| Previous changeset 1:d605800d956c (2019-06-25) Next changeset 3:b12ff7a3ee41 (2019-10-16) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada" |
|
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 |
|
added:
test-data/tn5gaps-sites1.txt test-data/transit-in-tn5.wig test-data/transit-in2-tn5.wig test-data/transit_tn5.prot |
|
removed:
test-data/transit-in1.gff3 |
| b |
| diff -r d605800d956c -r c1751dfb4d94 macros.xml --- a/macros.xml Tue Jun 25 17:44:17 2019 -0400 +++ b/macros.xml Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/gff_to_prot-in1.gff3 --- a/test-data/gff_to_prot-in1.gff3 Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/gff_to_prot-in1.gff3 Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/gff_to_prot-out1.txt --- a/test-data/gff_to_prot-out1.txt Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/gff_to_prot-out1.txt Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/gumbel-sites1.txt --- a/test-data/gumbel-sites1.txt Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/gumbel-sites1.txt Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/hmm-genes1.txt --- a/test-data/hmm-genes1.txt Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/hmm-genes1.txt Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/hmm-sites1.txt --- a/test-data/hmm-sites1.txt Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/hmm-sites1.txt Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/resampling-sites1.txt --- a/test-data/resampling-sites1.txt Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/resampling-sites1.txt Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/tn5gaps-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tn5gaps-sites1.txt Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/transit-co1-rep1.wig --- a/test-data/transit-co1-rep1.wig Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/transit-co1-rep1.wig Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 test-data/transit-co1-rep2.wig --- a/test-data/transit-co1-rep2.wig Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/transit-co1-rep2.wig Tue Oct 08 08:25:10 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 0\n-114705 105\n-114850 0\n-114858 0\n-114903 72\n-114912 68\n-114926 66\n-115035 47\n-115078 0\n-115297 83\n-115305 0\n-115339 0\n-115418 0\n-115435 0\n-115461 287\n-115491 0\n-115563 131\n-115650 76\n-115702 0\n-115717 214\n-115753 0\n-115761 43\n-115816 92\n-115836 0\n-115858 14\n-115926 6\n-115934 59\n-115944 0\n-116075 0\n-116098 76\n-116152 51\n-116320 13\n-116364 30\n-116474 0\n-116649 0\n-116708 0\n-116733 252\n-116803 1\n-116847 0\n-116955 11\n-117014 0\n-117039 0\n-117168 133\n-117197 0\n-117213 147\n-117240 0\n-117247 0\n-117380 0\n-117504 76\n-117517 20\n-117537 0\n-117551 0\n-117622 63\n-117640 0\n-117648 0\n-117702 23\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 18\n-119916 0\n-119936 0\n-120045 77\n-120121 0\n-120256 415\n-120310 35\n-120410 0\n-120574 0\n-120626 116\n-120791 3\n-120882 0\n-120892 53\n-120902 17\n-120940 142\n-120989 85\n-121171 0\n-121181 0\n-121251 0\n-121291 169\n-121391 44\n-121397 194\n-121442 44\n-121500 93\n-121548 144\n-121766 141\n-121770 40\n-121856 131\n-121916 0\n-121950 131\n-122045 0\n-122104 73\n-122193 0\n-122211 77\n-122220 0\n-122231 0\n-122243 0\n-122304 0\n-122388 3\n-122444 11\n-122494 0\n-122542 173\n-122566 3\n-122596 147\n-122609 20\n-122643 12\n-122655 0\n-122696 22\n-122764 0\n-122834 260\n-122836 38\n-122992 129\n-123012 25\n-123049 40\n-123122 61\n-123221 0\n-123243 0\n-123346 415\n-123470 0\n-123493 0\n-123520 0\n-123522 61\n-123612 274\n-123671 0\n-123772 1\n-123829 105\n-123873 0\n-123896 138\n-123906 141\n-123910 168\n-123912 21\n-124145 124\n-124149 246\n-124152 0\n-124168 0\n-124219 0\n-124298 2\n-124327 0\n-124343 0\n-124362 0\n-124379 28\n-124390 0\n-124603 86\n-124722 0\n-124786 14\n-125015 1\n-125021 23\n-125292 44\n-125337 132\n-125371 0\n-125377 39\n-125469 0\n-125579 0\n-125592 0\n-125605 43\n-125620 21\n-125644 0\n-125659 53\n-125666 105\n-125823 68\n-125843 0\n-125940 0\n-126059 0\n-126098 46\n-126163 0\n-126431 0\n-126693 0\n-126812 10\n-126829 119\n-126963 0\n-127059 0\n-127096 0\n-127119 0\n-127157 0\n-127160 0\n-127181 0\n-127232 0\n-127335 0\n-127344 0\n-127392 118\n-127503 40\n-127731 8\n-127839 0\n-127853 0\n-128018 0\n-128025 0\n-128073 10\n-128109 22\n-128148 0\n-128154 0\n-128165 86\n-128305 2\n-128379 0\n-128389 10\n-128616 0\n-128697 31\n-128777 131\n-128820 0\n-128904 77\n-128983 28\n-129116 0\n-129184 2\n-129231 26\n-129269 0\n-129321 108\n-129396 16\n-129431 37\n-129496 236\n-129708 0\n-129789 0\n-129812 0\n-129827 0\n-129860 10\n-129888 15\n-129969 0\n-130019 9\n-130074 249\n-130107 260\n-130130 0\n-130263 0\n-130353 60\n-130491 123\n-130558 14\n-130564 0\n-130573 3\n-130587 120\n-130602 0\n-130616 77\n-130699 93\n-130708 0\n-130787 0\n-130929 21\n-131037 178\n-131140 21\n-131149 0\n-131158 77\n-131328 2\n-131341 0\n-131441 0\n-131497 0\n-131542 1\n-131553 0\n-131565 43\n-131640 0\n-131740 36\n-131776 0\n-131867 0\n-131894 0\n-131929 105\n-132047 10\n-132077 1\n-132137 0\n-132276 1\n-132284 0\n-132353 0\n-13'..b' 0\n-4391253 0\n-4391265 12\n-4391329 7\n-4391395 316\n-4391430 14\n-4391592 0\n-4391599 15\n-4391632 6\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 0\n-4393177 18\n-4393219 27\n-4393222 