hypothetical protein\t2804266\t2804841\t+\t191\t-\t-\tSAOUHSC_03032\tSAOUHSC_03032\t-\r\n-high affinity nickel transporter%2C putative\t2805006\t2806022\t+\t338\t-\t-\tSAOUHSC_03033\tSAOUHSC_03033\t-\r\n-conserved hypothetical protein\t2806265\t2807059\t+\t264\t-\t-\tSAOUHSC_03034\tSAOUHSC_03034\t-\r\n-conserved hypothetical protein\t2807193\t2807705\t-\t170\t-\t-\tSAOUHSC_03035\tSAOUHSC_03035\t-\r\n-ABC transporter%2C ATP-binding protein%2C putative\t2807988\t2808746\t+\t252\t-\t-\tSAOUHSC_03036\tSAOUHSC_03036\t-\r\n-permease%2C putative\t2808736\t2810616\t+\t626\t-\t-\tSAOUHSC_03037\tSAOUHSC_03037\t-\r\n--\t2810709\t2810900\t+\t63\t-\t-\tSAOUHSC_03037a\tSAOUHSC_03037a\t-\r\n-integrase/recombinase\t2810912\t2811448\t+\t178\t-\t-\tSAOUHSC_03040\tSAOUHSC_03040\t-\r\n-conserved hypothetical protein\t2811508\t2812005\t-\t165\t-\t-\tSAOUHSC_03041\tSAOUHSC_03041\t-\r\n-integrase/recombinase%2C core domain family\t2812084\t2812434\t+\t116\t-\t-\tSAOUHSC_03042\tSAOUHSC_03042\t-\r\n--\t2812463\t2812654\t+\t63\t-\t-\tSAOUHSC_3042a\tSAOUHSC_3042a\t-\r\n-cold shock protein%2C putative\t2813020\t2813247\t+\t75\t-\t-\tSAOUHSC_03045\tSAOUHSC_03045\t-\r\n-Helix-turn-helix domain protein\t2813374\t2813943\t-\t189\t-\t-\tSAOUHSC_03046\tSAOUHSC_03046\t-\r\n-conserved hypothetical protein\t2814203\t2814598\t-\t131\t-\t-\tSAOUHSC_03047\tSAOUHSC_03047\t-\r\n-conserved hypothetical protein\t2814666\t2815019\t-\t117\t-\t-\tSAOUHSC_03048\tSAOUHSC_03048\t-\r\n-conserved hypothetical protein\t2815473\t2816312\t-\t279\t-\t-\tSAOUHSC_03049\tSAOUHSC_03049\t-\r\n-glucose-inhibited division protein B%3B SAM-dependent methyltransferase%3B methylates the N7 position of guanosine in position 527 of 16S rRNA\t2816355\t2817074\t-\t239\t-\t-\tgidB\tSAOUHSC_03051\t-\r\n-GidA%3B glucose-inhibited cell division protein A%3B involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs\t2817074\t2818951\t-\t625\t-\t-\tgidA\tSAOUHSC_03052\t-\r\n-in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine%2C which is found in the wobble position of some tRNAs and affects ribosomal frameshifting%3B shows potassium-dependent dimerization and GTP hydrolysis%3B also involved in regulation of glutamate-dependent acid resistance and activation of gadE\t2819018\t2820397\t-\t459\t-\t-\ttrmE\tSAOUHSC_03053\t-\r\n-protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus%3B this enzyme also cleaves other RNA substrates\t2820536\t2820889\t-\t117\t-\t-\trnpA\tSAOUHSC_03054\t-\r\n-in Escherichia coli transcription of this gene is enhanced by polyamines\t2821010\t2821147\t-\t45\t-\t-\trpmH\tSAOUHSC_03055\t-\r\n+-\t287570\t289414\t+\t614\t-\t-\tSAOUHSC_00268\tSAOUHSC_00268\t-\r\n" |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/gumbel-sites1.txt --- a/test-data/gumbel-sites1.txt Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/gumbel-sites1.txt Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b"@@ -1,4001 +1,1011 @@\n #Gumbel\n-#Console: python /home/inithello/miniconda3/envs/__transit@2.3.1/bin/transit gumbel input_file_0.wig,input_file_1.wig annotation.dat transit_out.txt -iN 0.0 -tC 0.0 -s 1000 -b 100 -m 1 -t 1\n-#Data: input_file_0.wig,input_file_1.wig\n-#Annotation path: annotation.dat\n-#FDR Corrected thresholds: 0.991000, 0.039000\n-#MH Acceptance-Rate:\t50.50%\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit gumbel transit-co1-rep1_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep3_smol.wig transit-in1_smol.prot gumbel-sites1_smol.txt -s 1000 -b 100\n+#Data: b'transit-co1-rep1_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep3_smol.wig'\n+#Annotation path: b'transit-in1_smol.prot'\n+#FDR Corrected thresholds: 0.989000, 0.529000\n+#MH Acceptance-Rate:\t79.07%\n #Total Iterations Performed:\t1099\n #Sample Size:\t1000\n-#phi estimate:\t0.337057\n-#Time: 24.356441021\n+#phi estimate:\t0.407618\n+#Time: 9.027700185775757\n #Orf\tName\tDesc\tk\tn\tr\ts\tzbar\tCall\n-Rv0001\tdnaA\tchromosomal replication initiation protein \t0\t31\t31\t1365\t0.995000\tE\n-Rv0002\tdnaN\tDNA polymerase III subunit beta \t0\t31\t31\t1167\t0.749000\tU\n-Rv0003\trecF\trecombination protein F \t13\t35\t7\t71\t0.000000\tNE\n-Rv0004\t-\thypothetical protein Rv0004 \t1\t7\t6\t308\t0.984000\tU\n-Rv0005\tgyrB\tDNA gyrase subunit B \t2\t42\t40\t1997\t0.981000\tU\n-Rv0006\tgyrA\tDNA gyrase subunit A \t1\t45\t44\t2243\t0.972000\tU\n-Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t3\t10\t5\t393\t0.676000\tU\n+Rv0001\tdnaA\tchromosomal replication initiation protein \t0\t31\t31\t1365\t1.000000\tE\n+Rv0002\tdnaN\tDNA polymerase III subunit beta \t0\t31\t31\t1167\t1.000000\tE\n+Rv0003\trecF\trecombination protein F \t10\t35\t9\t140\t0.001000\tNE\n+Rv0004\t-\thypothetical protein Rv0004 \t0\t7\t7\t327\t0.975000\tU\n+Rv0005\tgyrB\tDNA gyrase subunit B \t2\t42\t40\t1997\t1.000000\tE\n+Rv0006\tgyrA\tDNA gyrase subunit A \t1\t45\t44\t2243\t1.000000\tE\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t4\t10\t3\t256\t0.001000\tNE\n Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t3\t4\t1\t2\t0.000000\tNE\n-Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t7\t0\t0\t0.000000\tNE\n-Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t6\t10\t3\t29\t0.000000\tNE\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t3\t7\t2\t50\t0.000000\tNE\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t5\t10\t4\t119\t0.000000\tNE\n Rv0011c\t-\tputative septation inhibitor protein \t0\t3\t3\t133\t-1.000000\tS\n-Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t12\t16\t3\t89\t0.000000\tNE\n-Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t1\t15\t14\t640\t1.000000\tE\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t9\t16\t3\t89\t0.000000\tNE\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t2\t15\t12\t528\t0.989000\tU\n Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t0\t24\t24\t1784\t1.000000\tE\n Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t1\t16\t15\t1244\t1.000000\tE\n-Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t13\t37\t6\t133\t0.000000\tNE\n-Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t13\t27\t4\t149\t0.000000\tNE\n-Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t8\t25\t12\t695\t0.998000\tE\n-Rv0019c\t-\thypothetical protein Rv0019c \t8\t13\t2\t20\t0.000000\tNE\n-Rv0020c\tTB39.8\thypothetical protein Rv0020c \t7\t52\t43\t1029\t0.494000\tU\n-Rv0021c\t-\thypothetical protein Rv0021c \t19\t22\t1\t2\t0.000000\tNE\n+Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t9\t37\t8\t240\t0.001000\tNE\n+Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t14\t27\t4\t64\t0.000000\tNE\n+Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t6\t25\t12\t695\t0.965000\tU\n+Rv0019c\t-\thypothetical protein Rv0019c \t7\t13\t2\t20\t0.000000\tNE\n+Rv0020c\tTB39.8\thypothetical protein Rv0020c \t8\t52\t43\t1029\t0.529000\tU\n+Rv0021c\t-\thypothetical protein Rv0021c \t18\t22\t1\t2\t0.000000\tNE\n Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t8\t0\t0\t0.000000\tNE\n-Rv0023\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN \t0\t12\t12\t582\t1.000000\tE\n-"..b' PHOSPHATE-BINDING LIPOPROTEIN PSTS1 (PBP-1) (PSTS1) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0935\tpstC1\tPHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTC1 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0936\tpstA2\tPHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTA2 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0937c\t-\thypothetical protein Rv0937c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0938\t-\tATP-dependent DNA ligase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0939\t-\tPOSSIBLE BIFUNCTIONAL ENZYME: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE (HHDD ISOMERASE) + CYCLASE/DEHYDRASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0940c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0941c\t-\thypothetical protein Rv0941c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0942\t-\thypothetical protein Rv0942 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0943c\t-\tPROBABLE MONOOXYGENASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0944\t-\tPOSSIBLE FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FAPY-DNA GLYCOSYLASE) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0945\t-\tshort chain dehydrogenase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0946c\tpgi\tglucose-6-phosphate isomerase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0948c\t-\thypothetical protein Rv0948c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0949\tuvrD1\tPROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0950c\t-\thypothetical protein Rv0950c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0951\tsucC\tsuccinyl-CoA synthetase subunit beta \t0\t0\t0\t0\t-1.000000\tS\n+Rv0952\tsucD\tsuccinyl-CoA synthetase subunit alpha \t0\t0\t0\t0\t-1.000000\tS\n+Rv0953c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0954\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0955\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0956\tpurN\tphosphoribosylglycinamide formyltransferase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0957\tpurH\tbifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0958\t-\tPOSSIBLE MAGNESIUM CHELATASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0959\t-\thypothetical protein Rv0959 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0960\t-\thypothetical protein Rv0960 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0961\t-\tPROBABLE INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0962c\tlprP\tPOSSIBLE LIPOPROTEIN LPRP \t0\t0\t0\t0\t-1.000000\tS\n+Rv0963c\t-\thypothetical protein Rv0963c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0964c\t-\thypothetical protein Rv0964c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0965c\t-\thypothetical protein Rv0965c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0966c\t-\thypothetical protein Rv0966c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0967\t-\thypothetical protein Rv0967 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0968\t-\thypothetical protein Rv0968 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0969\tctpV\tPROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t0\t0\t0\t0\t-1.000000\tS\n+Rv0970\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0971c\techA7\tenoyl-CoA hydratase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0972c\tfadE12\tPROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0973c\taccA2\tPROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0974c\taccD2\tPROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0975c\tfadE13\tPROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0976c\t-\thypothetical protein Rv0976c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0977\tPE_PGRS16\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0978c\tPE_PGRS17\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0979A\trpmF\t50S ribosomal protein L32 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0979c\t-\thypothetical protein Rv0979c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0980c\tPE_PGRS18\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0981\tmprA\tMYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0982\tmprB\tPROBABLE TWO COMPONENT SENSOR KINASE MPRB \t0\t0\t0\t0\t-1.000000\tS\n+Rv0983\tpepD\tPROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0984\tmoaB2\tPOSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t0\t0\t0\t0\t-1.000000\tS\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/hmm-genes1.txt --- a/test-data/hmm-genes1.txt Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/hmm-genes1.txt Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -1,3991 +1,1004 @@\n #HMM - Genes\n-Rv0001\tdnaA\tchromosomal replication initiation protein \t32\t31\t0\t1\t0\t0.0312\t89.00\tES\n+#genes: ES=14, GD=6, NE=80, GA=0, N/A=900\n+#key: ES=essential, GD=insertions cause growth-defect, NE=non-essential, GA=insertions confer growth-advantage, N/A=not analyzed (genes with 0 TA sites)\n+#ORF\tgene\tannotation\tTAs\tES sites\tGD sites\tNE sites\tGA sites\tsaturation\tmean\tcall\n+Rv0001\tdnaA\tchromosomal replication initiation protein \t32\t31\t0\t1\t0\t0.0312\t110.00\tES\n Rv0002\tdnaN\tDNA polymerase III subunit beta \t31\t31\t0\t0\t0\t0.0000\t0.00\tES\n-Rv0003\trecF\trecombination protein F \t35\t5\t0\t30\t0\t0.3714\t48.08\tNE\n-Rv0004\t-\thypothetical protein Rv0004 \t8\t6\t0\t2\t0\t0.2500\t61.50\tES\n-Rv0005\tgyrB\tDNA gyrase subunit B \t43\t40\t0\t3\t0\t0.0698\t134.00\tES\n-Rv0006\tgyrA\tDNA gyrase subunit A \t46\t44\t0\t2\t0\t0.0435\t222.00\tES\n-Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t11\t0\t0\t11\t0\t0.3636\t68.75\tNE\n-Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t0\t0\t4\t0\t0.7500\t243.33\tNE\n-Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t0\t0\t7\t0\t1.0000\t137.29\tNE\n-Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t0\t0\t10\t0\t0.6000\t235.33\tNE\n+Rv0003\trecF\trecombination protein F \t35\t5\t0\t30\t0\t0.3714\t60.85\tNE\n+Rv0004\t-\thypothetical protein Rv0004 \t8\t6\t0\t2\t0\t0.2500\t78.00\tES\n+Rv0005\tgyrB\tDNA gyrase subunit B \t43\t40\t0\t3\t0\t0.0698\t174.33\tES\n+Rv0006\tgyrA\tDNA gyrase subunit A \t46\t44\t0\t2\t0\t0.0435\t279.00\tES\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t11\t0\t0\t11\t0\t0.3636\t86.50\tNE\n+Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t0\t0\t4\t0\t0.7500\t314.00\tNE\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t0\t0\t7\t0\t1.0000\t175.29\tNE\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t0\t0\t10\t0\t0.6000\t298.83\tNE\n Rv0011c\t-\tputative septation inhibitor protein \t3\t0\t0\t3\t0\t0.0000\t0.00\tNE\n-Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t0\t0\t16\t0\t0.7500\t260.25\tNE\n-Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t15\t0\t0\t0\t0.0667\t8.00\tES\n-Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t25\t25\t0\t0\t0\t0.0400\t8.00\tES\n-Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t16\t0\t15\t1\t0\t0.0625\t300.00\tGD\n-Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t37\t0\t33\t4\t0\t0.3514\t43.31\tGD\n-Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t27\t0\t0\t27\t0\t0.4815\t82.15\tNE\n-Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t25\t12\t0\t13\t0\t0.3200\t38.00\tES\n-Rv0019c\t-\thypothetical protein Rv0019c \t13\t1\t0\t12\t0\t0.6154\t223.12\tNE\n-Rv0020c\tTB39.8\thypothetical protein Rv0020c \t52\t43\t0\t9\t0\t0.1346\t73.43\tES\n-Rv0021c\t-\thypothetical protein Rv0021c \t23\t0\t0\t23\t0\t0.8696\t281.05\tNE\n-Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t0\t0\t8\t0\t1.0000\t334.50\tNE\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t0\t0\t16\t0\t0.7500\t330.08\tNE\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t15\t0\t0\t0\t0.0667\t11.00\tES\n+Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t25\t25\t0\t0\t0\t0.0400\t11.00\tES\n+Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t16\t0\t15\t1\t0\t0.0625\t377.00\tGD\n+Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t37\t0\t33\t4\t0\t0.3514\t55.38\tGD\n+Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t27\t0\t0\t27\t0\t0.4815\t104.69\tNE\n+Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t25\t12\t0\t13\t0\t0.3200\t48.62\tNE\n+Rv0019c\t-\thypothetical protein Rv0019c \t13\t1\t0\t12\t0\t0.6154\t289.25\tNE\n+Rv0020c\tTB39.8\thypothetical protein Rv0020c \t52\t43\t0\t9\t0\t0.1346\t94.29\tES\n+Rv0021c\t-\thypothetical protein Rv0021c \t23\t0\t0\t23\t0\t0.8696\t359.65\tNE\n+Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t0\t0\t8\t0\t1.0000\t421.75\tNE\n Rv0023\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN \t12\t12\t0\t0\t0\t0.0000\t0.00\tES\n-Rv0024\t-\tPUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN \t13\t0\t0\t13\t0\t0.8462\t209.00\tNE\n-Rv0025\t-\thypothetical protein Rv002'..b'protein Rv0937c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0938\t-\tATP-dependent DNA ligase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0939\t-\tPOSSIBLE BIFUNCTIONAL ENZYME: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE (HHDD ISOMERASE) + CYCLASE/DEHYDRASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0940c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0941c\t-\thypothetical protein Rv0941c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0942\t-\thypothetical protein Rv0942 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0943c\t-\tPROBABLE MONOOXYGENASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0944\t-\tPOSSIBLE FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FAPY-DNA GLYCOSYLASE) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0945\t-\tshort chain dehydrogenase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0946c\tpgi\tglucose-6-phosphate isomerase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0948c\t-\thypothetical protein Rv0948c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0949\tuvrD1\tPROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0950c\t-\thypothetical protein Rv0950c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0951\tsucC\tsuccinyl-CoA synthetase subunit beta \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0952\tsucD\tsuccinyl-CoA synthetase subunit alpha \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0953c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0954\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0955\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0956\tpurN\tphosphoribosylglycinamide formyltransferase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0957\tpurH\tbifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0958\t-\tPOSSIBLE MAGNESIUM CHELATASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0959\t-\thypothetical protein Rv0959 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0960\t-\thypothetical protein Rv0960 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0961\t-\tPROBABLE INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0962c\tlprP\tPOSSIBLE LIPOPROTEIN LPRP \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0963c\t-\thypothetical protein Rv0963c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0964c\t-\thypothetical protein Rv0964c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0965c\t-\thypothetical protein Rv0965c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0966c\t-\thypothetical protein Rv0966c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0967\t-\thypothetical protein Rv0967 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0968\t-\thypothetical protein Rv0968 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0969\tctpV\tPROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0970\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0971c\techA7\tenoyl-CoA hydratase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0972c\tfadE12\tPROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0973c\taccA2\tPROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0974c\taccD2\tPROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0975c\tfadE13\tPROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0976c\t-\thypothetical protein Rv0976c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0977\tPE_PGRS16\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0978c\tPE_PGRS17\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0979c\t-\thypothetical protein Rv0979c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0979A\trpmF\t50S ribosomal protein L32 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0980c\tPE_PGRS18\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0981\tmprA\tMYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0982\tmprB\tPROBABLE TWO COMPONENT SENSOR KINASE MPRB \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0983\tpepD\tPROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0984\tmoaB2\tPOSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/hmm-sites1.txt --- a/test-data/hmm-sites1.txt Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/hmm-sites1.txt Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -1,74623 +1,2016 @@\n #HMM - Sites\n # Tn-HMM\n-#Console: python /home/inithello/miniconda3/envs/__transit@2.5.2/bin/transit hmm input_file_0.wig,input_file_1.wig annotation.dat transit_out.txt -iN 0.0 -tC 0.0 -r Mean\n-# \n-# Mean:\t225.23\n-# Median:\t112.00\n-# Normalization:\tTTR\n-# LOESS Correction:\tFalse\n-# pins (obs):\t0.548435\n-# pins (est):\t0.668453\n-# Run length (r):\t5\n-# State means:\n-# ES: 1.0101 GD: 3.6959 NE: 169.5859 GA: 847.9294\n-# Self-Transition Prob:\n-# ES: -7.1294e-12 GD: -7.1294e-12 NE: -7.1294e-12 GA: -7.1294e-12\n-# State Emission Parameters (theta):\n-# ES: 0.9900 GD: 0.2706 NE: 0.0059 GA: 0.0012\n-# State Distributions:# ES: 16.17% GD: 4.51% NE: 78.02% GA: 1.31%\n-60\t0\t1.00e+00 \t1.28e-13 \t2.03e-15 \t4.05e-16 \tES\tRv0001_(dnaA)\n-72\t0\t1.00e+00 \t3.49e-14 \t1.21e-17 \t4.82e-19 \tES\tRv0001_(dnaA)\n-102\t0\t1.00e+00 \t9.54e-15 \t7.22e-20 \t5.75e-22 \tES\tRv0001_(dnaA)\n-188\t0\t1.00e+00 \t2.61e-15 \t4.30e-22 \t6.91e-25 \tES\tRv0001_(dnaA)\n-246\t0\t1.00e+00 \t7.13e-16 \t2.59e-24 \t7.56e-27 \tES\tRv0001_(dnaA)\n-333\t0\t1.00e+00 \t1.95e-16 \t4.93e-26 \t6.75e-27 \tES\tRv0001_(dnaA)\n-360\t0\t1.00e+00 \t5.34e-17 \t3.41e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-426\t0\t1.00e+00 \t1.47e-17 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-448\t0\t1.00e+00 \t4.11e-18 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-471\t0\t1.00e+00 \t1.22e-18 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-483\t0\t1.00e+00 \t4.33e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-494\t0\t1.00e+00 \t2.18e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-504\t0\t1.00e+00 \t1.59e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-514\t0\t1.00e+00 \t1.42e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-525\t0\t1.00e+00 \t1.38e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-534\t0\t1.00e+00 \t1.38e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-601\t0\t1.00e+00 \t1.40e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-653\t0\t1.00e+00 \t1.48e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-670\t0\t1.00e+00 \t1.79e-19 \t3.40e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-706\t0\t1.00e+00 \t2.94e-19 \t3.41e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-741\t0\t1.00e+00 \t7.14e-19 \t3.60e-26 \t6.74e-27 \tES\tRv0001_(dnaA)\n-784\t0\t1.00e+00 \t2.25e-18 \t3.69e-25 \t6.74e-27 \tES\tRv0001_(dnaA)\n-794\t0\t1.00e+00 \t7.86e-18 \t5.62e-23 \t6.74e-27 \tES\tRv0001_(dnaA)\n-843\t0\t1.00e+00 \t2.84e-17 \t9.44e-21 \t6.74e-27 \tES\tRv0001_(dnaA)\n-989\t0\t1.00e+00 \t1.04e-16 \t1.58e-18 \t6.78e-27 \tES\tRv0001_(dnaA)\n-1092\t0\t1.00e+00 \t3.79e-16 \t2.66e-16 \t3.26e-26 \tES\tRv0001_(dnaA)\n-1104\t0\t1.00e+00 \t1.39e-15 \t4.47e-14 \t2.16e-23 \tES\tRv0001_(dnaA)\n-1267\t0\t1.00e+00 \t5.07e-15 \t7.50e-12 \t1.81e-20 \tES\tRv0001_(dnaA)\n-1278\t0\t1.00e+00 \t1.85e-14 \t1.26e-09 \t1.52e-17 \tES\tRv0001_(dnaA)\n-1345\t0\t1.00e+00 \t6.78e-14 \t2.11e-07 \t1.27e-14 \tES\tRv0001_(dnaA)\n-1423\t0\t1.00e+00 \t2.48e-13 \t3.55e-05 \t1.07e-11 \tES\tRv0001_(dnaA)\n-1522\t89\t2.83e-176\t1.61e-22 \t1.00e+00 \t2.30e-06 \tNE\tRv0001_(dnaA)\n-1552\t31\t1.48e-83 \t5.27e-25 \t1.00e+00 \t1.75e-06 \tNE\t\n-1635\t160\t0.00e+00 \t9.28e-44 \t1.00e+00 \t3.21e-06 \tNE\t\n-1779\t0\t9.03e-13 \t1.40e-15 \t1.00e+00 \t1.51e-06 \tNE\t\n-1782\t0\t9.08e-13 \t1.43e-15 \t1.00e+00 \t1.51e-06 \tNE\t\n-1788\t0\t9.08e-13 \t1.43e-15 \t1.00e+00 \t1.51e-06 \tNE\t\n-1847\t0\t9.08e-13 \t1.43e-15 \t1.00e+00 \t1.51e-06 \tNE\t\n-1858\t275\t0.00e+00 \t1.49e-52 \t1.00e+00 \t5.54e-06 \tNE\t\n-1921\t15\t1.88e-51 \t6.34e-13 \t1.00e+00 \t1.62e-06 \tNE\t\n-2001\t0\t9.94e-01 \t1.28e-12 \t5.96e-03 \t8.98e-09 \tES\t\n-2012\t0\t1.00e+00 \t3.55e-13 \t3.55e-05 \t1.07e-11 \tES\t\n-2063\t0\t1.00e+00 \t9.71e-14 \t2.11e-07 \t1.27e-14 \tES\tRv0002_(dnaN)\n-2104\t0\t1.00e+00 \t2.65e-14 \t1.26e-09 \t1.52e-17 \tES\tRv0002_(dnaN)\n-2141\t0\t1.00e+00 \t7.26e-15 \t7.50e-12 \t1.81e-20 \tES\tRv0002_(dnaN)\n-2232\t0\t1.00e+00 \t1.98e-15 \t4.47e-14 \t2.16e-23 \tES\tRv0002_(dnaN)\n-2290\t0\t1.00e+00 \t5.42e-16 \t2.66e-16 \t3.26e-26 \tES\tRv0002_(dnaN)\n-2315\t0\t1.00e+00 \t1.48e-16 \t1.58e-18 \t6.78e-27 \tES\tRv0002_(dnaN)\n-2318\t0\t1.00e+00 \t4.05e-17 \t9.44e-21 \t6.74e-27 \tES\tRv0002_(dnaN)\n-2333\t0\t1.00e+00 \t1.11e-17 \t5.62e-23 \t6.74e-27 \tES\tRv0002_(dnaN)\n-2344\t0\t1.00e+00 \t3.05e-18 \t3.69e-25 \t6.74e-27 \tES\tRv0002_(dnaN)\n-2363\t0\t1.00e+00 \t8.55e-19 \t3.60e-26 \t6.74e-27 \tES\tRv0002_(dnaN)\n-2387\t0\t1.00e+00 \t2.54e-19 \t3.41e-26 \t6.74e-'..b'\t6.44e-104\t2.04e-26 \t1.00e+00 \t8.38e-25 \tNE\tRv0097_(-)\n+106858\t125\t5.08e-272\t1.92e-38 \t1.00e+00 \t9.58e-25 \tNE\tRv0097_(-)\n+106906\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t5.25e-25 \tNE\tRv0097_(-)\n+106926\t82\t7.91e-184\t2.14e-31 \t1.00e+00 \t6.94e-25 \tNE\tRv0097_(-)\n+106929\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t5.12e-25 \tNE\tRv0097_(-)\n+106941\t271\t0.00e+00 \t6.39e-55 \t1.00e+00 \t1.92e-24 \tNE\tRv0097_(-)\n+107024\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t6.37e-25 \tNE\tRv0097_(-)\n+107031\t142\t1.08e-303\t7.28e-39 \t1.00e+00 \t1.00e-24 \tNE\tRv0097_(-)\n+107033\t0\t1.00e-17 \t1.70e-19 \t1.00e+00 \t5.59e-25 \tNE\tRv0097_(-)\n+107039\t0\t1.01e-17 \t1.74e-19 \t1.00e+00 \t6.47e-25 \tNE\tRv0097_(-)\n+107106\t593\t0.00e+00 \t2.63e-93 \t1.00e+00 \t1.60e-23 \tNE\tRv0097_(-)\n+107226\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t1.41e-24 \tNE\tRv0097_(-)\n+107245\t147\t1.10e-313\t1.74e-39 \t1.00e+00 \t1.41e-24 \tNE\tRv0097_(-)\n+107278\t0\t5.19e-20 \t4.72e-21 \t1.00e+00 \t7.13e-25 \tNE\tRv0097_(-)\n+107288\t17\t5.67e-54 \t3.63e-23 \t1.00e+00 \t1.11e-24 \tNE\tRv0097_(-)\n+107328\t146\t5.66e-314\t9.21e-40 \t1.00e+00 \t5.48e-24 \tNE\tRv0097_(-)\n+107436\t7\t2.77e-36 \t7.02e-23 \t1.00e+00 \t8.55e-24 \tNE\tRv0097_(-)\n+107452\t331\t0.00e+00 \t3.30e-63 \t1.00e+00 \t1.33e-22 \tNE\tRv0097_(-)\n+107456\t1473\t0.00e+00 \t3.09e-206\t1.00e+00 \t2.85e-20 \tNE\tRv0097_(-)\n+107466\t110\t4.70e-242\t1.39e-36 \t1.00e+00 \t1.05e-22 \tNE\tRv0097_(-)\n+107553\t0\t1.94e-15 \t1.15e-17 \t1.00e+00 \t1.92e-23 \tNE\tRv0097_(-)\n+107592\t0\t1.95e-15 \t1.18e-17 \t1.00e+00 \t4.19e-24 \tNE\tRv0097_(-)\n+107696\t0\t1.95e-15 \t1.18e-17 \t1.00e+00 \t1.20e-24 \tNE\tRv0098_(-)\n+107717\t17\t2.12e-49 \t8.87e-20 \t1.00e+00 \t6.65e-25 \tNE\tRv0098_(-)\n+107735\t94\t4.33e-210\t6.34e-30 \t1.00e+00 \t8.59e-25 \tNE\tRv0098_(-)\n+107765\t0\t5.19e-20 \t3.46e-21 \t1.00e+00 \t7.23e-25 \tNE\tRv0098_(-)\n+107795\t47\t6.61e-114\t4.88e-27 \t1.00e+00 \t1.86e-24 \tNE\tRv0098_(-)\n+107797\t0\t5.19e-20 \t3.46e-21 \t1.00e+00 \t4.98e-24 \tNE\tRv0098_(-)\n+107858\t150\t1.12e-319\t7.38e-40 \t1.00e+00 \t4.12e-23 \tNE\tRv0098_(-)\n+107927\t97\t4.40e-216\t1.18e-34 \t1.00e+00 \t1.02e-22 \tNE\tRv0098_(-)\n+107947\t35\t3.29e-92 \t7.51e-17 \t1.00e+00 \t2.59e-22 \tNE\tRv0098_(-)\n+108059\t4\t5.45e-20 \t2.50e-10 \t1.00e+00 \t9.13e-22 \tNE\tRv0098_(-)\n+108129\t0\t2.70e-06 \t8.37e-10 \t1.00e+00 \t4.19e-21 \tNE\tRv0098_(-)\n+108149\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t2.19e-23 \tNE\tRv0098_(-)\n+108179\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t1.04e-24 \tNE\tRv0099_(fadD10)\n+108197\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t2.94e-24 \tNE\tRv0099_(fadD10)\n+108272\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t1.30e-23 \tNE\tRv0099_(fadD10)\n+108285\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t7.94e-23 \tNE\tRv0099_(fadD10)\n+108344\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t1.58e-20 \tNE\tRv0099_(fadD10)\n+108356\t156\t6.03e-318\t3.14e-29 \t1.00e+00 \t2.84e-17 \tNE\tRv0099_(fadD10)\n+108393\t0\t2.70e-06 \t5.00e-11 \t1.00e+00 \t1.49e-17 \tNE\tRv0099_(fadD10)\n+108565\t0\t2.72e-06 \t5.10e-11 \t1.00e+00 \t1.68e-20 \tNE\tRv0099_(fadD10)\n+108586\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t1.11e-21 \tNE\tRv0099_(fadD10)\n+108596\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t1.07e-21 \tNE\tRv0099_(fadD10)\n+108692\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t1.20e-21 \tNE\tRv0099_(fadD10)\n+108718\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t2.13e-21 \tNE\tRv0099_(fadD10)\n+108807\t0\t2.72e-06 \t5.10e-11 \t1.00e+00 \t2.23e-19 \tNE\tRv0099_(fadD10)\n+108850\t272\t0.00e+00 \t6.97e-45 \t1.00e+00 \t6.42e-16 \tNE\tRv0099_(fadD10)\n+108854\t220\t0.00e+00 \t2.83e-50 \t1.00e+00 \t5.19e-16 \tNE\tRv0099_(fadD10)\n+108899\t0\t5.19e-20 \t8.51e-20 \t1.00e+00 \t2.10e-16 \tNE\tRv0099_(fadD10)\n+108952\t90\t8.24e-200\t5.44e-31 \t1.00e+00 \t3.05e-16 \tNE\tRv0099_(fadD10)\n+108976\t0\t1.49e-08 \t5.33e-12 \t1.00e+00 \t2.11e-16 \tNE\tRv0099_(fadD10)\n+109024\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t2.16e-16 \tNE\tRv0099_(fadD10)\n+109032\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t2.42e-16 \tNE\tRv0099_(fadD10)\n+109070\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t3.67e-16 \tNE\tRv0099_(fadD10)\n+109079\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t9.98e-16 \tNE\tRv0099_(fadD10)\n+109104\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t5.15e-15 \tNE\tRv0099_(fadD10)\n+109197\t10\t1.57e-28 \t3.09e-13 \t1.00e+00 \t1.03e-12 \tNE\tRv0099_(fadD10)\n+109215\t115\t6.69e-252\t2.11e-26 \t1.00e+00 \t1.72e-12 \tNE\tRv0099_(fadD10)\n+109226\t0\t2.27e-10 \t5.87e-11 \t1.00e+00 \t1.30e-12 \tNE\tRv0099_(fadD10)\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/resampling-sites1.txt --- a/test-data/resampling-sites1.txt Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/resampling-sites1.txt Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b"@@ -1,3997 +1,1007 @@\n #Resampling\n-#Console: python /home/inithello/miniconda3/envs/__transit@2.3.1/bin/transit resampling input_file_0.wig,input_file_1.wig control_file_0.wig,control_file_1.wig,control_file_2.wig annotation.dat transit_out.txt -iN 0.0 -tC 0.0 -s 1000 -n TTR\n-#Control Data: input_file_0.wig,input_file_1.wig\n-#Experimental Data: control_file_0.wig,control_file_1.wig,control_file_2.wig\n-#Annotation path: annotation.dat\n-#Time: 88.9293761253\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit resampling transit-in1-rep2_smol.wig,transit-in1-rep1_smol.wig transit-co1-rep3_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep1_smol.wig transit-in1_smol.prot resampling-sites1_smol.txt\n+#Control Data: b'transit-in1-rep2_smol.wig,transit-in1-rep1_smol.wig'\n+#Experimental Data: b'transit-co1-rep3_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep1_smol.wig'\n+#Annotation path: b'transit-in1_smol.prot' \n+#Time: 64.01395511627197\n #Orf\tName\tDesc\tSites\tMean Ctrl\tMean Exp\tlog2FC\tSum Ctrl\tSum Exp\tDelta Mean\tp-value\tAdj. p-value\n Rv0001\tdnaA\tchromosomal replication initiation protein \t31\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n Rv0002\tdnaN\tDNA polymerase III subunit beta \t31\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n-Rv0003\trecF\trecombination protein F \t35\t17.9\t21.7\t0.28\t1250.8\t2278.69\t3.8\t0.66900\t1.00000\n-Rv0004\t-\thypothetical protein Rv0004 \t7\t2.4\t0.0\t-1.75\t33.1\t0.00\t-2.4\t0.40700\t1.00000\n-Rv0005\tgyrB\tDNA gyrase subunit B \t42\t8.7\t2.8\t-1.66\t733.2\t348.51\t-6.0\t0.39400\t1.00000\n-Rv0006\tgyrA\tDNA gyrase subunit A \t45\t4.4\t1.9\t-1.23\t399.7\t255.54\t-2.5\t0.47600\t1.00000\n-Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t10\t13.0\t42.2\t1.69\t260.6\t1264.90\t29.1\t0.46500\t1.00000\n-Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t182.8\t153.2\t-0.25\t1462.2\t1838.43\t-29.6\t0.70900\t1.00000\n-Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t137.2\t71.6\t-0.94\t1921.3\t1503.03\t-65.7\t0.27200\t1.00000\n-Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t141.2\t135.8\t-0.06\t2823.7\t4075.38\t-5.3\t0.94400\t1.00000\n+Rv0003\trecF\trecombination protein F \t35\t22.6\t27.7\t0.30\t1579.1\t2907.67\t5.1\t0.66630\t1.00000\n+Rv0004\t-\thypothetical protein Rv0004 \t7\t2.9\t0.0\t-1.97\t40.8\t0.00\t-2.9\t0.40810\t1.00000\n+Rv0005\tgyrB\tDNA gyrase subunit B \t42\t11.3\t3.6\t-1.66\t951.9\t450.90\t-7.8\t0.40760\t1.00000\n+Rv0006\tgyrA\tDNA gyrase subunit A \t45\t5.7\t2.4\t-1.22\t511.8\t330.34\t-3.2\t0.50960\t1.00000\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t10\t16.2\t53.7\t1.73\t323.1\t1610.25\t37.5\t0.47710\t1.00000\n+Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t235.5\t195.4\t-0.27\t1884.3\t2345.17\t-40.1\t0.74730\t1.00000\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t175.3\t89.0\t-0.98\t2453.5\t1869.11\t-86.2\t0.24570\t1.00000\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t179.3\t172.9\t-0.05\t3586.6\t5186.87\t-6.4\t0.94490\t1.00000\n Rv0011c\t-\tputative septation inhibitor protein \t3\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n-Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t195.2\t82.7\t-1.24\t6247.1\t3967.58\t-112.6\t0.03000\t0.64355\n-Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t0.5\t2.2\t2.06\t16.0\t100.42\t1.7\t0.90500\t1.00000\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t247.6\t104.1\t-1.25\t7922.3\t4996.36\t-143.5\t0.02820\t1.00000\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t0.7\t2.9\t2.03\t21.1\t129.04\t2.2\t0.90500\t1.00000\n Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t24\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n-Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t16\t18.7\t9.5\t-0.98\t599.2\t454.54\t-9.3\t0.70700\t1.00000\n-Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t37\t15.2\t10.2\t-0.58\t1127.7\t1133.31\t-5.0\t0.43100\t1.00000\n-Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t27\t39.6\t39.4\t-0.01\t2139.5\t3187.58\t-0.3\t0.98900\t1.00000\n-Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t25\t12.1\t9.6\t-0.34\t607.2\t719.85\t-2.5\t0.72800\t1"..b'hosphate isomerase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0948c\t-\thypothetical protein Rv0948c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0949\tuvrD1\tPROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0950c\t-\thypothetical protein Rv0950c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0951\tsucC\tsuccinyl-CoA synthetase subunit beta \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0952\tsucD\tsuccinyl-CoA synthetase subunit alpha \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0953c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0954\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0955\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0956\tpurN\tphosphoribosylglycinamide formyltransferase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0957\tpurH\tbifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0958\t-\tPOSSIBLE