34\n-4393301 94\n-4393372 62\n-4393408 128\n-4393429 0\n-4393436 32\n-4393439 47\n-4393517 7\n-4393670 0\n-4393747 0\n-4393860 14\n-4393908 1107\n-4393924 0\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 45\n-4398413 20\n-4398714 0\n-4398724 0\n-4398752 166\n-4398870 0\n-4398950 0\n-4398980 0\n-4399141 0\n-4399204 0\n-4399376 2\n-4399403 42\n-4399510 24\n-4399607 0\n-4399819 86\n-4399821 0\n-4399842 0\n-4399983 0\n-4400082 119\n-4400137 6\n-4400185 22\n-4400204 74\n-4400285 6\n-4400325 12\n-4400426 0\n-4400520 14\n-4400531 2\n-4400645 0\n-4400728 1\n-4400745 17\n-4400797 185\n-4400822 0\n-4400837 0\n-4400902 15\n-4401048 13\n-4401135 40\n-4401392 8\n-4401433 142\n-4401458 0\n-4401499 0\n-4401519 37\n-4401531 19\n-4401595 0\n-4401610 0\n-4401677 63\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 0\n-4402719 2\n-4402767 0\n-4402796 0\n-4402859 0\n-4402974 0\n-4403031 0\n-4403080 0\n-4403093 0\n-4403134 0\n-4403171 0\n-4403191 5\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 0\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 28\n-4405245 52\n-4405250 60\n-4405266 0\n-4405277 0\n-4405420 0\n-4405454 10\n-4405458 0\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 4\n-4407690 33\n-4407744 0\n-4407921 0\n-4407930 0\n-4407939 0\n-4407960 0\n-4407995 0\n-4408001 0\n-4408056 0\n-4408071 0\n-4408076 0\n-4408138 0\n-4408203 18\n-4408299 0\n-4408335 0\n-4408553 1\n-4408742 55\n-4408755 118\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 0\n-4410158 0\n-4410240 0\n-4410264 2\n-4410271 0\n-4410277 20\n-4410305 0\n-4410327 0\n-4410337 0\n-4410367 0\n-4410373 0\n-4410403 0\n-4410423 19\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 1\n-4411182 0\n-4411245 0\n-4411258 0\n-4411273 2\n-4411277 107\n-4411337 0\n-4411397 0\n-4411412 0\n-4411421 0\n-4411440 164\n-4411479 25\n-4411508 0\n-4411526 0\n' |
| b |
| diff -r d605800d956c -r c1751dfb4d94 test-data/transit-co1-rep3.wig --- a/test-data/transit-co1-rep3.wig Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/transit-co1-rep3.wig Tue Oct 08 08:25:10 2019 -0400 |
| b |
| b'@@ -1998,72610 +1998,3 @@\n 109197 0\n 109215 52\n 109226 0\n-109244 0\n-109285 0\n-109292 0\n-109317 0\n-109410 74\n-109521 35\n-109822 0\n-109824 0\n-109916 2\n-110017 0\n-110040 0\n-110060 0\n-110074 0\n-110076 0\n-110094 0\n-110149 45\n-110199 0\n-110221 0\n-110315 76\n-110340 105\n-110424 0\n-110473 0\n-110574 0\n-110600 0\n-110711 0\n-110916 1\n-110929 0\n-110958 0\n-110970 0\n-111013 0\n-111083 0\n-111148 52\n-111211 0\n-111405 7\n-111528 0\n-111578 0\n-111726 92\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 0\n-112703 0\n-112777 0\n-112906 0\n-112922 502\n-112926 28\n-112970 0\n-112992 0\n-113033 0\n-113095 0\n-113113 3\n-113133 80\n-113166 0\n-113174 0\n-113227 0\n-113395 0\n-113462 19\n-113517 98\n-113571 98\n-113580 38\n-113652 0\n-113675 45\n-113712 0\n-113827 0\n-113924 0\n-114033 0\n-114049 2\n-114229 0\n-114251 0\n-114285 15\n-114326 14233\n-114437 0\n-114512 0\n-114558 184\n-114589 0\n-114705 192\n-114850 0\n-114858 0\n-114903 99\n-114912 30\n-114926 4\n-115035 182\n-115078 1\n-115297 304\n-115305 0\n-115339 0\n-115418 0\n-115435 0\n-115461 324\n-115491 0\n-115563 45\n-115650 3\n-115702 0\n-115717 155\n-115753 2\n-115761 0\n-115816 0\n-115836 0\n-115858 0\n-115926 0\n-115934 3\n-115944 0\n-116075 0\n-116098 0\n-116152 122\n-116320 0\n-116364 0\n-116474 0\n-116649 0\n-116708 0\n-116733 170\n-116803 0\n-116847 0\n-116955 0\n-117014 0\n-117039 70\n-117168 1\n-117197 0\n-117213 98\n-117240 0\n-117247 0\n-117380 0\n-117504 0\n-117517 0\n-117537 0\n-117551 0\n-117622 411\n-117640 0\n-117648 0\n-117702 1\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 59\n-119748 0\n-119916 0\n-119936 0\n-120045 57\n-120121 0\n-120256 680\n-120310 0\n-120410 0\n-120574 0\n-120626 227\n-120791 0\n-120882 0\n-120892 0\n-120902 26\n-120940 192\n-120989 2\n-121171 0\n-121181 0\n-121251 0\n-121291 25\n-121391 32\n-121397 93\n-121442 0\n-121500 101\n-121548 66\n-121766 228\n-121770 4\n-121856 44\n-121916 265\n-121950 4\n-122045 0\n-122104 82\n-122193 40\n-122211 0\n-122220 0\n-122231 0\n-122243 0\n-122304 0\n-122388 42\n-122444 0\n-122494 167\n-122542 169\n-122566 0\n-122596 114\n-122609 0\n-122643 0\n-122655 8\n-122696 3\n-122764 7\n-122834 33\n-122836 1\n-122992 35\n-123012 4\n-123049 0\n-123122 0\n-123221 0\n-123243 0\n-123346 362\n-123470 0\n-123493 0\n-123520 0\n-123522 53\n-123612 174\n-123671 0\n-123772 150\n-123829 3\n-123873 0\n-123896 354\n-123906 404\n-123910 249\n-123912 0\n-124145 10\n-124149 367\n-124152 0\n-124168 0\n-124219 0\n-124298 0\n-124327 0\n-124343 0\n-124362 0\n-124379 0\n-124390 0\n-124603 2\n-124722 0\n-124786 120\n-125015 113\n-125021 0\n-125292 19\n-125337 71\n-125371 0\n-125377 0\n-125469 42\n-125579 0\n-125592 0\n-125605 130\n-125620 0\n-125644 0\n-125659 226\n-125666 232\n-125823 0\n-125843 0\n-125940 0\n-126059 0\n-126098 265\n-126163 0\n-126431 0\n-126693 0\n-126812 0\n-126829 0\n-126963 112\n-127059 0\n-127096 0\n-127119 0\n-127157 0\n-127160 0\n-127181 0\n-127232 0\n-127335 0\n-127344 0\n-127392 219\n-127503 104\n-127731 0\n-127839 0\n-127853 0\n-128018 0\n-128025 0\n-128073 0\n-128109 31\n-128148 0\n-128154 0\n-128165 139\n-128305 0\n-128379 0\n-128389 0\n-128616 68\n-128697 57\n-128777 221\n-128820 0\n-128904 46\n-128983 0\n-129116 0\n-129184 0\n-129231 3\n-129269 0\n-129321 23\n-129396 0\n-129431 0\n-129496 269\n-129708 0\n-129789 0\n-129812 0\n-129827 0\n-129860 4\n-129888 101\n-129969 0\n-130019 46\n-130074 107\n-130107 525\n-130130 0\n-130263 0\n-130353 75\n-130491 0\n-130558 0\n-130564 0\n-130573 0\n-130587 74\n-130602 0\n-130616 37\n-130699 31\n-130708 28\n-130787 0\n-130929 35\n-131037 218\n-131140 5\n-131149 0\n-131158 0\n-131328 80\n-131341 0\n-131441 0\n-131497 0\n-131542 0\n-131553 0\n-131565 0\n-131640 0\n-131740 116\n-131776 0\n-131867 0\n-131894 0\n-131929 89\n-132047 27\n-132077 72\n-132137 0\n-132276 0\n-132284 0\n-132353 0\n-132374 0\n-132392 0\n-132401 0\n-132529 134\n-1325'..b'-4391246 0\n-4391253 0\n-4391265 58\n-4391329 97\n-4391395 77\n-4391430 1\n-4391592 0\n-4391599 113\n-4391632 0\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 1\n-4393177 0\n-4393219 1\n-4393222 45\n-4393301 66\n-4393372 139\n-4393408 190\n-4393429 0\n-4393436 47\n-4393439 0\n-4393517 0\n-4393670 0\n-4393747 0\n-4393860 92\n-4393908 610\n-4393924 0\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 83\n-4398413 0\n-4398714 0\n-4398724 0\n-4398752 141\n-4398870 0\n-4398950 0\n-4398980 54\n-4399141 0\n-4399204 0\n-4399376 97\n-4399403 149\n-4399510 1\n-4399607 0\n-4399819 313\n-4399821 0\n-4399842 141\n-4399983 0\n-4400082 7\n-4400137 2\n-4400185 16\n-4400204 133\n-4400285 87\n-4400325 9\n-4400426 0\n-4400520 1\n-4400531 0\n-4400645 2\n-4400728 44\n-4400745 0\n-4400797 380\n-4400822 0\n-4400837 0\n-4400902 0\n-4401048 4\n-4401135 70\n-4401392 22\n-4401433 162\n-4401458 0\n-4401499 0\n-4401519 39\n-4401531 0\n-4401595 0\n-4401610 0\n-4401677 347\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 0\n-4402719 2\n-4402767 0\n-4402796 0\n-4402859 0\n-4402974 0\n-4403031 0\n-4403080 0\n-4403093 0\n-4403134 0\n-4403171 0\n-4403191 23\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 8\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 3\n-4405245 2\n-4405250 0\n-4405266 0\n-4405277 0\n-4405420 0\n-4405454 0\n-4405458 0\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 0\n-4407690 101\n-4407744 0\n-4407921 0\n-4407930 0\n-4407939 2\n-4407960 0\n-4407995 0\n-4408001 0\n-4408056 0\n-4408071 0\n-4408076 0\n-4408138 0\n-4408203 31\n-4408299 0\n-4408335 0\n-4408553 65\n-4408742 1\n-4408755 14\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 0\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 0\n-4411182 147\n-4411245 0\n-4411258 0\n-4411273 0\n-4411277 0\n-4411337 0\n-4411397 0\n-4411412 0\n-4411421 0\n-4411440 134\n-4411479 0\n-4411508 0\n-4411526 0\n' |
| b |
| diff -r d605800d956c -r c1751dfb4d94 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 08:25:10 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\n+27\t3\n+31\t1\n+37\t1\n+39\t2\n+47\t2\n+57\t4\n+69\t15\n+77\t2\n+79\t8\n+87\t4\n+153\t3\n+159\t1\n+174\t4\n+176\t48\n+182\t14\n+184\t23\n+200\t6\n+205\t10\n+208\t21\n+215\t36\n+216\t34\n+226\t9\n+234\t2\n+236\t3\n+244\t14\n+252\t1\n+257\t3\n+265\t13\n+325\t4\n+326\t39\n+327\t18\n+334\t12\n+350\t1\n+358\t5\n+366\t7\n+378\t4\n+381\t6\n+415\t6\n+423\t2\n+425\t10\n+431\t20\n+434\t8\n+439\t9\n+445\t2\n+452\t3\n+476\t11\n+481\t4\n+506\t1\n+508\t5\n+513\t3\n+516\t11\n+518\t5\n+521\t21\n+526\t4\n+534\t8\n+555\t1\n+572\t2\n+574\t6\n+576\t8\n+581\t1\n+589\t1\n+595\t9\n+640\t13\n+648\t6\n+655\t14\n+674\t7\n+675\t24\n+683\t16\n+686\t35\n+688\t1\n+694\t43\n+701\t22\n+704\t6\n+732\t2\n+740\t23\n+745\t19\n+751\t11\n+766\t3\n+768\t2\n+774\t6\n+795\t1\n+807\t7\n+809\t1\n+810\t1\n+812\t25\n+814\t17\n+817\t6\n+822\t9\n+828\t1\n+832\t3\n+838\t1\n+840\t15\n+845\t15\n+857\t2\n+869\t9\n+886\t24\n+892\t1\n+896\t25\n+932\t5\n+936\t5\n+940\t2\n+952\t10\n+959\t1\n+960\t2\n+961\t13\n+964\t1\n+972\t19\n+979\t1\n+1016\t1\n+1025\t3\n+1027\t18\n+1028\t14\n+1029\t68\n+1031\t5\n+1036\t7\n+1037\t29\n+1039\t14\n+1042\t2\n+1044\t5\n+1053\t4\n+1076\t4\n+1090\t12\n+1095\t2\n+1105\t15\n+1128\t1\n+1141\t76\n+1149\t11\n+1168\t50\n+1176\t2\n+1202\t1\n+1209\t7\n+1210\t4\n+1212\t11\n+1217\t27\n+1222\t16\n+1225\t21\n+1236\t8\n+1238\t5\n+1246\t1\n+1269\t23\n+1271\t3\n+1276\t4\n+1277\t5\n+1286\t5\n+1294\t1\n+1327\t4\n+1340\t4\n+1345\t4\n+1347\t26\n+1350\t20\n+1368\t7\n+1374\t9\n+1395\t3\n+1444\t25\n+1450\t14\n+1458\t8\n+1464\t22\n+1466\t7\n+1471\t2\n+1473\t11\n+1474\t11\n+1487\t1\n+1501\t8\n+1513\t1\n+1524\t2\n+1536\t5\n+1544\t7\n+1551\t14\n+1555\t2\n+1556\t2\n+1590\t45\n+1593\t1\n+1595\t1\n+1598\t13\n+1607\t10\n+1613\t4\n+1615\t2\n+1626\t11\n+1631\t2\n+1634\t26\n+1661\t12\n+1667\t2\n+1679\t7\n+1681\t8\n+1689\t6\n+1691\t9\n+1696\t10\n+1702\t10\n+1704\t4\n+1712\t41\n+1715\t16\n+1717\t15\n+1720\t38\n+1725\t15\n+1739\t10\n+1768\t6\n+1773\t14\n+1781\t2\n+1792\t15\n+1818\t5\n+1832\t2\n+1833\t9\n+1840\t11\n+1841\t21\n+1856\t10\n+1857\t5\n+1858\t12\n+1860\t5\n+1862\t1\n+1868\t3\n+1870\t6\n+1872\t8\n+1875\t1\n+1878\t14\n+1881\t3\n+1887\t3\n+1936\t24\n+1989\t3\n+1997\t7\n+2006\t1\n+2019\t13\n+2021\t1\n+2029\t25\n+2047\t4\n+2056\t5\n+2066\t32\n+2075\t19\n+2081\t11\n+2083\t4\n+2084\t16\n+2101\t13\n+2102\t6\n+2107\t7\n+2111\t38\n+2119\t22\n+2145\t27\n+2158\t10\n+2169\t6\n+2177\t20\n+2178\t9\n+2201\t2\n+2209\t3\n+2212\t1\n+2264\t1\n+2273\t6\n+2290\t16\n+2291\t5\n+2297\t1\n+2301\t21\n+2318\t14\n+2324\t12\n+2326\t21\n+2332\t26\n+2337\t16\n+2361\t19\n+2369\t15\n+2375\t6\n+2403\t4\n+2410\t8\n+2445