MAGNESIUM CHELATASE \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0959\t-\thypothetical protein Rv0959 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0960\t-\thypothetical protein Rv0960 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0961\t-\tPROBABLE INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0962c\tlprP\tPOSSIBLE LIPOPROTEIN LPRP \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0963c\t-\thypothetical protein Rv0963c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0964c\t-\thypothetical protein Rv0964c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0965c\t-\thypothetical protein Rv0965c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0966c\t-\thypothetical protein Rv0966c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0967\t-\thypothetical protein Rv0967 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0968\t-\thypothetical protein Rv0968 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0969\tctpV\tPROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0970\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0971c\techA7\tenoyl-CoA hydratase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0972c\tfadE12\tPROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0973c\taccA2\tPROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0974c\taccD2\tPROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0975c\tfadE13\tPROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0976c\t-\thypothetical protein Rv0976c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0977\tPE_PGRS16\tPE-PGRS FAMILY PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0978c\tPE_PGRS17\tPE-PGRS FAMILY PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0979A\trpmF\t50S ribosomal protein L32 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0979c\t-\thypothetical protein Rv0979c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0980c\tPE_PGRS18\tPE-PGRS FAMILY PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0981\tmprA\tMYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0982\tmprB\tPROBABLE TWO COMPONENT SENSOR KINASE MPRB \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0983\tpepD\tPROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0984\tmoaB2\tPOSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/tn5gaps-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tn5gaps-sites1.txt Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b"@@ -0,0 +1,512 @@\n+#Tn5 Gaps\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit tn5gaps transit-in-tn5_smoll.wig,transit-in2-tn5_smol.wig transit_tn5_smol.prot tn5gaps-sites1_smol.txt\n+#Data: b'transit-in-tn5_smoll.wig,transit-in2-tn5_smol.wig'\n+#Annotation path: b'transit_tn5_smol.prot'\n+#Time: 1.1462020874023438\n+#Essential gene count: 1\n+#Minimum reads: 1\n+#Replicate combination method: Sum\n+#Minimum significant run length: 216\n+#Expected run length: 6.88000\n+#Expected max run length: 52.61348258987123\n+#Orf\tName\tDesc\tk\tn\tr\tovr\tlenovr\tpval\tpadj\tcall\n+BW25113_0001\tthrL\t-\t14\t63\t10\t8\t8\t1.00000\t1.00000\tNon-essential\n+BW25113_0002\tthrA\tbifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal)\t356\t2460\t48\t48\t48\t0.72170\t1.00000\tNon-essential\n+BW25113_0003\tthrB\t-\t160\t930\t32\t32\t32\t1.00000\t1.00000\tNon-essential\n+BW25113_0004\tthrC\t-\t194\t1284\t54\t54\t54\t0.38483\t1.00000\tNon-essential\n+BW25113_0005\tyaaX\t-\t48\t294\t32\t32\t32\t1.00000\t1.00000\tNon-essential\n+BW25113_0006\tyaaA\t-\t115\t774\t41\t41\t41\t0.98087\t1.00000\tNon-essential\n+BW25113_0007\tyaaJ\tinner membrane transport protein\t214\t1428\t46\t46\t46\t0.82900\t1.00000\tNon-essential\n+BW25113_0008\ttalB\t-\t181\t951\t54\t54\t54\t0.38483\t1.00000\tNon-essential\n+BW25113_0009\tmog\tputative molybdochetalase in molybdopterine biosynthesis\t95\t585\t45\t24\t24\t1.00000\t1.00000\tNon-essential\n+BW25113_0010\tsatP\t-\t108\t564\t37\t37\t37\t0.99947\t1.00000\tNon-essential\n+BW25113_0011\tyaaW\t-\t113\t711\t34\t34\t34\t1.00000\t1.00000\tNon-essential\n+BW25113_0013\tyaaI\t-\t77\t402\t26\t26\t26\t1.00000\t1.00000\tNon-essential\n+BW25113_0014\tdnaK\tchaperone Hsp70%3B DNA biosynthesis%3B autoregulated heat shock proteins\t34\t1914\t835\t216\t216\t0.00000\t0.00000\tEssential\n+BW25113_0015\tdnaJ\tchaperone with DnaK%3B heat shock protein\t169\t1128\t67\t67\t67\t0.05791\t1.00000\tNon-essential\n+BW25113_0016\tinsL1\t-\t235\t1110\t36\t36\t36\t0.99986\t1.00000\tNon-essential\n+BW25113_0018\tmokC\tregulatory peptide whose translation enables hokC (gef) expression%3B completely contained in another CDS\t68\t207\t12\t12\t12\t1.00000\t1.00000\tNon-essential\n+BW25113_0019\tnhaA\tNa+/H antiporter%2C pH dependent\t171\t1164\t36\t36\t36\t0.99986\t1.00000\tNon-essential\n+BW25113_0020\tnhaR\t-\t116\t903\t38\t38\t38\t0.99837\t1.00000\tNon-essential\n+BW25113_0021\tinsB1\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0022\tinsA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0023\trpsT\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0024\tyaaY\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0025\tribF\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0026\tileS\tisoleucine tRNA synthetase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0027\tlspA\tprolipoprotein signal peptidase (SPase II)\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0028\tfkpB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0029\tispH\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0030\trihC\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0031\tdapB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0032\tcarA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0033\tcarB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0034\tcaiF\ttranscriptional regulator of cai operon\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0035\tcaiE\tpossible synthesis of cofactor for carnitine racemase and dehydratase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0036\tcaiD\tcarnitine racemase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0037\tcaiC\tprobable crotonobetaine/carnitine-CoA ligase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0038\tcaiB\tl-carnitine dehydratase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0039\tcaiA\tprobable carnitine operon oxidoreductase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0040\tcaiT\tprobable carnitine transporter\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0041\tfixA\tprobable flavoprotein subunit%2C carnitine metabolism\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0042\tfixB\tprobable flavoprotein subunit%2C carnitine metabolism\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_"..b'\t1.00000\tNon-essential\n+BW25113_0489\tqmcA\tputative protease\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0490\tfetA\tputative ATP-binding component of a transport system\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0491\tfetB\tputative metal resistance protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0492\tybbN\tputative thioredoxin-like protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0493\tybbO\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0494\ttesA\tacyl-CoA thioesterase I%3B also functions as protease I\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0495\tybbA\tputative ATP-binding component of a transport system\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0496\tybbP\tputative oxidoreductase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0497\trhsD\trhsD protein in rhs element\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0498\tybbC\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0503\tmnmH\tputative capsule anchoring protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0504\tallS\tputative transcriptional regulator LYSR-type\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0505\tallA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0506\tallR\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0507\tgcl\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0508\thyi\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0509\tglxR\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0511\tybbW\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0512\tallB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0513\tybbY\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0514\tglxK\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0515\tallE\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0516\tallC\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0517\tallD\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0518\tfdrA\tinvolved in protein transport%3B multicopy suppressor of dominant negative ftsH mutants\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0520\tylbF\tputative carboxylase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0521\tybcF\tputative carbamate kinase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0522\tpurK\tphosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C CO(2)-fixing subunit\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0523\tpurE\tphosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C catalytic subunit\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0524\tlpxH\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0525\tppiB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0526\tcysS\tcysteine tRNA synthetase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0527\tybcI\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0528\tybcJ\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0529\tfolD\t5%2C10-methylene-tetrahydrofolate dehydrogenase%3B 5%2C10-methylene-tetrahydrofolate cyclohydrolase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0530\tsfmA\tputative fimbrial-like protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0531\tsfmC\tputative chaperone\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4406\tyaeP\tconserved hypothetical protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4412\thokC\tsmall toxic membrane polypeptide%3B completely contained in another CDS\t36\t150\t12\t12\t12\t1.00000\t1.00000\tNon-essential\n+BW25113_4413\tsokC\t-\t20\t52\t12\t12\t12\t1.00000\t1.00000\tNon-essential\n+BW25113_4414\ttff\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4504\tykfH\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4506\tykgO\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4572\tylbE\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4577\tsgrS\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4585\tchiX\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4586\tykfM\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4662\tsgrT\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4671\tykgR\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4690\teyeA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-co1-rep1.wig --- a/test-data/transit-co1-rep1.wig Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/transit-co1-rep1.wig Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -1998,72610 +1998,3 @@\n 109197 0\n 109215 126\n 109226 0\n-109244 0\n-109285 0\n-109292 16\n-109317 0\n-109410 8\n-109521 0\n-109822 169\n-109824 0\n-109916 0\n-110017 0\n-110040 0\n-110060 0\n-110074 0\n-110076 27\n-110094 0\n-110149 10\n-110199 0\n-110221 0\n-110315 73\n-110340 141\n-110424 0\n-110473 0\n-110574 0\n-110600 0\n-110711 0\n-110916 21\n-110929 0\n-110958 0\n-110970 0\n-111013 