\t1\n+2448\t1\n+2450\t4\n+2453\t14\n+2459\t22\n+2467\t19\n+2479\t12\n+2480\t7\n+2518\t13\n+2526\t5\n+2539\t6\n+2577\t38\n+2587\t25\n+2592\t11\n+2626\t7\n+2629\t13\n+2634\t5\n+2670\t4\n+2672\t8\n+2683\t6\n+2684\t18\n+2686\t9\n+2689\t2\n+2694\t20\n+2701\t7\n+2706\t2\n+2707\t1\n+2709\t11\n+2721\t2\n+2724\t36\n+2727\t1\n+2734\t19\n+2735\t3\n+2745\t4\n+2751\t18\n+2755\t8\n+2758\t1\n+2760\t6\n+2763\t6\n+2765\t3\n+2771\t1\n+2774\t13\n+2777\t3\n+2783\t3\n+2785\t7\n+2800\t14\n+2801\t3\n+2809\t7\n+2830\t2\n+2836\t9\n+2838\t13\n+2842\t4\n+2846\t9\n+2849\t2\n+2854\t28\n+2856\t1\n+2869\t3\n+2874\t6\n+2875\t38\n+2882\t34\n+2886\t2\n+2893\t1\n+2899\t5\n+2900\t13\n+2904\t2\n+2917\t15\n+2919\t17\n+2967\t31\n+2969\t1\n+2975\t4\n+2977\t9\n+2995\t4\n+3003\t7\n+3030\t4\n+3035\t1\n+3040\t2\n+3045\t9\n+3058\t12\n+3063\t19\n+3065\t3\n+3077\t10\n+3085\t18\n+3090\t4\n+3095\t10\n+3100\t6\n+3103\t5\n+3129\t1\n+3130\t18\n+3138\t16\n+3140\t10\n+3185\t1\n+3187\t17\n+3193\t10\n+3195\t13\n+3207\t3\n+3211\t1\n+3217\t1\n+3222\t6\n+3224\t7\n+3232\t5\n+3237\t9\n+3248\t1\n+3253\t6\n+3255\t21\n+3256\t9\n+3263\t5\n+3299\t16\n+3300\t23\n+3307\t3\n+3312\t9\n+3315\t2\n+3319\t24\n+3320\t1\n+3335\t4\n+3365\t6\n+3374\t6\n+3379\t18\n+3381\t4\n+3384\t12\n+3387\t4\n+3388\t1\n+3401\t23\n+3410\t13\n+3426\t1\n+3446\t3\n+3448\t1\n+3452\t16\n+3489\t5\n+3491\t4\n+3495\t6\n+3496\t2\n+3498\t9\n+3501\t1\n+3503\t5\n+3508\t4\n+3510\t3\n+3522\t10\n+3526\t14\n+3529\t2\n+3562\t12\n+3582\t11\n+3584\t23\n+3594\t4\n+3596\t25\n+3612\t6\n+3614\t15\n+3616\t4\n+3623\t17\n+3625\t1\n+3638\t12\n+3649\t25\n+3652\t9\n+3654\t16\n+3656\t2\n+3657\t16\n+3685\t24\n+3696\t1\n+3707\t16\n+3710\t8\n+3741\t2\n+3744\t8\n+3746\t3\n+3763\t24\n+3768\t25\n+3773\t5\n+3781\t25\n+3783\t6\n+3790\t19\n+3791\t18\n+3792\t1\n+3793\t17\n+3798\t2\n+3799\t1\n+3842\t1\n+3870\t6\n+3871\t1\n+3876\t4\n+3886\t10\n+3896\t10\n+3899\t8\n+3906\t4\n+3915\t4\n+3944\t11\n+3954\t8\n+3972\t6\n+3975\t11\n+3990\t3\n+4005\t15\n+4016\t2\n+4032\t7\n+4034\t46\n+4042\t29\n+4086\t1\n+4088\t7\n+4096\t5\n+4101\t39\n+4112\t5\n+4116\t1\n+4157\t2\n+4158\t2\n+4163\t20\n+4164\t1\n+4165\t14\n+4192\t2\n+4205\t2\n+4227\t9\n+4239\t37\n+4241\t2\n+4244\t6\n+4250\t3\n+4252\t3\n+4259\t7\n+4273\t1\n+4296\t16\n+4298\t15\n+4305\t1\n+4314\t8\n+4316\t6\n+4335\t23\n+4341\t17\n+4351\t11\n+4359\t50\n+4369\t5\n+4409\t10\n+4410\t14\n+4417\t7\n+4435\t5\n+4437\t4\n+4439\t17\n+4451\t'..b'\n+15646\t3\n+15647\t2\n+15657\t2\n+15663\t1\n+15664\t6\n+15672\t3\n+15674\t4\n+15680\t15\n+15682\t6\n+15703\t6\n+15709\t4\n+15747\t8\n+15753\t3\n+15755\t4\n+15765\t1\n+15774\t1\n+15783\t11\n+15790\t7\n+15792\t2\n+15797\t4\n+15798\t2\n+15800\t4\n+15802\t5\n+15828\t2\n+15836\t5\n+15844\t5\n+15851\t4\n+15852\t5\n+15853\t1\n+15859\t31\n+15860\t4\n+15867\t10\n+15877\t1\n+15887\t1\n+15892\t5\n+15893\t1\n+15895\t11\n+15906\t1\n+15911\t2\n+15914\t1\n+15926\t1\n+15937\t3\n+15951\t1\n+15954\t2\n+15961\t14\n+15968\t5\n+15970\t6\n+15971\t1\n+15976\t5\n+15978\t1\n+15980\t1\n+16002\t4\n+16012\t6\n+16016\t2\n+16017\t6\n+16030\t2\n+16035\t2\n+16038\t9\n+16043\t6\n+16045\t8\n+16051\t6\n+16053\t4\n+16059\t3\n+16061\t1\n+16066\t7\n+16067\t1\n+16101\t2\n+16128\t11\n+16130\t1\n+16131\t9\n+16168\t5\n+16179\t1\n+16186\t13\n+16189\t7\n+16194\t1\n+16196\t5\n+16197\t3\n+16219\t2\n+16232\t4\n+16233\t1\n+16271\t1\n+16290\t5\n+16296\t2\n+16298\t3\n+16302\t3\n+16304\t12\n+16305\t2\n+16311\t16\n+16322\t1\n+16325\t7\n+16328\t1\n+16335\t1\n+16348\t2\n+16352\t7\n+16355\t18\n+16358\t10\n+16359\t1\n+16360\t5\n+16362\t1\n+16383\t1\n+16391\t5\n+16392\t4\n+16394\t3\n+16402\t3\n+16409\t3\n+16411\t4\n+16412\t1\n+16414\t1\n+16420\t1\n+16429\t2\n+16434\t5\n+16435\t2\n+16470\t3\n+16471\t4\n+16495\t16\n+16503\t3\n+16524\t5\n+16550\t5\n+16560\t2\n+16563\t1\n+16592\t6\n+16593\t6\n+16594\t6\n+16600\t6\n+16602\t2\n+16607\t4\n+16608\t2\n+16610\t1\n+16616\t7\n+16617\t1\n+16618\t14\n+16620\t25\n+16626\t25\n+16628\t24\n+16630\t16\n+16638\t20\n+16650\t2\n+16654\t2\n+16664\t20\n+16665\t6\n+16672\t17\n+16683\t10\n+16691\t1\n+16692\t6\n+16693\t5\n+16701\t3\n+16702\t8\n+16707\t25\n+16708\t1\n+16709\t5\n+16710\t8\n+16714\t2\n+16715\t3\n+16719\t13\n+16726\t4\n+16728\t14\n+16730\t7\n+16732\t5\n+16734\t5\n+16736\t12\n+16741\t7\n+16749\t22\n+16759\t11\n+16776\t5\n+16786\t1\n+16789\t4\n+16794\t20\n+16796\t30\n+16799\t23\n+16801\t22\n+16804\t21\n+16816\t6\n+16817\t2\n+16819\t10\n+16826\t1\n+16842\t13\n+16850\t1\n+16856\t10\n+16859\t6\n+16861\t13\n+16863\t17\n+16869\t8\n+16872\t2\n+16876\t10\n+16880\t1\n+16886\t30\n+16887\t3\n+16894\t114\n+16896\t12\n+16907\t4\n+16912\t45\n+16914\t10\n+16917\t15\n+16919\t8\n+16926\t8\n+16927\t44\n+16929\t17\n+16931\t15\n+16933\t9\n+16934\t5\n+16935\t11\n+16938\t11\n+16939\t70\n+16941\t58\n+16943\t9\n+16946\t22\n+16949\t145\n+16951\t3\n+16956\t37\n+16958\t9\n+16959\t12\n+16960\t21\n+16962\t8\n+16964\t143\n+16966\t15\n+16967\t13\n+16968\t9\n+16969\t17\n+16975\t9\n+16980\t11\n+16981\t12\n+16989\t1\n+17004\t7\n+17013\t14\n+17015\t20\n+17018\t20\n+17020\t19\n+17021\t6\n+17026\t30\n+17030\t15\n+17034\t24\n+17035\t9\n+17038\t15\n+17040\t82\n+17046\t21\n+17047\t18\n+17048\t27\n+17054\t1\n+17057\t23\n+17058\t13\n+17059\t25\n+17062\t5\n+17065\t27\n+17072\t19\n+17078\t1\n+17094\t20\n+17095\t10\n+17096\t3\n+17103\t29\n+17109\t13\n+17110\t2\n+17111\t2\n+17128\t6\n+17164\t8\n+17174\t6\n+17184\t2\n+17192\t8\n+17218\t22\n+17222\t39\n+17227\t13\n+17233\t1\n+17267\t1\n+17274\t52\n+17282\t5\n+17287\t3\n+17294\t1\n+17295\t2\n+17296\t12\n+17297\t1\n+17298\t7\n+17302\t3\n+17303\t13\n+17304\t16\n+17305\t2\n+17307\t1\n+17309\t33\n+17310\t33\n+17311\t11\n+17316\t17\n+17317\t17\n+17318\t21\n+17321\t15\n+17326\t1\n+17328\t1\n+17329\t13\n+17330\t16\n+17331\t2\n+17337\t10\n+17338\t26\n+17345\t2\n+17352\t2\n+17354\t1\n+17360\t2\n+17373\t2\n+17375\t14\n+17381\t4\n+17449\t27\n+17488\t6\n+17508\t12\n+17516\t30\n+17524\t1\n+17531\t20\n+17539\t25\n+17544\t1\n+17549\t2\n+17554\t10\n+17559\t4\n+17562\t9\n+17571\t2\n+17572\t1\n+17573\t5\n+17574\t2\n+17585\t1\n+17587\t8\n+17588\t2\n+17591\t10\n+17596\t3\n+17598\t12\n+17599\t9\n+17607\t4\n+17626\t5\n+17628\t11\n+17633\t17\n+17636\t22\n+17673\t3\n+17714\t3\n+17722\t21\n+17734\t6\n+17746\t4\n+17755\t2\n+17773\t1\n+17812\t7\n+17820\t39\n+17832\t2\n+17835\t2\n+17840\t11\n+17845\t22\n+17860\t2\n+17862\t1\n+17869\t1\n+17887\t13\n+17908\t1\n+17916\t5\n+17924\t1\n+17932\t1\n+17964\t1\n+17967\t1\n+17980\t10\n+17986\t7\n+17997\t11\n+17999\t13\n+18006\t2\n+18014\t40\n+18021\t12\n+18029\t12\n+18036\t1\n+18043\t1\n+18061\t2\n+18073\t16\n+18084\t13\n+18086\t1\n+18087\t2\n+18089\t7\n+18092\t9\n+18097\t2\n+18102\t10\n+18104\t5\n+18107\t11\n+18108\t13\n+18112\t12\n+18118\t2\n+18127\t26\n+18129\t5\n+18137\t2\n+18145\t14\n+18166\t22\n+18189\t10\n+18226\t7\n+18249\t8\n+18250\t23\n+18255\t14\n+18256\t9\n+18257\t3\n+18261\t7\n+18293\t10\n+18302\t1\n+18313\t5\n+18316\t2\n+18334\t3\n+18342\t7\n+18359\t2\n+18370\t20\n+18395\t1\n+18400\t15\n+18403\t5\n+18408\t1\n+18413\t5\n+18444\t8\n+18452\t13\n+18470\t11\n+18494\t5\n+18532\t1\n+18540\t2\n+18548\t9\n+18556\t2\n+18566\t17\n+18586\t14\n+18588\t1\n+18593\t10\n+18598\t25\n+18599\t1\n+18607\t2\n+18612\t4\n+18613\t10\n+18621\t20\n+18623\t2\n+18655\t10\n+18670\t3\n+18674\t8\n+18682\t59\n+18688\t1\n+18699\t1\n+18708\t1\n+18712\t20\n+18716\t13\n+18717\t2\n+18731\t3\n' |
| b |
| diff -r d605800d956c -r c1751dfb4d94 test-data/transit-in1-rep1.wig --- a/test-data/transit-in1-rep1.wig Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/transit-in1-rep1.wig Tue Oct 08 08:25:10 2019 -0400 |
| b |
| b'@@ -1998,72610 +1998,3 @@\n 109197 0\n 109215 0\n 109226 0\n-109244 0\n-109285 0\n-109292 58\n-109317 0\n-109410 39\n-109521 18\n-109822 182\n-109824 0\n-109916 121\n-110017 0\n-110040 0\n-110060 0\n-110074 0\n-110076 2\n-110094 0\n-110149 26\n-110199 0\n-110221 0\n-110315 368\n-110340 0\n-110424 0\n-110473 0\n-110574 0\n-110600 0\n-110711 1\n-110916 162\n-110929 0\n-110958 0\n-110970 0\n-111013 0\n-111083 0\n-111148 41\n-111211 0\n-111405 0\n-111528 57\n-111578 0\n-111726 0\n-111749 0\n-111822 0\n-111938 0\n-112087 0\n-112112 0\n-112173 8\n-112273 0\n-112324 0\n-112338 0\n-112502 0\n-112513 404\n-112703 0\n-112777 0\n-112906 94\n-112922 332\n-112926 2\n-112970 0\n-112992 0\n-113033 69\n-113095 0\n-113113 111\n-113133 2\n-113166 91\n-113174 0\n-113227 0\n-113395 0\n-113462 0\n-113517 51\n-113571 178\n-113580 47\n-113652 0\n-113675 14\n-113712 0\n-113827 107\n-113924 41\n-114033 0\n-114049 64\n-114229 0\n-114251 0\n-114285 0\n-114326 142\n-114437 0\n-114512 0\n-114558 323\n-114589 0\n-114705 185\n-114850 6\n-114858 0\n-114903 72\n-114912 136\n-114926 11\n-115035 45\n-115078 196\n-115297 155\n-115305 0\n-115339 0\n-115418 4\n-115435 0\n-115461 344\n-115491 0\n-115563 493\n-115650 137\n-115702 0\n-115717 198\n-115753 204\n-115761 0\n-115816 92\n-115836 0\n-115858 32\n-115926 0\n-115934 187\n-115944 0\n-116075 0\n-116098 74\n-116152 36\n-116320 22\n-116364 5\n-116474 0\n-116649 0\n-116708 0\n-116733 249\n-116803 51\n-116847 0\n-116955 6\n-117014 0\n-117039 2\n-117168 0\n-117197 0\n-117213 270\n-117240 0\n-117247 0\n-117380 0\n-117504 34\n-117517 0\n-117537 0\n-117551 0\n-117622 132\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 84\n-119916 0\n-119936 0\n-120045 83\n-120121 2\n-120256 553\n-120310 0\n-120410 1\n-120574 0\n-120626 49\n-120791 0\n-120882 0\n-120892 24\n-120902 59\n-120940 325\n-120989 0\n-121171 0\n-121181 0\n-121251 0\n-121291 42\n-121391 61\n-121397 22\n-121442 0\n-121500 105\n-121548 64\n-121766 367\n-121770 279\n-121856 154\n-121916 0\n-121950 108\n-122045 26\n-122104 22\n-122193 0\n-122211 20\n-122220 0\n-122231 0\n-122243 0\n-122304 58\n-122388 50\n-122444 0\n-122494 0\n-122542 208\n-122566 0\n-122596 18\n-122609 131\n-122643 144\n-122655 11\n-122696 144\n-122764 0\n-122834 53\n-122836 39\n-122992 54\n-123012 39\n-123049 269\n-123122 0\n-123221 0\n-123243 0\n-123346 165\n-123470 0\n-123493 0\n-123520 0\n-123522 75\n-123612 184\n-123671 0\n-123772 1\n-123829 9\n-123873 0\n-123896 194\n-123906 291\n-123910 351\n-123912 0\n-124145 0\n-124149 179\n-124152 0\n-124168 0\n-124219 0\n-124298 0\n-124327 0\n-124343 0\n-124362 0\n-124379 1\n-124390 0\n-124603 0\n-124722 0\n-124786 0\n-125015 22\n-125021 61\n-125292 42\n-125337 56\n-125371 0\n-125377 17\n-125469 55\n-125579 0\n-125592 0\n-125605 38\n-125620 34\n-125644 52\n-125659 310\n-125666 406\n-125823 0\n-125843 0\n-125940 0\n-126059 0\n-126098 179\n-126163 0\n-126431 0\n-126693 0\n-126812 0\n-126829 0\n-126963 6\n-127059 0\n-127096 0\n-127119 0\n-127157 0\n-127160 0\n-127181 0\n-127232 0\n-127335 0\n-127344 0\n-127392 65\n-127503 0\n-127731 1\n-127839 0\n-127853 0\n-128018 0\n-128025 0\n-128073 2\n-128109 14\n-128148 0\n-128154 75\n-128165 