0\n-111083 0\n-111148 27\n-111211 0\n-111405 0\n-111528 52\n-111578 0\n-111726 0\n-111749 0\n-111822 0\n-111938 0\n-112087 0\n-112112 0\n-112173 0\n-112273 0\n-112324 0\n-112338 0\n-112502 0\n-112513 54\n-112703 0\n-112777 0\n-112906 73\n-112922 286\n-112926 36\n-112970 0\n-112992 0\n-113033 0\n-113095 0\n-113113 74\n-113133 25\n-113166 20\n-113174 0\n-113227 0\n-113395 0\n-113462 0\n-113517 11\n-113571 53\n-113580 150\n-113652 0\n-113675 21\n-113712 0\n-113827 27\n-113924 2\n-114033 0\n-114049 118\n-114229 0\n-114251 0\n-114285 124\n-114326 2647\n-114437 0\n-114512 0\n-114558 183\n-114589 0\n-114705 130\n-114850 1\n-114858 0\n-114903 88\n-114912 124\n-114926 16\n-115035 0\n-115078 26\n-115297 23\n-115305 0\n-115339 0\n-115418 25\n-115435 0\n-115461 193\n-115491 0\n-115563 217\n-115650 13\n-115702 0\n-115717 51\n-115753 10\n-115761 0\n-115816 71\n-115836 0\n-115858 7\n-115926 0\n-115934 2\n-115944 0\n-116075 0\n-116098 10\n-116152 45\n-116320 32\n-116364 23\n-116474 0\n-116649 0\n-116708 0\n-116733 233\n-116803 0\n-116847 0\n-116955 35\n-117014 0\n-117039 0\n-117168 0\n-117197 0\n-117213 229\n-117240 0\n-117247 0\n-117380 0\n-117504 8\n-117517 11\n-117537 0\n-117551 0\n-117622 262\n-117640 0\n-117648 0\n-117702 0\n-117731 0\n-117787 0\n-117861 0\n-117882 0\n-118006 0\n-118072 0\n-118109 0\n-118139 0\n-118150 0\n-118239 0\n-118313 0\n-118341 0\n-118447 0\n-118482 0\n-118500 0\n-118564 0\n-118687 0\n-118703 0\n-118761 0\n-118786 0\n-118817 0\n-118857 0\n-118892 0\n-118948 0\n-118969 0\n-118977 0\n-119092 0\n-119211 0\n-119213 0\n-119220 0\n-119240 0\n-119253 0\n-119301 0\n-119310 0\n-119355 0\n-119435 0\n-119447 0\n-119454 0\n-119530 0\n-119570 0\n-119634 0\n-119658 0\n-119730 0\n-119748 1\n-119916 0\n-119936 0\n-120045 31\n-120121 12\n-120256 169\n-120310 0\n-120410 0\n-120574 0\n-120626 48\n-120791 0\n-120882 0\n-120892 92\n-120902 169\n-120940 43\n-120989 0\n-121171 0\n-121181 0\n-121251 0\n-121291 20\n-121391 48\n-121397 58\n-121442 11\n-121500 80\n-121548 110\n-121766 563\n-121770 93\n-121856 223\n-121916 0\n-121950 0\n-122045 0\n-122104 106\n-122193 0\n-122211 21\n-122220 0\n-122231 0\n-122243 0\n-122304 8\n-122388 8\n-122444 35\n-122494 0\n-122542 309\n-122566 0\n-122596 85\n-122609 61\n-122643 0\n-122655 0\n-122696 33\n-122764 9\n-122834 217\n-122836 2\n-122992 43\n-123012 0\n-123049 34\n-123122 0\n-123221 0\n-123243 19\n-123346 151\n-123470 0\n-123493 0\n-123520 0\n-123522 67\n-123612 140\n-123671 0\n-123772 125\n-123829 95\n-123873 0\n-123896 145\n-123906 85\n-123910 190\n-123912 0\n-124145 0\n-124149 234\n-124152 0\n-124168 0\n-124219 0\n-124298 131\n-124327 0\n-124343 0\n-124362 0\n-124379 35\n-124390 0\n-124603 9\n-124722 0\n-124786 0\n-125015 0\n-125021 2\n-125292 3\n-125337 1\n-125371 0\n-125377 0\n-125469 165\n-125579 0\n-125592 0\n-125605 19\n-125620 115\n-125644 0\n-125659 75\n-125666 263\n-125823 54\n-125843 0\n-125940 0\n-126059 0\n-126098 54\n-126163 0\n-126431 0\n-126693 0\n-126812 23\n-126829 3\n-126963 11\n-127059 0\n-127096 0\n-127119 0\n-127157 32\n-127160 0\n-127181 0\n-127232 0\n-127335 0\n-127344 0\n-127392 138\n-127503 37\n-127731 111\n-127839 0\n-127853 0\n-128018 0\n-128025 0\n-128073 0\n-128109 0\n-128148 0\n-128154 0\n-128165 32\n-128305 12\n-128379 0\n-128389 0\n-128616 23\n-128697 31\n-128777 126\n-128820 0\n-128904 11\n-128983 0\n-129116 0\n-129184 1\n-129231 104\n-129269 0\n-129321 15\n-129396 0\n-129431 0\n-129496 745\n-129708 0\n-129789 0\n-129812 0\n-129827 0\n-129860 0\n-129888 172\n-129969 0\n-130019 24\n-130074 681\n-130107 277\n-130130 0\n-130263 0\n-130353 4\n-130491 20\n-130558 23\n-130564 0\n-130573 3\n-130587 171\n-130602 0\n-130616 40\n-130699 104\n-130708 19\n-130787 0\n-130929 2\n-131037 83\n-131140 164\n-131149 0\n-131158 14\n-131328 72\n-131341 23\n-131441 0\n-131497 0\n-131542 12\n-131553 23\n-131565 34\n-131640 0\n-131740 1\n-131776 0\n-131867 0\n-131894 0\n-131929 125\n-132047 0\n-132077 0\n-132137 0\n-132276 0\n-132284 0\n-132353 0\n-132374 0\n-132392 0'..b'3\n-4391265 7\n-4391329 70\n-4391395 211\n-4391430 52\n-4391592 5\n-4391599 169\n-4391632 16\n-4391706 0\n-4391725 0\n-4391863 0\n-4391943 0\n-4391965 0\n-4392004 0\n-4392028 0\n-4392067 0\n-4392268 0\n-4392344 0\n-4392368 0\n-4392579 0\n-4392720 0\n-4392748 0\n-4392794 0\n-4392827 0\n-4392955 0\n-4393002 0\n-4393041 0\n-4393086 32\n-4393177 23\n-4393219 37\n-4393222 5\n-4393301 88\n-4393372 274\n-4393408 165\n-4393429 0\n-4393436 2\n-4393439 8\n-4393517 72\n-4393670 0\n-4393747 11\n-4393860 4\n-4393908 639\n-4393924 47\n-4393957 0\n-4393966 0\n-4394007 0\n-4394026 0\n-4394092 0\n-4394280 0\n-4394419 0\n-4394493 0\n-4394525 0\n-4394565 0\n-4394590 0\n-4394654 0\n-4394690 0\n-4395030 0\n-4395062 0\n-4395099 0\n-4395171 0\n-4395238 0\n-4395415 0\n-4395462 0\n-4395469 0\n-4395501 0\n-4395568 0\n-4395572 0\n-4395576 0\n-4395685 0\n-4395798 0\n-4395857 0\n-4395924 0\n-4395983 0\n-4395996 0\n-4396032 0\n-4396042 0\n-4396139 0\n-4396183 0\n-4396215 0\n-4396269 0\n-4396280 0\n-4396290 0\n-4396296 0\n-4396406 0\n-4396434 0\n-4396455 0\n-4396534 0\n-4396566 0\n-4396596 0\n-4396667 0\n-4396751 0\n-4396847 0\n-4397010 0\n-4397038 0\n-4397048 0\n-4397065 0\n-4397081 0\n-4397168 0\n-4397176 0\n-4397389 0\n-4397424 0\n-4397467 0\n-4397473 0\n-4397483 0\n-4397571 0\n-4397600 0\n-4397673 0\n-4397689 0\n-4397719 0\n-4397764 0\n-4397771 0\n-4397786 0\n-4397797 0\n-4397883 0\n-4397886 0\n-4397914 0\n-4397928 0\n-4397965 0\n-4397968 0\n-4397972 0\n-4398095 0\n-4398098 0\n-4398104 0\n-4398331 72\n-4398413 0\n-4398714 0\n-4398724 0\n-4398752 120\n-4398870 0\n-4398950 22\n-4398980 0\n-4399141 0\n-4399204 0\n-4399376 108\n-4399403 124\n-4399510 14\n-4399607 0\n-4399819 456\n-4399821 0\n-4399842 70\n-4399983 0\n-4400082 1\n-4400137 35\n-4400185 0\n-4400204 38\n-4400285 52\n-4400325 9\n-4400426 0\n-4400520 8\n-4400531 34\n-4400645 60\n-4400728 0\n-4400745 9\n-4400797 235\n-4400822 0\n-4400837 0\n-4400902 62\n-4401048 52\n-4401135 1\n-4401392 31\n-4401433 155\n-4401458 0\n-4401499 0\n-4401519 31\n-4401531 0\n-4401595 0\n-4401610 0\n-4401677 282\n-4401784 0\n-4401806 0\n-4401821 0\n-4401908 0\n-4401994 0\n-4402014 0\n-4402109 0\n-4402240 0\n-4402344 0\n-4402410 0\n-4402449 0\n-4402529 0\n-4402549 0\n-4402607 0\n-4402621 0\n-4402651 0\n-4402705 51\n-4402719 13\n-4402767 0\n-4402796 0\n-4402859 0\n-4402974 0\n-4403031 0\n-4403080 1\n-4403093 0\n-4403134 0\n-4403171 0\n-4403191 0\n-4403283 0\n-4403326 0\n-4403429 0\n-4403453 0\n-4403477 0\n-4403501 0\n-4403518 0\n-4403552 0\n-4403609 0\n-4403621 0\n-4403641 0\n-4403672 0\n-4403679 0\n-4403809 0\n-4403893 0\n-4403899 0\n-4403932 0\n-4404076 0\n-4404135 0\n-4404208 0\n-4404215 0\n-4404308 0\n-4404315 0\n-4404394 0\n-4404410 134\n-4404434 0\n-4404466 0\n-4404559 0\n-4404572 0\n-4404688 0\n-4404802 0\n-4404843 0\n-4404876 0\n-4404917 0\n-4404926 0\n-4405144 0\n-4405155 0\n-4405168 0\n-4405208 21\n-4405245 244\n-4405250 43\n-4405266 0\n-4405277 0\n-4405420 0\n-4405454 6\n-4405458 16\n-4405483 0\n-4405514 0\n-4405523 0\n-4405558 0\n-4405610 0\n-4405654 0\n-4405675 0\n-4405871 0\n-4405986 0\n-4406003 0\n-4406018 0\n-4406029 0\n-4406059 0\n-4406144 0\n-4406151 0\n-4406281 0\n-4406313 0\n-4406357 0\n-4406552 0\n-4406582 0\n-4406603 0\n-4406669 0\n-4406689 0\n-4406720 0\n-4406727 0\n-4406793 0\n-4406819 0\n-4406822 0\n-4406915 0\n-4407061 0\n-4407090 0\n-4407101 0\n-4407135 0\n-4407219 0\n-4407240 0\n-4407462 0\n-4407484 0\n-4407619 36\n-4407690 46\n-4407744 0\n-4407921 14\n-4407930 0\n-4407939 0\n-4407960 0\n-4407995 0\n-4408001 0\n-4408056 24\n-4408071 0\n-4408076 0\n-4408138 1\n-4408203 106\n-4408299 0\n-4408335 0\n-4408553 23\n-4408742 197\n-4408755 68\n-4409010 0\n-4409166 0\n-4409255 0\n-4409280 0\n-4409297 0\n-4409338 0\n-4409353 0\n-4409357 0\n-4409424 0\n-4409444 0\n-4409546 0\n-4409581 0\n-4409607 0\n-4409615 0\n-4409676 0\n-4409682 0\n-4409702 0\n-4409822 0\n-4409903 0\n-4409974 0\n-4409996 0\n-4410026 0\n-4410029 0\n-4410146 26\n-4410158 0\n-4410240 0\n-4410264 0\n-4410271 0\n-4410277 0\n-4410305 0\n-4410327 0\n-4410337 0\n-4410367 0\n-4410373 0\n-4410403 0\n-4410423 0\n-4410624 0\n-4410668 0\n-4410693 0\n-4410769 0\n-4410851 0\n-4410861 0\n-4410944 0\n-4411049 0\n-4411098 0\n-4411102 0\n-4411164 37\n-4411182 0\n-4411245 0\n-4411258 0\n-4411273 0\n-4411277 1\n-4411337 0\n-4411397 1\n-4411412 0\n-4411421 0\n-4411440 23\n-4411479 88\n-4411508 0\n-4411526 0\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-co1-rep2.wig --- a/test-data/transit-co1-rep2.wig Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/transit-co1-rep2.wig Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -1998,72610 +1998,3 @@\n 109197 0\n 109215 0\n 109226 0\n-109244 0\n-109285 4\n-109292 24\n-109317 0\n-109410 15\n-109521 176\n-109822 36\n-109824 0\n-109916 23\n-110017 0\n-110040 0\n-110060 0\n-110074 0\n-110076 18\n-110094 0\n-110149 0\n-110199 0\n-110221 0\n-110315 83\n-110340 138\n-110424 0\n-110473 0\n-110574 0\n-110600 0\n-110711 0\n-110916 23\n-110929 0\n-110958 0\n-110970 0\n-111013 0\n-111083 0\n-111148 77\n-111211 0\n-111405 0\n-111528 46\n-111578 0\n-111726 1\n-111749 0\n-111822 0\n-111938 0\n-112087 0\n-112112 0\n-112173 0\n-112273 0\n-112324 0\n-112338 0\n-112502 0\n-112513 358\n-112703 0\n-112777 0\n-112906 1\n-112922 175\n-112926 24\n-112970 0\n-112992 0\n-113033 1\n-113095 0\n-113113 0\n-113133 26\n-113166 1\n-113174 0\n-113227 0\n-113395 0\n-113462 3\n-113517 21\n-113571 120\n-113580 10\n-113652 20\n-113675 0\n-113712 0\n-113827 12\n-113924 0\n-114033 0\n-114049 79\n-114229 0\n-114251 0\n-114285 78\n-114326 7263\n-114437 0\n-114512 0\n-114558 122\n-114589 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| diff -r 202a99525669 -r c980be2c002c test-data/transit-co1-rep3.wig --- a/test-data/transit-co1-rep3.wig Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/transit-co1-rep3.wig Tue Oct 08 08:24:12 2019 -0400 |
| b |
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| diff -r 202a99525669 -r c980be2c002c test-data/transit-in-tn5.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in-tn5.wig Tue Oct 08 08:24:12 2019 -0400 |
| b |
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|
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-in1-rep1.wig --- a/test-data/transit-in1-rep1.wig Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/transit-in1-rep1.wig Tue Oct 08 08:24:12 2019 -0400 |
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| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-in1-rep2.wig --- a/test-data/transit-in1-rep2.wig Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/transit-in1-rep2.wig Tue Oct 08 08:24:12 2019 -0400 |
| b |