192\n-128305 43\n-128379 0\n-128389 0\n-128616 0\n-128697 56\n-128777 97\n-128820 0\n-128904 23\n-128983 41\n-129116 0\n-129184 0\n-129231 2\n-129269 0\n-129321 77\n-129396 39\n-129431 0\n-129496 620\n-129708 0\n-129789 0\n-129812 0\n-129827 0\n-129860 52\n-129888 41\n-129969 0\n-130019 32\n-130074 211\n-130107 404\n-130130 0\n-130263 0\n-130353 0\n-130491 117\n-130558 142\n-130564 0\n-130573 4\n-130587 254\n-130602 0\n-130616 186\n-130699 504\n-130708 0\n-130787 0\n-130929 0\n-131037 261\n-131140 81\n-131149 0\n-131158 5\n-131328 97\n-131341 80\n-131441 0\n-131497 0\n-131542 0\n-131553 0\n-131565 0\n-131640 0\n-131740 26\n-131776 0\n-131867 0\n-131894 0\n-131929 68\n-132047 0\n-132077 0\n-132137 0\n-132276 9\n-132284 0\n-132353 0\n-132374 0\n-'..b'91253 0\n-4391265 69\n-4391329 71\n-4391395 254\n-4391430 0\n-4391592 0\n-4391599 158\n-4391632 22\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 4\n-4393177 80\n-4393219 2\n-4393222 13\n-4393301 38\n-4393372 18\n-4393408 98\n-4393429 0\n-4393436 70\n-4393439 0\n-4393517 42\n-4393670 0\n-4393747 0\n-4393860 0\n-4393908 316\n-4393924 0\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 154\n-4398413 0\n-4398714 0\n-4398724 0\n-4398752 219\n-4398870 0\n-4398950 2\n-4398980 0\n-4399141 0\n-4399204 0\n-4399376 0\n-4399403 0\n-4399510 0\n-4399607 0\n-4399819 105\n-4399821 0\n-4399842 0\n-4399983 0\n-4400082 45\n-4400137 0\n-4400185 24\n-4400204 55\n-4400285 214\n-4400325 8\n-4400426 0\n-4400520 255\n-4400531 5\n-4400645 107\n-4400728 0\n-4400745 0\n-4400797 110\n-4400822 0\n-4400837 14\n-4400902 26\n-4401048 0\n-4401135 4\n-4401392 238\n-4401433 83\n-4401458 0\n-4401499 0\n-4401519 2\n-4401531 0\n-4401595 0\n-4401610 0\n-4401677 95\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 0\n-4402719 55\n-4402767 0\n-4402796 0\n-4402859 0\n-4402974 0\n-4403031 0\n-4403080 264\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 11\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 10\n-4405245 287\n-4405250 32\n-4405266 0\n-4405277 0\n-4405420 0\n-4405454 0\n-4405458 0\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 15\n-4407690 0\n-4407744 0\n-4407921 0\n-4407930 0\n-4407939 118\n-4407960 0\n-4407995 0\n-4408001 0\n-4408056 108\n-4408071 12\n-4408076 0\n-4408138 111\n-4408203 292\n-4408299 0\n-4408335 3\n-4408553 1\n-4408742 0\n-4408755 121\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 0\n-4410158 0\n-4410240 42\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 0\n-4411182 88\n-4411245 0\n-4411258 0\n-4411273 0\n-4411277 45\n-4411337 0\n-4411397 0\n-4411412 0\n-4411421 12\n-4411440 44\n-4411479 0\n-4411508 0\n-4411526 0\n' |
| b |
| diff -r d605800d956c -r c1751dfb4d94 test-data/transit-in1-rep2.wig --- a/test-data/transit-in1-rep2.wig Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/transit-in1-rep2.wig Tue Oct 08 08:25:10 2019 -0400 |
| b |
| b'@@ -1998,72610 +1998,3 @@\n 109197 11\n 109215 130\n 109226 0\n-109244 0\n-109285 124\n-109292 86\n-109317 16\n-109410 42\n-109521 56\n-109822 94\n-109824 0\n-109916 0\n-110017 0\n-110040 0\n-110060 0\n-110074 0\n-110076 0\n-110094 0\n-110149 92\n-110199 0\n-110221 0\n-110315 281\n-110340 177\n-110424 0\n-110473 0\n-110574 0\n-110600 0\n-110711 12\n-110916 93\n-110929 0\n-110958 0\n-110970 0\n-111013 0\n-111083 0\n-111148 65\n-111211 0\n-111405 32\n-111528 157\n-111578 0\n-111726 0\n-111749 0\n-111822 0\n-111938 0\n-112087 18\n-112112 42\n-112173 53\n-112273 22\n-112324 0\n-112338 0\n-112502 0\n-112513 129\n-112703 0\n-112777 0\n-112906 0\n-112922 1066\n-112926 147\n-112970 0\n-112992 0\n-113033 21\n-113095 47\n-113113 135\n-113133 75\n-113166 6\n-113174 0\n-113227 2\n-113395 0\n-113462 93\n-113517 293\n-113571 178\n-113580 52\n-113652 0\n-113675 4\n-113712 0\n-113827 191\n-113924 6\n-114033 0\n-114049 136\n-114229 0\n-114251 0\n-114285 77\n-114326 60\n-114437 0\n-114512 66\n-114558 296\n-114589 0\n-114705 241\n-114850 0\n-114858 0\n-114903 257\n-114912 279\n-114926 1\n-115035 64\n-115078 0\n-115297 185\n-115305 0\n-115339 0\n-115418 64\n-115435 0\n-115461 687\n-115491 22\n-115563 329\n-115650 117\n-115702 19\n-115717 182\n-115753 26\n-115761 43\n-115816 19\n-115836 0\n-115858 8\n-115926 0\n-115934 168\n-115944 0\n-116075 0\n-116098 40\n-116152 17\n-116320 80\n-116364 0\n-116474 0\n-116649 0\n-116708 0\n-116733 408\n-116803 78\n-116847 0\n-116955 24\n-117014 0\n-117039 35\n-117168 11\n-117197 0\n-117213 489\n-117240 0\n-117247 0\n-117380 0\n-117504 114\n-117517 107\n-117537 4\n-117551 0\n-117622 158\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 9\n-119916 0\n-119936 0\n-120045 194\n-120121 147\n-120256 387\n-120310 34\n-120410 0\n-120574 0\n-120626 24\n-120791 30\n-120882 0\n-120892 34\n-120902 40\n-120940 429\n-120989 127\n-121171 0\n-121181 0\n-121251 140\n-121291 34\n-121391 77\n-121397 85\n-121442 22\n-121500 12\n-121548 342\n-121766 941\n-121770 156\n-121856 205\n-121916 81\n-121950 166\n-122045 58\n-122104 47\n-122193 26\n-122211 182\n-122220 43\n-122231 0\n-122243 0\n-122304 0\n-122388 13\n-122444 0\n-122494 0\n-122542 303\n-122566 37\n-122596 447\n-122609 127\n-122643 53\n-122655 28\n-122696 279\n-122764 47\n-122834 821\n-122836 249\n-122992 92\n-123012 17\n-123049 245\n-123122 131\n-123221 0\n-123243 111\n-123346 570\n-123470 0\n-123493 0\n-123520 0\n-123522 299\n-123612 272\n-123671 0\n-123772 1\n-123829 96\n-123873 0\n-123896 337\n-123906 787\n-123910 497\n-123912 0\n-124145 7\n-124149 358\n-124152 0\n-124168 35\n-124219 0\n-124298 89\n-124327 0\n-124343 0\n-124362 0\n-124379 55\n-124390 0\n-124603 100\n-124722 0\n-124786 435\n-125015 19\n-125021 54\n-125292 18\n-125337 0\n-125371 0\n-125377 193\n-125469 164\n-125579 0\n-125592 0\n-125605 2\n-125620 26\n-125644 0\n-125659 115\n-125666 241\n-125823 178\n-125843 0\n-125940 0\n-126059 0\n-126098 143\n-126163 0\n-126431 0\n-126693 0\n-126812 0\n-126829 77\n-126963 49\n-127059 0\n-127096 0\n-127119 0\n-127157 0\n-127160 0\n-127181 0\n-127232 0\n-127335 0\n-127344 0\n-127392 419\n-127503 230\n-127731 81\n-127839 0\n-127853 0\n-128018 0\n-128025 0\n-128073 10\n-128109 159\n-128148 0\n-128154 0\n-128165 273\n-128305 141\n-128379 0\n-128389 14\n-128616 16\n-128697 0\n-128777 135\n-128820 1\n-128904 74\n-128983 160\n-129116 0\n-129184 90\n-129231 105\n-129269 0\n-129321 129\n-129396 19\n-129431 0\n-129496 829\n-129708 21\n-129789 0\n-129812 0\n-129827 0\n-129860 0\n-129888 104\n-129969 0\n-130019 260\n-130074 430\n-130107 411\n-130130 0\n-130263 0\n-130353 133\n-130491 93\n-130558 31\n-130564 98\n-130573 0\n-130587 211\n-130602 0\n-130616 189\n-130699 390\n-130708 0\n-130787 0\n-130929 70\n-131037 162\n-131140 7\n-131149 4\n-131158 18\n-131328 119\n-131341 23\n-131441 0\n-131497 0\n-131542 3\n-131553 14\n-131565 47\n-131640 0\n-131740 24\n-131776 0\n-131867 0\n-131894 0\n-131929 '..b'\n-4391430 71\n-4391592 2\n-4391599 412\n-4391632 137\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 85\n-4393177 173\n-4393219 131\n-4393222 42\n-4393301 140\n-4393372 198\n-4393408 173\n-4393429 0\n-4393436 186\n-4393439 312\n-4393517 115\n-4393670 0\n-4393747 0\n-4393860 41\n-4393908 799\n-4393924 135\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 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 d605800d956c -r c1751dfb4d94 test-data/transit-in1.gff3 --- a/test-data/transit-in1.gff3 Tue Jun 25 17:44:17 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 d605800d956c -r c1751dfb4d94 test-data/transit-in1.prot --- a/test-data/transit-in1.prot Tue Jun 25 17:44:17 2019 -0400 +++ b/test-data/transit-in1.prot Tue Oct 08 08:25:10 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 d605800d956c -r c1751dfb4d94 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 08:25:10 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\n+1\t2\n+27\t3\n+33\t1\n+58\t8\n+65\t1\n+69\t1\n+77\t1\n+87\t19\n+150\t6\n+153\t4\n+166\t2\n+176\t63\n+179\t1\n+184\t76\n+187\t1\n+200\t1\n+205\t25\n+210\t17\n+215\t37\n+217\t7\n+226\t5\n+227\t4\n+238\t1\n+244\t2\n+252\t5\n+256\t18\n+283\t3\n+286\t4\n+291\t9\n+293\t1\n+301\t10\n+326\t24\n+327\t10\n+334\t4\n+341\t1\n+342\t14\n+344\t4\n+358\t14\n+363\t1\n+366\t13\n+415\t28\n+423\t22\n+431\t10\n+434\t1\n+438\t10\n+439\t18\n+446\t10\n+480\t1\n+481\t3\n+506\t8\n+508\t15\n+513\t16\n+521\t1\n+526\t4\n+576\t9\n+595\t7\n+634\t9\n+640\t3\n+655\t20\n+679\t20\n+682\t1\n+683\t4\n+684\t3\n+686\t43\n+694\t2\n+701\t11\n+704\t5\n+730\t13\n+740\t10\n+745\t9\n+751\t8\n+753\t3\n+758\t2\n+760\t19\n+764\t24\n+766\t10\n+814\t7\n+840\t14\n+842\t15\n+861\t3\n+888\t4\n+896\t14\n+932\t2\n+936\t42\n+940\t21\n+951\t1\n+956\t8\n+964\t12\n+972\t7\n+1025\t8\n+1027\t15\n+1029\t51\n+1036\t9\n+1037\t75\n+1039\t3\n+1053\t7\n+1064\t2\n+1087\t1\n+1133\t15\n+1141\t84\n+1149\t1\n+1158\t8\n+1168\t22\n+1176\t17\n+1212\t1\n+1217\t18\n+1222\t12\n+1225\t5\n+1233\t2\n+1236\t6\n+1237\t3\n+1253\t1\n+1258\t1\n+1269\t1\n+1276\t18\n+1289\t1\n+1297\t7\n+1302\t4\n+1322\t7\n+1327\t4\n+1339\t1\n+1350\t1\n+1374\t3\n+1395\t5\n+1403\t14\n+1422\t12\n+1433\t13\n+1437\t1\n+1439\t11\n+1450\t3\n+1458\t8\n+1464\t45\n+1473\t1\n+1474\t3\n+1487\t8\n+1496\t1\n+1500\t8\n+1501\t6\n+1536\t6\n+1548\t2\n+1551\t18\n+1590\t90\n+1598\t50\n+1626\t45\n+1634\t13\n+1669\t8\n+1681\t1\n+1687\t1\n+1689\t11\n+1712\t42\n+1715\t7\n+1720\t54\n+1722\t1\n+1725\t4\n+1727\t1\n+1747\t17\n+1768\t6\n+1773\t6\n+1781\t14\n+1791\t8\n+1792\t3\n+1818\t21\n+1832\t4\n+1833\t24\n+1840\t4\n+1850\t8\n+1858\t9\n+1860\t33\n+1862\t33\n+1867\t26\n+1870\t1\n+1872\t2\n+1875\t4\n+1881\t13\n+1887\t4\n+1892\t11\n+1985\t10\n+1997\t20\n+1999\t18\n+2010\t2\n+2011\t4\n+2019\t11\n+2029\t6\n+2031\t2\n+2046\t6\n+2055\t4\n+2066\t12\n+2083\t7\n+2084\t2\n+2091\t7\n+2102\t18\n+2107\t13\n+2111\t11\n+2119\t5\n+2145\t36\n+2152\t19\n+2153\t3\n+2167\t7\n+2169\t2\n+2230\t6\n+2263\t11\n+2264\t12\n+2273\t2\n+2280\t5\n+2290\t4\n+2297\t1\n+2300\t2\n+2305\t11\n+2308\t14\n+2324\t5\n+2326\t9\n+2332\t12\n+2335\t1\n+2337\t16\n+2361\t4\n+2362\t14\n+2369\t6\n+2371\t4\n+2412\t1\n+2435\t1\n+2448\t7\n+2450\t9\n+2453\t11\n+2457\t9\n+2459\t3\n+2467\t20\n+2479\t11\n+2480\t22\n+2485\t9\n+2507\t6\n+2518\t2\n+2524\t2\n+2531\t14\n+2533\t9\n+2577\t21\n+2663\t13\n+2670\t9\n+2672\t2\n+2686\t1\n+2689\t8\n+2691\t2\n+2694\t12\n+2701\t11\n+2703\t17\n+2706\t8\n+2708\t7\n+2714\t17\n+2751\t5\n+2755\t1\n+2777\t5\n+2811\t6\n+2829\t1\n+2830\t1\n+2836\t18\n+2838\t1\n+2849\t9\n+2851\t4\n+2854\t45\n+2856\t1\n+2864\t7\n+2873\t8\n+2874\t20\n+2881\t3\n+2882\t2\n+2883\t31\n+2899\t2\n+2900\t8\n+2902\t1\n+2933\t10\n+2935\t1\n+2969\t11\n+3003\t1\n+3030\t9\n+3045\t8\n+3046\t21\n+3047\t5\n+3067\t38\n+3069\t5\n+3077\t17\n+3085\t2\n+3090\t25\n+3098\t21\n+3099\t26\n+3103\t1\n+3138\t11\n+3150\t13\n+3163\t4\n+3171\