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0\n-4394525 0\n-4394565 0\n-4394590 0\n-4394654 0\n-4394690 0\n-4395030 0\n-4395062 0\n-4395099 0\n-4395171 0\n-4395238 0\n-4395415 0\n-4395462 0\n-4395469 0\n-4395501 0\n-4395568 0\n-4395572 0\n-4395576 0\n-4395685 0\n-4395798 0\n-4395857 0\n-4395924 0\n-4395983 0\n-4395996 0\n-4396032 0\n-4396042 0\n-4396139 0\n-4396183 0\n-4396215 0\n-4396269 0\n-4396280 0\n-4396290 0\n-4396296 0\n-4396406 0\n-4396434 0\n-4396455 0\n-4396534 0\n-4396566 0\n-4396596 0\n-4396667 0\n-4396751 0\n-4396847 0\n-4397010 0\n-4397038 0\n-4397048 0\n-4397065 0\n-4397081 0\n-4397168 0\n-4397176 0\n-4397389 0\n-4397424 0\n-4397467 0\n-4397473 0\n-4397483 0\n-4397571 0\n-4397600 0\n-4397673 0\n-4397689 0\n-4397719 0\n-4397764 0\n-4397771 0\n-4397786 0\n-4397797 0\n-4397883 0\n-4397886 0\n-4397914 0\n-4397928 0\n-4397965 0\n-4397968 0\n-4397972 0\n-4398095 0\n-4398098 0\n-4398104 0\n-4398331 169\n-4398413 7\n-4398714 0\n-4398724 0\n-4398752 5\n-4398870 0\n-4398950 0\n-4398980 0\n-4399141 0\n-4399204 7\n-4399376 98\n-4399403 29\n-4399510 60\n-4399607 0\n-4399819 183\n-4399821 0\n-4399842 152\n-4399983 0\n-4400082 76\n-4400137 0\n-4400185 149\n-4400204 167\n-4400285 293\n-4400325 31\n-4400426 0\n-4400520 317\n-4400531 114\n-4400645 101\n-4400728 0\n-4400745 41\n-4400797 417\n-4400822 0\n-4400837 0\n-4400902 112\n-4401048 0\n-4401135 162\n-4401392 397\n-4401433 45\n-4401458 0\n-4401499 0\n-4401519 220\n-4401531 2\n-4401595 0\n-4401610 0\n-4401677 118\n-4401784 0\n-4401806 0\n-4401821 0\n-4401908 0\n-4401994 0\n-4402014 0\n-4402109 0\n-4402240 0\n-4402344 0\n-4402410 0\n-4402449 0\n-4402529 0\n-4402549 0\n-4402607 0\n-4402621 0\n-4402651 0\n-4402705 2\n-4402719 42\n-4402767 0\n-4402796 0\n-4402859 0\n-4402974 0\n-4403031 0\n-4403080 40\n-4403093 0\n-4403134 0\n-4403171 0\n-4403191 0\n-4403283 0\n-4403326 0\n-4403429 0\n-4403453 0\n-4403477 0\n-4403501 0\n-4403518 0\n-4403552 0\n-4403609 0\n-4403621 0\n-4403641 0\n-4403672 0\n-4403679 0\n-4403809 0\n-4403893 0\n-4403899 0\n-4403932 0\n-4404076 0\n-4404135 0\n-4404208 0\n-4404215 0\n-4404308 0\n-4404315 0\n-4404394 0\n-4404410 194\n-4404434 52\n-4404466 0\n-4404559 0\n-4404572 0\n-4404688 0\n-4404802 0\n-4404843 5\n-4404876 0\n-4404917 0\n-4404926 0\n-4405144 0\n-4405155 0\n-4405168 0\n-4405208 4\n-4405245 137\n-4405250 16\n-4405266 0\n-4405277 0\n-4405420 0\n-4405454 0\n-4405458 45\n-4405483 0\n-4405514 0\n-4405523 0\n-4405558 0\n-4405610 0\n-4405654 0\n-4405675 0\n-4405871 0\n-4405986 0\n-4406003 0\n-4406018 0\n-4406029 0\n-4406059 0\n-4406144 0\n-4406151 0\n-4406281 0\n-4406313 0\n-4406357 0\n-4406552 0\n-4406582 0\n-4406603 0\n-4406669 0\n-4406689 0\n-4406720 0\n-4406727 0\n-4406793 0\n-4406819 0\n-4406822 0\n-4406915 0\n-4407061 0\n-4407090 0\n-4407101 0\n-4407135 0\n-4407219 0\n-4407240 0\n-4407462 0\n-4407484 37\n-4407619 154\n-4407690 38\n-4407744 0\n-4407921 54\n-4407930 0\n-4407939 117\n-4407960 18\n-4407995 0\n-4408001 0\n-4408056 85\n-4408071 0\n-4408076 0\n-4408138 106\n-4408203 275\n-4408299 1\n-4408335 54\n-4408553 29\n-4408742 119\n-4408755 415\n-4409010 2\n-4409166 0\n-4409255 0\n-4409280 0\n-4409297 0\n-4409338 0\n-4409353 0\n-4409357 0\n-4409424 0\n-4409444 0\n-4409546 0\n-4409581 0\n-4409607 0\n-4409615 0\n-4409676 0\n-4409682 0\n-4409702 0\n-4409822 0\n-4409903 0\n-4409974 0\n-4409996 0\n-4410026 0\n-4410029 0\n-4410146 2\n-4410158 0\n-4410240 41\n-4410264 0\n-4410271 0\n-4410277 0\n-4410305 0\n-4410327 0\n-4410337 0\n-4410367 0\n-4410373 14\n-4410403 0\n-4410423 12\n-4410624 0\n-4410668 0\n-4410693 0\n-4410769 1\n-4410851 0\n-4410861 0\n-4410944 0\n-4411049 0\n-4411098 0\n-4411102 0\n-4411164 125\n-4411182 118\n-4411245 0\n-4411258 0\n-4411273 72\n-4411277 173\n-4411337 0\n-4411397 0\n-4411412 0\n-4411421 0\n-4411440 99\n-4411479 0\n-4411508 0\n-4411526 0\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-in1.gff3 --- a/test-data/transit-in1.gff3 Tue Jun 25 17:43:58 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,3990 +0,0 @@\n-chromosomal replication initiation protein \t1\t1524\t+\t507\t15607143\t885041\tdnaA\tRv0001\tCOG0593L\t\r\n-DNA polymerase III subunit beta \t2052\t3260\t+\t402\t15607144\t887092\tdnaN\tRv0002\tCOG0592L\t\r\n-recombination protein F \t3280\t4437\t+\t385\t15607145\t887089\trecF\tRv0003\tCOG1195L\t\r\n-hypothetical protein Rv0004 \t4434\t4997\t+\t187\t15607146\t887088\t-\tRv0004\tCOG5512R\t\r\n-DNA gyrase subunit B \t5123\t7267\t+\t714\t15607147\t887081\tgyrB\tRv0005\tCOG0187L\t\r\n-DNA gyrase subunit A \t7302\t9818\t+\t838\t15607148\t887105\tgyrA\tRv0006\tCOG0188L\t\r\n-POSSIBLE CONSERVED MEMBRANE PROTEIN \t9914\t10828\t+\t304\t15607149\t885982\t-\tRv0007\t-\t\r\n-POSSIBLE MEMBRANE PROTEIN \t11874\t12311\t-\t145\t15607150\t887085\t-\tRv0008c\t-\t\r\n-PROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t12468\t13016\t+\t182\t15607151\t887087\tppiA\tRv0009\tCOG0652O\t\r\n-PROBABLE CONSERVED MEMBRANE PROTEIN \t13133\t13558\t-\t141\t15607152\t887082\t-\tRv0010c\t-\t\r\n-putative septation inhibitor protein \t13714\t13995\t-\t93\t15607153\t887074\t-\tRv0011c\t-\t\r\n-PROBABLE CONSERVED MEMBRANE PROTEIN \t14089\t14877\t+\t262\t15607154\t887083\t-\tRv0012\tCOG3879S\t\r\n-para-aminobenzoate synthase component II \t14914\t15612\t+\t232\t57116682\t885955\ttrpG\tRv0013\tCOG0512EH\t\r\n-TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t15590\t17470\t-\t626\t15607156\t887072\tpknB\tRv0014c\tCOG0515RTKL, COG2815S\t\r\n-TRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t17467\t18762\t-\t431\t15607157\t885953\tpknA\tRv0015c\tCOG0515RTKL\t\r\n-PROBABLE PENICILLIN-BINDING PROTEIN PBPA \t18759\t20234\t-\t491\t15607158\t887078\tpbpA\tRv0016c\tCOG0768M\t\r\n-PROBABLE CELL DIVISION PROTEIN RODA \t20231\t21640\t-\t469\t15607159\t887075\trodA\tRv0017c\tCOG0772D\t\r\n-POSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t21637\t23181\t-\t514\t15607160\t887070\tppp\tRv0018c\tCOG0631T\t\r\n-hypothetical protein Rv0019c \t23270\t23737\t-\t155\t15607161\t887079\t-\tRv0019c\tCOG1716T\t\r\n-hypothetical protein Rv0020c \t23861\t25444\t-\t527\t15607162\t887067\tTB39.8\tRv0020c\tCOG1716T\t\r\n-hypothetical protein Rv0021c \t25913\t26881\t-\t322\t15607163\t887066\t-\tRv0021c\tCOG2070R\t\r\n-PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t27023\t27442\t-\t139\t15607164\t887071\twhiB5\tRv0022c\t-\t\r\n-POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN \t27595\t28365\t+\t256\t15607165\t887062\t-\tRv0023\tCOG1396K\t\r\n-PUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN \t28362\t29207\t+\t281\t15607166\t887061\t-\tRv0024\tCOG0791M\t\r\n-hypothetical protein Rv0025 \t29245\t29607\t+\t120\t15607167\t887060\t-\tRv0025\t-\t\r\n-hypothetical protein Rv0026 \t29722\t31068\t+\t448\t15607168\t887057\t-\tRv0026\t-\t\r\n-hypothetical protein Rv0027 \t31189\t31506\t+\t105\t15607169\t887054\t-\tRv0027\t-\t\r\n-hypothetical protein Rv0028 \t31514\t31819\t+\t101\t15607170\t885812\t-\tRv0028\t-\t\r\n-hypothetical protein Rv0029 \t32057\t33154\t+\t365\t15607171\t887053\t-\tRv0029\t-\t\r\n-hypothetical protein Rv0030 \t33224\t33553\t+\t109\t15607172\t887051\t-\tRv0030\t-\t\r\n-POSSIBLE REMNANT OF A TRANSPOSASE \t33582\t33794\t+\t70\t15607173\t887049\t-\tRv0031\t-\t\r\n-POSSIBLE 8-AMINO-7-OXONONANOATE SYNTHASE BIOF2 (AONS) (8-AMINO-7-KETOPELARGONATE SYNTHASE) (7-KETO-8-AMINO-PELARGONIC ACID SYNTHETASE) (7-KAP SYNTHETASE) (L-ALANINE--PIMELYL CoA LIGASE) \t34295\t36610\t+\t771\t15607174\t887050\tbioF2\tRv0032\tCOG0156H\t\r\n-PROBABLE ACYL CARRIER PROTEIN ACPA (ACP) \t36607\t36870\t+\t87\t15607175\t887052\tacpA\tRv0033\tCOG0236IQ\t\r\n-hypothetical protein Rv0034 \t36867\t37262\t+\t131\t15607176\t887046\t-\tRv0034\tCOG3631R\t\r\n-PROBABLE FATTY-ACID-CoA LIGASE FADD34 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) \t37259\t38947\t+\t562\t57116683\t887048\tfadD34\tRv0035\tCOG0318IQ\t\r\n-hypothetical protein Rv0036c \t39056\t39829\t-\t257\t15607178\t887043\t-\tRv0036c\t-\t\r\n-PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t39877\t41202\t-\t441\t15607179\t887042\t-\tRv0037c\tCOG0477GEPR\t\r\n-hypothetical protein Rv0038 \t41304\t41912\t+\t202\t15607180\t887045\t-\tRv0038\tCOG1678K\t\r\n-POSSIBLE CONSERVED TRANSMEMBRANE PROTEIN \t42004\t42351\t-\t115\t15607181\t887038\t-\tRv0039c\t-\t\r\n-SECRETED PROLINE RICH PROTEIN MTC28 (PROLINE RICH 28 KDA ANTIGEN) \t42433\t43365\t-\t310\t57116684\t887037\tmtc28\tRv0040c\t-\t\r\n-leucyl-tRNA synth'..b'v3885c\t-\t\r\n-PROBABLE ALANINE AND PROLINE RICH MEMBRANE-ANCHORED MYCOSIN MYCP2 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-2) \t4368518\t4370170\t-\t550\t15611022\t886215\tmycP2\tRv3886c\tCOG1404O\t\r\n-PROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t4370155\t4371684\t-\t509\t15611023\t886211\t-\tRv3887c\t-\t\r\n-PROBABLE CONSERVED MEMBRANE PROTEIN \t4371681\t4372706\t-\t341\t15611024\t886219\t-\tRv3888c\tCOG0455D, COG3640D\t\r\n-hypothetical protein Rv3889c \t4372800\t4373630\t-\t276\t15611025\t886223\t-\tRv3889c\t-\t\r\n-ESAT-6 LIKE PROTEIN ESXC (ESAT-6 like protein 11) \t4373726\t4374013\t-\t95\t15611026\t886222\tesxC\tRv3890c\tCOG4842S\t\r\n-POSSIBLE ESAT-6 LIKE PROTEIN ESXD \t4374049\t4374372\t-\t107\t15611027\t886218\tesxD\tRv3891c\t-\t\r\n-PPE FAMILY PROTEIN \t4374484\t4375683\t-\t399\t57117166\t886227\tPPE69\tRv3892c\t-\t\r\n-PE FAMILY PROTEIN \t4375762\t4375995\t-\t77\t57117167\t886213\tPE36\tRv3893c\t-\t\r\n-POSSIBLE CONSERVED MEMBRANE PROTEIN \t4376262\t4380452\t-\t1396\t15611030\t886230\t-\tRv3894c\tCOG1674D\t\r\n-PROBABLE CONSERVED MEMBRANE PROTEIN \t4380453\t4381940\t-\t495\t15611031\t886231\t-\tRv3895c\t-\t\r\n-hypothetical protein Rv3896c \t4381943\t4382851\t-\t302\t15611032\t886216\t-\tRv3896c\tCOG3953R\t\r\n-hypothetical protein Rv3897c \t4383008\t4383640\t-\t210\t15611033\t886225\t-\tRv3897c\t-\t\r\n-hypothetical protein Rv3898c \t4383653\t4383985\t-\t110\t15611034\t886233\t-\tRv3898c\t-\t\r\n-hypothetical protein Rv3899c \t4384147\t4385379\t-\t410\t15611035\t886228\t-\tRv3899c\t-\t\r\n-CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t4385373\t4386308\t-\t311\t15611036\t886235\t-\tRv3900c\t-\t\r\n-POSSIBLE MEMBRANE PROTEIN \t4386365\t4386814\t-\t149\t15611037\t886226\t-\tRv3901c\t-\t\r\n-hypothetical protein Rv3902c \t4387365\t4387895\t-\t176\t15611038\t886236\t-\tRv3902c\t-\t\r\n-HYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t4387892\t4390432\t-\t846\t15611039\t886229\t-\tRv3903c\t-\t\r\n-PUTATIVE ESAT-6 LIKE PROTEIN ESXE (HYPOTHETICAL ALANINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 12) \t4390437\t4390709\t-\t90\t15611040\t886237\tesxE\tRv3904c\t-\t\r\n-PUTATIVE ESAT-6 LIKE PROTEIN ESXF (HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 13) \t4390720\t4391031\t-\t103\t15611041\t886239\tesxF\tRv3905c\tCOG4842S\t\r\n-hypothetical protein Rv3906c \t4391097\t4391606\t-\t169\t15611042\t886221\t-\tRv3906c\t-\t\r\n-PROBABLE POLY(A) POLYMERASE PCNA (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) (NTP POLYMERASE) (RNA ADENYLATING ENZYME) (POLY(A) POLYMERASE) \t4391631\t4393073\t-\t480\t57117168\t886240\tpcnA\tRv3907c\tCOG0617J\t\r\n-hypothetical protein Rv3908 \t4393449\t4394195\t+\t248\t15611044\t886242\t-\tRv3908\tCOG0494LR\t\r\n-hypothetical protein Rv3909 \t4394192\t4396600\t+\t802\t15611045\t886245\t-\tRv3909\t-\t\r\n-PROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t4396597\t4400151\t+\t1184\t15611046\t886247\t-\tRv3910\tCOG0515RTKL, COG0728R\t\r\n-RNA polymerase sigma factor SigM \t4400186\t4400854\t+\t222\t15611047\t886246\tsigM\tRv3911\tCOG1595K\t\r\n-HYPOTHETICAL ALANINE RICH PROTEIN \t4400870\t4401634\t+\t254\t15611048\t886234\t-\tRv3912\t-\t\r\n-PROBABLE THIOREDOXIN REDUCTASE TRXB2 (TRXR) (TR) \t4401728\t4402735\t+\t335\t15611049\t886232\ttrxB2\tRv3913\tCOG0492O\t\r\n-THIOREDOXIN TRXC (TRX) (MPT46) \t4402732\t4403082\t+\t116\t15611050\t886241\ttrxC\tRv3914\tCOG0526OC\t\r\n-PROBABLE HYDROLASE \t4403192\t4404412\t+\t406\t57117169\t886250\t-\tRv3915\tCOG0860M, COG3409M\t\r\n-hypothetical protein Rv3916c \t4404433\t4405167\t-\t244\t15611052\t886249\t-\tRv3916c\t-\t\r\n-PROBABLE CHROMOSOME PARTITIONING PROTEIN PARB \t4405457\t4406491\t-\t344\t57117170\t886244\tparB\tRv3917c\tCOG1475K\t\r\n-PROBABLE CHROMOSOME PARTITIONING PROTEIN PARA \t4406488\t4407531\t-\t347\t57117171\t886224\tparA\tRv3918c\tCOG1192D\t\r\n-glucose-inhibited division protein B \t4407528\t4408202\t-\t224\t15611055\t886243\tgidB\tRv3919c\tCOG0357M\t\r\n-HYPOTHETICAL PROTEIN SIMILAR TO JAG PROTEIN \t4408334\t4408897\t-\t187\t15611056\t886255\t-\tRv3920c\tCOG1847R\t\r\n-putative inner membrane protein translocase component YidC \t4408969\t4410069\t-\t366\t15611057\t886238\t-\tRv3921c\tCOG0706U\t\r\n-hypothetical protein Rv3922c \t4410053\t4410415\t-\t120\t15611058\t886256\t-\tRv3922c\tCOG0759S\t\r\n-ribonuclease P \t4410412\t4410762\t-\t116\t161352458\t886248\trnpA\tRv3923c\tCOG0594J\t\r\n-50S ribosomal protein L34 \t4410786\t4410929\t-\t47\t15611060\t886258\trpmH\tRv3924c\tCOG0230J\t\r\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-in1.prot --- a/test-data/transit-in1.prot Tue Jun 25 17:43:58 2019 -0400 +++ b/test-data/transit-in1.prot Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -998,2993 +998,3 @@\n PROBABLE TWO COMPONENT SENSOR KINASE MPRB \t1097508\t1099022\t+\t504\t15608122\t885062\tmprB\tRv0982\tCOG0642T\t\r\n PROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t1099066\t1100460\t+\t464\t15608123\t885382\tpepD\tRv0983\tCOG0265O\t\r\n POSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t1100460\t1101005\t+\t181\t15608124\t885378\tmoaB2\tRv0984\tCOG0521H\t\r\n-large-conductance mechanosensitive channel \t1101025\t1101480\t-\t151\t15608125\t885368\tmscL\tRv0985c\tCOG1970M\t\r\n-PROBABLE ADHESION COMPONENT TRANSPORT ATP-BINDING PROTEIN ABC TRANSPORTER \t1101803\t1102549\t+\t248\t15608126\t885364\t-\tRv0986\tCOG1136V\t\r\n-PROBABLE ADHESION COMPONENT TRANSPORT TRANSMEMBRANE PROTEIN ABC TRANSPORTER \t1102542\t1105109\t+\t855\t15608127\t885363\t-\tRv0987\tCOG0577V\t\r\n-POSSIBLE CONSERVED EXPORTED PROTEIN \t1105116\t1106276\t+\t386\t15608128\t885353\t-\tRv0988\tCOG5621R\t\r\n-PROBABLE POLYPRENYL-DIPHOSPHATE SYNTHASE GRCC2 (POLYPRENYL PYROPHOSPHATE SYNTHETASE) \t1106405\t1107382\t-\t325\t15608129\t885355\tgrcC2\tRv0989c\tCOG0142H\t\r\n-hypothetical protein Rv0990c \t1107443\t1108099\t-\t218\t15608130\t885343\t-\tRv0990c\t-\t\r\n-CONSERVED HYPOTHETICAL SERINE RICH PROTEIN \t1108172\t1108504\t-\t110\t15608131\t885350\t-\tRv0991c\tCOG2331S\t\r\n-hypothetical protein Rv0992c \t1108578\t1109171\t-\t197\t15608132\t885337\t-\tRv0992c\tCOG0212H\t\r\n-PROBABLE UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE GALU (UDP-GLUCOSE PYROPHOSPHORYLASE) (UDPGP) (ALPHA-D-GLUCOSYL-1-PHOSPHATE URIDYLYLTRANSFERASE) (URIDINE DIPHOSPHOGLUCOSE PYROPHOSPHORYLASE) \t1109272\t1110192\t+\t306\t15608133\t885341\tgalU\tRv0993\tCOG1210M\t\r\n-PROBABLE MOLYBDOPTERIN BIOSYNTHESIS PROTEIN MOEA1 \t1110269\t1111549\t+\t426\t57116810\t885404\tmoeA1\tRv0994\tCOG0303H\t\r\n-POSSIBLE RIBOSOMAL-PROTEIN-ALANINE ACETYLTRANSFERASE RIMJ (ACETYLATING ENZYME FOR N-TERMINAL OF RIBOSOMAL PROTEIN S5) \t1111612\t1112223\t+\t203\t15608135\t885399\trimJ\tRv0995\tCOG1670J\t\r\n-PROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t1112384\t1113460\t+\t358\t15608136\t885393\t-\tRv0996\t-\t\r\n-hypothetical protein Rv0997 \t1114293\t1114724\t+\t143\t15608137\t885386\t-\tRv0997\t-\t\r\n-hypothetical protein Rv0998 \t1114748\t1115749\t+\t333\t15608138\t885385\t-\tRv0998\tCOG0454KR, COG0664T\t\r\n-hypothetical protein Rv0999 \t1115767\t1116525\t+\t252\t15608139\t886043\t-\tRv0999\t-\t\r\n-hypothetical protein Rv1000c \t1116531\t1117148\t-\t205\t57116811\t886266\t-\tRv1000c\tCOG3145L\t\r\n-arginine deiminase \t1117185\t1118393\t+\t402\t15608141\t888313\tarcA\tRv1001\tCOG2235E\t\r\n-hypothetical protein Rv1002c \t1118428\t1119939\t-\t503\t15608142\t887882\t-\tRv1002c\tCOG1928O\t\r\n-hypothetical protein Rv1003 \t1120022\t1120879\t+\t285\t15608143\t887935\t-\tRv1003\tCOG0313R\t\r\n-PROBABLE MEMBRANE PROTEIN \t1120889\t1122148\t-\t419\t15608144\t886039\t-\tRv1004c\t-\t\r\n-para-aminobenzoate synthase component I \t1122222\t1123598\t-\t458\t15608145\t888205\tpabB\tRv1005c\tCOG0147EH\t\r\n-hypothetical protein Rv1006 \t1123714\t1125417\t+\t567\t15608146\t888234\t-\tRv1006\t-\t\r\n-methionyl-tRNA synthetase \t1125444\t1127003\t-\t519\t15608147\t886050\tmetG\tRv1007c\tCOG0143J\t\r\n-PROBABLE DEOXYRIBONUCLEASE TATD (YJJV PROTEIN) \t1127089\t1127883\t+\t264\t15608148\t886047\ttatD\tRv1008\tCOG0084L\t\r\n-Probable resuscitation-promoting factor rpfB \t1128091\t1129179\t+\t362\t15608149\t886048\trpfB\tRv1009\tCOG3583S\t\r\n-dimethyladenosine transferase \t1129152\t1130105\t+\t317\t15608150\t888792\tksgA\tRv1010\tCOG0030J\t\r\n-4-diphosphocytidyl-2-C-methyl-D-erythritol kinase \t1130191\t1131111\t+\t306\t15608151\t886034\tispE\tRv1011\tCOG1947I\t\r\n-hypothetical protein Rv1012 \t1131128\t1131421\t+\t97\t15608152\t886045\t-\tRv1012\t-\t\r\n-acyl-CoA synthetase \t1131625\t1133259\t+\t544\t15608153\t886035\tpks16\tRv1013\tCOG0318IQ\t\r\n-peptidyl-tRNA hydrolase \t1133333\t1133908\t-\t191\t15608154\t886037\tpth\tRv1014c\tCOG0193J\t\r\n-50S ribosomal protein L25/general stress protein Ctc \t1133921\t1134568\t-\t215\t15608155\t885992\trplY\tRv1015c\tCOG1825J\t\r\n-PROBABLE CONSERVED LIPOPROTEIN LPQT \t1134785\t1135465\t-\t226\t15608156\t886066\tlpqT\tRv1016c\t-\t\r\n-ribose-phosphate pyrophosphokinase \t11355'..b'v3885c\t-\t\r\n-PROBABLE ALANINE AND PROLINE RICH MEMBRANE-ANCHORED MYCOSIN MYCP2 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-2) \t4368518\t4370170\t-\t550\t15611022\t886215\tmycP2\tRv3886c\tCOG1404O\t\r\n-PROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t4370155\t4371684\t-\t509\t15611023\t886211\t-\tRv3887c\t-\t\r\n-PROBABLE CONSERVED MEMBRANE PROTEIN \t4371681\t4372706\t-\t341\t15611024\t886219\t-\tRv3888c\tCOG0455D, COG3640D\t\r\n-hypothetical protein Rv3889c \t4372800\t4373630\t-\t276\t15611025\t886223\t-\tRv3889c\t-\t\r\n-ESAT-6 LIKE PROTEIN ESXC (ESAT-6 like protein 11) \t4373726\t4374013\t-\t95\t15611026\t886222\tesxC\tRv3890c\tCOG4842S\t\r\n-POSSIBLE ESAT-6 LIKE PROTEIN ESXD \t4374049\t4374372\t-\t107\t15611027\t886218\tesxD\tRv3891c\t-\t\r\n-PPE FAMILY PROTEIN \t4374484\t4375683\t-\t399\t57117166\t886227\tPPE69\tRv3892c\t-\t\r\n-PE FAMILY PROTEIN \t4375762\t4375995\t-\t77\t57117167\t886213\tPE36\tRv3893c\t-\t\r\n-POSSIBLE CONSERVED MEMBRANE PROTEIN \t4376262\t4380452\t-\t1396\t15611030\t886230\t-\tRv3894c\tCOG1674D\t\r\n-PROBABLE CONSERVED MEMBRANE PROTEIN \t4380453\t4381940\t-\t495\t15611031\t886231\t-\tRv3895c\t-\t\r\n-hypothetical protein Rv3896c \t4381943\t4382851\t-\t302\t15611032\t886216\t-\tRv3896c\tCOG3953R\t\r\n-hypothetical protein Rv3897c \t4383008\t4383640\t-\t210\t15611033\t886225\t-\tRv3897c\t-\t\r\n-hypothetical protein Rv3898c \t4383653\t4383985\t-\t110\t15611034\t886233\t-\tRv3898c\t-\t\r\n-hypothetical protein Rv3899c \t4384147\t4385379\t-\t410\t15611035\t886228\t-\tRv3899c\t-\t\r\n-CONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t4385373\t4386308\t-\t311\t15611036\t886235\t-\tRv3900c\t-\t\r\n-POSSIBLE MEMBRANE PROTEIN \t4386365\t4386814\t-\t149\t15611037\t886226\t-\tRv3901c\t-\t\r\n-hypothetical protein Rv3902c \t4387365\t4387895\t-\t176\t15611038\t886236\t-\tRv3902c\t-\t\r\n-HYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t4387892\t4390432\t-\t846\t15611039\t886229\t-\tRv3903c\t-\t\r\n-PUTATIVE ESAT-6 LIKE PROTEIN ESXE (HYPOTHETICAL ALANINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 12) \t4390437\t4390709\t-\t90\t15611040\t886237\tesxE\tRv3904c\t-\t\r\n-PUTATIVE ESAT-6 LIKE PROTEIN ESXF (HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 13) \t4390720\t4391031\t-\t103\t15611041\t886239\tesxF\tRv3905c\tCOG4842S\t\r\n-hypothetical protein Rv3906c \t4391097\t4391606\t-\t169\t15611042\t886221\t-\tRv3906c\t-\t\r\n-PROBABLE POLY(A) POLYMERASE PCNA (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) (NTP POLYMERASE) (RNA ADENYLATING ENZYME) (POLY(A) POLYMERASE) \t4391631\t4393073\t-\t480\t57117168\t886240\tpcnA\tRv3907c\tCOG0617J\t\r\n-hypothetical protein Rv3908 \t4393449\t4394195\t+\t248\t15611044\t886242\t-\tRv3908\tCOG0494LR\t\r\n-hypothetical protein Rv3909 \t4394192\t4396600\t+\t802\t15611045\t886245\t-\tRv3909\t-\t\r\n-PROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t4396597\t4400151\t+\t1184\t15611046\t886247\t-\tRv3910\tCOG0515RTKL, COG0728R\t\r\n-RNA polymerase sigma factor SigM \t4400186\t4400854\t+\t222\t15611047\t886246\tsigM\tRv3911\tCOG1595K\t\r\n-HYPOTHETICAL ALANINE RICH PROTEIN \t4400870\t4401634\t+\t254\t15611048\t886234\t-\tRv3912\t-\t\r\n-PROBABLE THIOREDOXIN REDUCTASE TRXB2 (TRXR) (TR) \t4401728\t4402735\t+\t335\t15611049\t886232\ttrxB2\tRv3913\tCOG0492O\t\r\n-THIOREDOXIN TRXC (TRX) (MPT46) \t4402732\t4403082\t+\t116\t15611050\t886241\ttrxC\tRv3914\tCOG0526OC\t\r\n-PROBABLE HYDROLASE \t4403192\t4404412\t+\t406\t57117169\t886250\t-\tRv3915\tCOG0860M, COG3409M\t\r\n-hypothetical protein Rv3916c \t4404433\t4405167\t-\t244\t15611052\t886249\t-\tRv3916c\t-\t\r\n-PROBABLE CHROMOSOME PARTITIONING PROTEIN PARB \t4405457\t4406491\t-\t344\t57117170\t886244\tparB\tRv3917c\tCOG1475K\t\r\n-PROBABLE CHROMOSOME PARTITIONING PROTEIN PARA \t4406488\t4407531\t-\t347\t57117171\t886224\tparA\tRv3918c\tCOG1192D\t\r\n-glucose-inhibited division protein B \t4407528\t4408202\t-\t224\t15611055\t886243\tgidB\tRv3919c\tCOG0357M\t\r\n-HYPOTHETICAL PROTEIN SIMILAR TO JAG PROTEIN \t4408334\t4408897\t-\t187\t15611056\t886255\t-\tRv3920c\tCOG1847R\t\r\n-putative inner membrane protein translocase component YidC \t4408969\t4410069\t-\t366\t15611057\t886238\t-\tRv3921c\tCOG0706U\t\r\n-hypothetical protein Rv3922c \t4410053\t4410415\t-\t120\t15611058\t886256\t-\tRv3922c\tCOG0759S\t\r\n-ribonuclease P \t4410412\t4410762\t-\t116\t161352458\t886248\trnpA\tRv3923c\tCOG0594J\t\r\n-50S ribosomal protein L34 \t4410786\t4410929\t-\t47\t15611060\t886258\trpmH\tRv3924c\tCOG0230J\t\r\n' |
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit-in2-tn5.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in2-tn5.wig Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 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|
| b |
| diff -r 202a99525669 -r c980be2c002c test-data/transit_tn5.prot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit_tn5.prot Tue Oct 08 08:24:12 2019 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+-\t190\t255\t+\t21\t-\t-\tthrL\tBW25113_0001\t-\r\n+bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal)\t337\t2799\t+\t820\t-\t-\tthrA\tBW25113_0002\t-\r\n+-\t2801\t3733\t+\t310\t-\t-\tthrB\tBW25113_0003\t-\r\n+-\t3734\t5020\t+\t428\t-\t-\tthrC\tBW25113_0004\t-\r\n+-\t5234\t5530\t+\t98\t-\t-\tyaaX\tBW25113_0005\t-\r\n+-\t5683\t6459\t-\t258\t-\t-\tyaaA\tBW25113_0006\t-\r\n+inner membrane transport protein\t6529\t7959\t-\t476\t-\t-\tyaaJ\tBW25113_0007\t-\r\n+-\t8238\t9191\t+\t317\t-\t-\ttalB\tBW25113_0008\t-\r\n+putative molybdochetalase in molybdopterine biosynthesis\t9306\t9893\t+\t195\t-\t-\tmog\tBW25113_0009\t-\r\n+-\t9928\t10494\t-\t188\t-\t-\tsatP\tBW25113_0010\t-\r\n+-\t10643\t11356\t-\t237\t-\t-\tyaaW\tBW25113_0011\t-\r\n+-\t11382\t11786\t-\t134\t-\t-\tyaaI\tBW25113_0013\t-\r\n+chaperone Hsp70%3B DNA biosynthesis%3B autoregulated heat shock proteins\t12163\t14079\t+\t638\t-\t-\tdnaK\tBW25113_0014\t-\r\n+chaperone with DnaK%3B heat shock protein\t14168\t15298\t+\t376\t-\t-\tdnaJ\tBW25113_0015\t-\r\n+-\t15445\t16557\t+\t370\t-\t-\tinsL1\tBW25113_0016\t-\r\n+regulatory peptide whose translation enables hokC (gef) expression%3B completely contained in another CDS\t16751\t16960\t-\t69\t-\t-\tmokC\tBW25113_0018\t-\r\n+small toxic membrane polypeptide%3B completely contained in another CDS\t16751\t16903\t-\t50\t-\t-\thokC\tBW25113_4412\t-\r\n+-\t16952\t17006\t+\t18\t-\t-\tsokC\tBW25113_4413\t-\r\n+Na+/H antiporter%2C pH dependent\t17489\t18655\t+\t388\t-\t-\tnhaA\tBW25113_0019\t-\r\n+-\t18715\t19620\t+\t301\t-\t-\tnhaR\tBW25113_0020\t-\r\n+-\t19811\t20314\t-\t167\t-\t-\tinsB1\tBW25113_0021\t-\r\n+-\t20233\t20508\t-\t91\t-\t-\tinsA\tBW25113_0022\t-\r\n+-\t20815\t21078\t-\t87\t-\t-\trpsT\tBW25113_0023\t-\r\n+-\t21181\t21399\t+\t72\t-\t-\tyaaY\tBW25113_0024\t-\r\n+-\t21407\t22348\t+\t313\t-\t-\tribF\tBW25113_0025\t-\r\n+isoleucine tRNA synthetase\t22391\t25207\t+\t938\t-\t-\tileS\tBW25113_0026\t-\r\n+prolipoprotein signal peptidase (SPase II)\t25207\t25701\t+\t164\t-\t-\tlspA\tBW25113_0027\t-\r\n+-\t25826\t26275\t+\t149\t-\t-\tfkpB\tBW25113_0028\t-\r\n+-\t26277\t27227\t+\t316\t-\t-\tispH\tBW25113_0029\t-\r\n+-\t27293\t28207\t+\t304\t-\t-\trihC\tBW25113_0030\t-\r\n+-\t28374\t29195\t+\t273\t-\t-\tdapB\tBW25113_0031\t-\r\n+-\t29651\t30799\t+\t382\t-\t-\tcarA\tBW25113_0032\t-\r\n+-\t30817\t34038\t+\t1073\t-\t-\tcarB\tBW25113_0033\t-\r\n+transcriptional regulator of cai operon\t34300\t34695\t+\t131\t-\t-\tcaiF\tBW25113_0034\t-\r\n+possible synthesis of cofactor for carnitine racemase and dehydratase\t34781\t35371\t-\t196\t-\t-\tcaiE\tBW25113_0035\t-\r\n+carnitine racemase\t35377\t36162\t-\t261\t-\t-\tcaiD\tBW25113_0036\t-\r\n+probable crotonobetaine/carnitine-CoA ligase\t36271\t37824\t-\t517\t-\t-\tcaiC\tBW25113_0037\t-\r\n+l-carnitine dehydratase\t37898\t39115\t-\t405\t-\t-\tcaiB\tBW25113_0038\t-\r\n+probable carnitine operon oxidoreductase\t39244\t40386\t-\t380\t-\t-\tcaiA\tBW25113_0039\t-\r\n+probable carnitine transporter\t40417\t41931\t-\t504\t-\t-\tcaiT\tBW25113_0040\t-\r\n+probable flavoprotein subunit%2C carnitine metabolism\t42403\t43173\t+\t256\t-\t-\tfixA\tBW25113_0041\t-\r\n+probable flavoprotein subunit%2C carnitine metabolism\t43188\t44129\t+\t313\t-\t-\tfixB\tBW25113_0042\t-\r\n+flavoprotein%3B electron transport\t44180\t45466\t+\t428\t-\t-\tfixC\tBW25113_0043\t-\r\n+putative ferredoxin\t45463\t45750\t+\t95\t-\t-\tfixX\tBW25113_0044\t-\r\n+putative transport protein\t45807\t47138\t+\t443\t-\t-\tyaaU\tBW25113_0045\t-\r\n+putative NAD(P)H oxidoreductase\t47246\t47776\t+\t176\t-\t-\tkefF\tBW25113_0046\t-\r\n+K+ efflux antiporter%2C glutathione-regulated\t47769\t49631\t+\t620\t-\t-\tkefC\tBW25113_0047\t-\r\n+dihydrofolate reductase type I%3B trimethoprim resistance\t49823\t50302\t+\t159\t-\t-\tfolA\tBW25113_0048\t-\r\n+-\t50380\t51222\t-\t280\t-\t-\tapaH\tBW25113_0049\t-\r\n+-\t51229\t51606\t-\t125\t-\t-\tapaG\tBW25113_0050\t-\r\n+-\t51609\t52430\t-\t273\t-\t-\trsmA\tBW25113_0051\t-\r\n+pyridoxine biosynthesis\t52427\t53416\t-\t329\t-\t-\tpdxA\tBW25113_0052\t-\r\n+survival protein\t53416\t54702\t-\t428\t-\t-\tsurA\tBW25113_0053\t-\r\n+organic solvent tolerance\t54755\t57109\t-\t784\t-\t-\tlptD\tBW25113_0054\t-\r\n+-\t57364\t58179\t+\t271\t-\t-\tdjlA\tBW25113_0055\t-\r\n+-\t59687\t60346\t-\t219\t-\t-\trluA\tBW25113_0058\t-\r\n+probable ATP-dependent RNA helicase\t60358\t63264\t-\t968\t-\t-\trapA\tBW25113_0059\t-\r\n+-\t63429\t65780\t-\t783\t-\t-\tpolB\tBW25113_0060\t-\r\n+transcriptional regulator for ara operon\t66874\t67752\t+\t292\t-\t-\taraC\tBW25113_0064\t-\r\n+-\t67838\t68602\t+\t254\t-\t-\tyabI\tBW25113_0065\t-'..b"or III\t487548\t489479\t+\t643\t-\t-\tdnaX\tBW25113_0470\t-\r\n+-\t489532\t489861\t+\t109\t-\t-\tybaB\tBW25113_0471\t-\r\n+recombination and repair\t489861\t490466\t+\t201\t-\t-\trecR\tBW25113_0472\t-\r\n+chaperone Hsp90%2C heat shock protein C 62.5\t490576\t492450\t+\t624\t-\t-\thtpG\tBW25113_0473\t-\r\n+adenylate kinase activity%3B pleiotropic effects on glycerol-3-phosphate acyltransferase activity\t492631\t493275\t+\t214\t-\t-\tadk\tBW25113_0474\t-\r\n+ferrochelatase: final enzyme of heme biosynthesis\t493511\t494473\t+\t320\t-\t-\themH\tBW25113_0475\t-\r\n+-\t494470\t495429\t-\t319\t-\t-\taes\tBW25113_0476\t-\r\n+inosine-guanosine kinase\t495581\t496885\t+\t434\t-\t-\tgsk\tBW25113_0477\t-\r\n+putative transport protein\t497018\t498694\t-\t558\t-\t-\tybaL\tBW25113_0478\t-\r\n+fosmidomycin resistance protein\t498932\t500152\t-\t406\t-\t-\tfsr\tBW25113_0479\t-\r\n+UDP-sugar hydrolase (5'-nucleotidase)\t500370\t502022\t+\t550\t-\t-\tushA\tBW25113_0480\t-\r\n+-\t502059\t502538\t-\t159\t-\t-\tybaK\tBW25113_0481\t-\r\n+-\t502660\t502743\t+\t27\t-\t-\tchiX\tBW25113_4585\t-\r\n+putative ligase\t502742\t503536\t-\t264\t-\t-\tybaP\tBW25113_0482\t-\r\n+-\t503674\t504015\t+\t113\t-\t-\tybaQ\tBW25113_0483\t-\r\n+-\t504331\t506835\t-\t834\t-\t-\tcopA\tBW25113_0484\t-\r\n+putative glutaminase\t507097\t508029\t+\t310\t-\t-\tglsA\tBW25113_0485\t-\r\n+putative amino acid/amine transport protein\t508032\t509324\t+\t430\t-\t-\tybaT\tBW25113_0486\t-\r\n+-\t509449\t509856\t+\t135\t-\t-\tcueR\tBW25113_0487\t-\r\n+-\t509857\t510315\t-\t152\t-\t-\tybbJ\tBW25113_0488\t-\r\n+putative protease\t510312\t511229\t-\t305\t-\t-\tqmcA\tBW25113_0489\t-\r\n+putative ATP-binding component of a transport system\t511375\t512052\t+\t225\t-\t-\tfetA\tBW25113_0490\t-\r\n+putative metal resistance protein\t512039\t512818\t+\t259\t-\t-\tfetB\tBW25113_0491\t-\r\n+putative thioredoxin-like protein\t512881\t513735\t-\t284\t-\t-\tybbN\tBW25113_0492\t-\r\n+-\t513796\t514605\t-\t269\t-\t-\tybbO\tBW25113_0493\t-\r\n+acyl-CoA thioesterase I%3B also functions as protease I\t514595\t515221\t-\t208\t-\t-\ttesA\tBW25113_0494\t-\r\n+putative ATP-binding component of a transport system\t515189\t515875\t+\t228\t-\t-\tybbA\tBW25113_0495\t-\r\n+putative oxidoreductase\t515872\t518286\t+\t804\t-\t-\tybbP\tBW25113_0496\t-\r\n+rhsD protein in rhs element\t518717\t522997\t+\t1426\t-\t-\trhsD\tBW25113_0497\t-\r\n+-\t523037\t523405\t+\t122\t-\t-\tybbC\tBW25113_0498\t-\r\n+putative capsule anchoring protein\t525588\t526682\t-\t364\t-\t-\tmnmH\tBW25113_0503\t-\r\n+putative transcriptional regulator LYSR-type\t526751\t527677\t-\t308\t-\t-\tallS\tBW25113_0504\t-\r\n+-\t527907\t528389\t+\t160\t-\t-\tallA\tBW25113_0505\t-\r\n+-\t528467\t529282\t+\t271\t-\t-\tallR\tBW25113_0506\t-\r\n+-\t529372\t531153\t+\t593\t-\t-\tgcl\tBW25113_0507\t-\r\n+-\t531166\t531942\t+\t258\t-\t-\thyi\tBW25113_0508\t-\r\n+-\t532042\t532920\t+\t292\t-\t-\tglxR\tBW25113_0509\t-\r\n+-\t533089\t534543\t+\t484\t-\t-\tybbW\tBW25113_0511\t-\r\n+-\t534603\t535964\t+\t453\t-\t-\tallB\tBW25113_0512\t-\r\n+-\t536021\t537322\t+\t433\t-\t-\tybbY\tBW25113_0513\t-\r\n+-\t537344\t538489\t+\t381\t-\t-\tglxK\tBW25113_0514\t-\r\n+-\t538717\t539502\t-\t261\t-\t-\tallE\tBW25113_0515\t-\r\n+-\t539513\t540748\t-\t411\t-\t-\tallC\tBW25113_0516\t-\r\n+-\t540770\t541819\t-\t349\t-\t-\tallD\tBW25113_0517\t-\r\n+involved in protein transport%3B multicopy suppressor of dominant negative ftsH mutants\t542136\t543803\t+\t555\t-\t-\tfdrA\tBW25113_0518\t-\r\n+-\t543813\t545072\t+\t419\t-\t-\tylbE\tBW25113_4572\t-\r\n+putative carboxylase\t545083\t545898\t+\t271\t-\t-\tylbF\tBW25113_0520\t-\r\n+putative carbamate kinase\t545895\t546788\t+\t297\t-\t-\tybcF\tBW25113_0521\t-\r\n+phosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C CO(2)-fixing subunit\t546983\t548050\t-\t355\t-\t-\tpurK\tBW25113_0522\t-\r\n+phosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C catalytic subunit\t548047\t548556\t-\t169\t-\t-\tpurE\tBW25113_0523\t-\r\n+-\t548674\t549396\t-\t240\t-\t-\tlpxH\tBW25113_0524\t-\r\n+-\t549399\t549893\t-\t164\t-\t-\tppiB\tBW25113_0525\t-\r\n+cysteine tRNA synthetase\t550067\t551452\t+\t461\t-\t-\tcysS\tBW25113_0526\t-\r\n+-\t551488\t552009\t-\t173\t-\t-\tybcI\tBW25113_0527\t-\r\n+-\t552117\t552329\t-\t70\t-\t-\tybcJ\tBW25113_0528\t-\r\n+5%2C10-methylene-tetrahydrofolate dehydrogenase%3B 5%2C10-methylene-tetrahydrofolate cyclohydrolase\t552331\t553197\t-\t288\t-\t-\tfolD\tBW25113_0529\t-\r\n+putative fimbrial-like protein\t553668\t554210\t+\t180\t-\t-\tsfmA\tBW25113_0530\t-\r\n+putative chaperone\t554430\t555122\t+\t230\t-\t-\tsfmC\tBW25113_0531\t-\r\n" |
| b |
| diff -r 202a99525669 -r c980be2c002c transit_gumbel.xml --- a/transit_gumbel.xml Tue Jun 25 17:43:58 2019 -0400 +++ b/transit_gumbel.xml Tue Oct 08 08:24:12 2019 -0400 |
| b |
| @@ -26,8 +26,7 @@ <tests> <test> <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" /> - <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" /> - <param name="annotation" ftype="gff3" value="transit-in1.gff3" /> + <param name="annotation" ftype="tabular" value="transit-in1.prot" /> <param name="samples" value="1000" /> <param name="burnin" value="100" /> <param name="replicates" value="Replicates" /> @@ -52,7 +51,7 @@ ------------------- -Input files for HMM need to be: +Input files for Gumnbel need to be: - .wig files: Tabulated files containing one column with the TA site coordinate and one column with the read count at this site. - annotation .prot_table: Annotation file generated by the `Convert Gff3 to prot_table for TRANSIT` tool. @@ -72,6 +71,7 @@ -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0 --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0 + -n <string> := Determines which normalization method to use. Default -n TTR - Samples: Gumbel uses Metropolis-Hastings (MH) to generate samples of posterior distributions. The default setting is to run the simulation for 10,000 iterations. This is usually enough to assure convergence of the sampler and to provide accurate estimates of posterior probabilities. Less iterations may work, but at the risk of lower accuracy. @@ -79,6 +79,14 @@ - Trim: The MH sampler produces Markov samples that are correlated. This parameter dictates how many samples must be attempted for every sampled obtained. Increasing this parameter will decrease the auto-correlation, at the cost of dramatically increasing the run-time. For most situations, this parameter should be left at the default of “1”. - Minimum Read: The minimum read count that is considered a true read. Because the Gumbel method depends on determining gaps of TA sites lacking insertions, it may be susceptible to spurious reads (e.g. errors). The default value of 1 will consider all reads as true reads. A value of 2, for example, will ignore read counts of 1. - Replicates: Determines how to deal with replicates by averaging the read-counts or summing read counts across datasets. This should not have an affect for the Gumbel method, aside from potentially affecting spurious reads. +- Normalisation : + - TTR (Default) : Trimmed Total Reads (TTR), normalized by the total read-counts (like totreads), but trims top and bottom 5% of read-counts. This is the recommended normalization method for most cases as it has the beneffit of normalizing for difference in saturation in the context of resampling. + - nzmean : Normalizes datasets to have the same mean over the non-zero sites. + - totreads : Normalizes datasets by total read-counts, and scales them to have the same mean over all counts. + - zinfnb : Fits a zero-inflated negative binomial model, and then divides read-counts by the mean. The zero-inflated negative binomial model will treat some empty sites as belonging to the “true” negative binomial distribution responsible for read-counts while treating the others as “essential” (and thus not influencing its parameters). + - quantile : Normalizes datasets using the quantile normalization method described by Bolstad et al. (2003). In this normalization procedure, datasets are sorted, an empirical distribution is estimated as the mean across the sorted datasets at each site, and then the original (unsorted) datasets are assigned values from the empirical distribution based on their quantiles. + - betageom : Normalizes the datasets to fit an “ideal” Geometric distribution with a variable probability parameter p. Specially useful for datasets that contain a large skew. See Beta-Geometric Correction . + - nonorm : No normalization is performed. ------------------- @@ -119,4 +127,4 @@ <expand macro="citations" /> -</tool> \ No newline at end of file +</tool> |