t13\n+3187\t6\n+3195\t1\n+3202\t14\n+3203\t10\n+3207\t8\n+3222\t13\n+3245\t39\n+3248\t23\n+3256\t3\n+3258\t2\n+3261\t7\n+3273\t1\n+3287\t10\n+3299\t11\n+3300\t46\n+3312\t1\n+3320\t16\n+3327\t13\n+3345\t14\n+3350\t6\n+3384\t10\n+3393\t12\n+3401\t2\n+3406\t9\n+3418\t1\n+3425\t13\n+3433\t1\n+3438\t1\n+3439\t21\n+3452\t23\n+3474\t1\n+3488\t13\n+3489\t1\n+3495\t2\n+3498\t5\n+3501\t8\n+3503\t6\n+3508\t5\n+3510\t10\n+3522\t18\n+3565\t16\n+3581\t3\n+3584\t21\n+3586\t12\n+3592\t4\n+3600\t25\n+3614\t4\n+3615\t7\n+3623\t1\n+3625\t16\n+3638\t12\n+3640\t3\n+3649\t19\n+3652\t14\n+3654\t17\n+3657\t5\n+3685\t7\n+3699\t11\n+3710\t15\n+3713\t13\n+3744\t9\n+3746\t8\n+3762\t8\n+3763\t14\n+3766\t9\n+3768\t3\n+3776\t15\n+3781\t17\n+3785\t10\n+3790\t15\n+3791\t9\n+3798\t20\n+3799\t21\n+3876\t10\n+3904\t11\n+3915\t1\n+3921\t12\n+3944\t5\n+3972\t11\n+3980\t19\n+3985\t1\n+4005\t1\n+4024\t1\n+4034\t20\n+4042\t34\n+4088\t3\n+4101\t29\n+4109\t4\n+4115\t9\n+4150\t1\n+4158\t6\n+4163\t13\n+4170\t4\n+4173\t31\n+4181\t8\n+4192\t1\n+4196\t4\n+4197\t13\n+4204\t13\n+4210\t1\n+4223\t12\n+4239\t14\n+4242\t17\n+4247\t20\n+4249\t3\n+4252\t1\n+4273\t4\n+4296\t1\n+4298\t10\n+4316\t12\n+4335\t39\n+4351\t15\n+4352\t16\n+4359\t13\n+4360\t26\n+4369\t13\n+4406\t18\n+4409\t14\n+4426\t2\n+4438\t13\n+4439\t8\n+4450\t3\n+4451\t6\n+4459\t6\n+4473\t1\n+4546\t3\n+4551\t2\n+4553\t6\n+4557\t14\n+4576\t3\n+4588\t31\n+4594\t1\n+4596\t9\n+4597\t15\n+4601\t6\n+4604\t1\n+4609\t1\n+4618\t32\n+4623\t16\n+4633\t18\n+4639\t9\n+4644\t21\n+4645\t3\n+4648\t1\n+4655\t9\n+4664\t5\n+4672\t24\n+4674\t1\n+4705\t9\n+4710\t18\n+4713\t13\n+4718\t5\n+4720\t13\n+4728\t22\n+4765\t20\n+4778\t15\n+4784\t1\n+4786\t10\n+4795\t16\n+4805\t1\n+4808\t14\n+4815\t11\n+4817\t1\n+4822\t12\n+4830\t9\n+4832\t27\n+4834\t1\n+4837\t2\n+4843\t5\n+4845\t8\n+4848\t8\n+4851\t10\n+4864\t1\n+4882\t13\n+4886\t1\n+4895\t7\n+4908\t3\n+4918\t18\n+4919\t27\n+4920\t3\n+4932\t5\n+4950\t12\n+4953\t1\n+4961\t4\n+4982\t1\n+4992\t8\n+5000\t10\n+5009\t12\n+5020\t17\n+5040\t11\n+5046\t3\n+5156\t1\n+5166\t14\n+5167\t14\n+5169\t12\n+5175\t'..b'6560\t4\n+16579\t3\n+16584\t4\n+16585\t7\n+16597\t4\n+16600\t8\n+16607\t1\n+16608\t10\n+16610\t1\n+16616\t12\n+16618\t30\n+16620\t23\n+16624\t5\n+16626\t34\n+16628\t25\n+16630\t15\n+16638\t16\n+16650\t17\n+16664\t29\n+16671\t1\n+16672\t4\n+16677\t1\n+16686\t6\n+16693\t1\n+16701\t3\n+16702\t23\n+16707\t38\n+16709\t5\n+16710\t7\n+16715\t3\n+16717\t1\n+16719\t26\n+16726\t1\n+16727\t6\n+16728\t15\n+16732\t5\n+16741\t13\n+16742\t4\n+16747\t13\n+16749\t14\n+16753\t3\n+16759\t22\n+16768\t3\n+16776\t2\n+16781\t11\n+16791\t8\n+16794\t1\n+16796\t11\n+16801\t2\n+16814\t1\n+16818\t2\n+16821\t5\n+16829\t8\n+16842\t3\n+16853\t16\n+16861\t16\n+16872\t1\n+16880\t8\n+16886\t26\n+16887\t8\n+16894\t83\n+16899\t1\n+16904\t10\n+16907\t3\n+16913\t20\n+16914\t3\n+16917\t1\n+16919\t6\n+16920\t15\n+16921\t2\n+16925\t1\n+16926\t18\n+16927\t77\n+16928\t5\n+16929\t33\n+16931\t37\n+16933\t1\n+16935\t25\n+16937\t26\n+16939\t40\n+16941\t88\n+16943\t13\n+16946\t18\n+16948\t11\n+16949\t147\n+16951\t45\n+16955\t2\n+16956\t35\n+16958\t6\n+16959\t18\n+16964\t111\n+16966\t7\n+16967\t8\n+16968\t1\n+16969\t1\n+16974\t6\n+16975\t11\n+16977\t26\n+16985\t2\n+16986\t10\n+16989\t7\n+17002\t9\n+17004\t5\n+17013\t9\n+17015\t1\n+17016\t1\n+17018\t2\n+17020\t22\n+17023\t5\n+17026\t31\n+17028\t7\n+17030\t3\n+17031\t9\n+17034\t44\n+17035\t22\n+17038\t8\n+17040\t68\n+17042\t7\n+17046\t3\n+17047\t11\n+17048\t56\n+17052\t3\n+17057\t35\n+17065\t45\n+17067\t7\n+17070\t12\n+17072\t26\n+17078\t10\n+17079\t16\n+17089\t15\n+17095\t12\n+17103\t7\n+17109\t30\n+17118\t13\n+17181\t9\n+17218\t1\n+17228\t23\n+17230\t19\n+17234\t1\n+17241\t1\n+17244\t5\n+17272\t10\n+17274\t52\n+17275\t1\n+17282\t1\n+17289\t12\n+17294\t4\n+17295\t17\n+17296\t4\n+17297\t4\n+17302\t6\n+17303\t33\n+17305\t20\n+17309\t18\n+17310\t28\n+17311\t7\n+17316\t7\n+17317\t34\n+17318\t23\n+17321\t3\n+17324\t1\n+17329\t27\n+17330\t28\n+17331\t10\n+17338\t17\n+17357\t2\n+17360\t1\n+17375\t6\n+17449\t25\n+17508\t24\n+17516\t36\n+17524\t17\n+17528\t7\n+17529\t9\n+17531\t3\n+17539\t6\n+17562\t9\n+17566\t6\n+17569\t1\n+17572\t2\n+17574\t13\n+17585\t9\n+17587\t7\n+17588\t1\n+17591\t22\n+17598\t14\n+17606\t6\n+17608\t4\n+17614\t6\n+17618\t1\n+17626\t6\n+17628\t11\n+17629\t14\n+17633\t7\n+17636\t31\n+17641\t19\n+17686\t29\n+17714\t1\n+17724\t5\n+17746\t13\n+17754\t6\n+17755\t1\n+17759\t7\n+17767\t2\n+17781\t11\n+17786\t6\n+17791\t1\n+17812\t9\n+17820\t39\n+17825\t7\n+17835\t12\n+17862\t7\n+17868\t20\n+17887\t5\n+17899\t17\n+17903\t8\n+17909\t5\n+17911\t8\n+17924\t3\n+17932\t5\n+17964\t2\n+17968\t17\n+17986\t5\n+17989\t15\n+17997\t1\n+18006\t15\n+18013\t1\n+18014\t41\n+18021\t1\n+18029\t9\n+18035\t2\n+18036\t19\n+18041\t11\n+18061\t4\n+18069\t1\n+18081\t1\n+18082\t11\n+18089\t23\n+18092\t7\n+18094\t11\n+18102\t8\n+18104\t4\n+18108\t13\n+18111\t7\n+18124\t9\n+18127\t3\n+18129\t48\n+18135\t1\n+18139\t2\n+18145\t8\n+18149\t9\n+18161\t5\n+18174\t1\n+18232\t22\n+18255\t11\n+18256\t4\n+18265\t1\n+18310\t1\n+18313\t5\n+18346\t7\n+18352\t3\n+18359\t11\n+18395\t3\n+18400\t18\n+18405\t3\n+18443\t2\n+18444\t3\n+18450\t5\n+18452\t21\n+18458\t6\n+18518\t12\n+18532\t11\n+18535\t1\n+18548\t24\n+18550\t4\n+18556\t7\n+18598\t1\n+18618\t2\n+18662\t12\n+18670\t3\n+18672\t15\n+18674\t1\n+18675\t21\n+18682\t9\n+18706\t7\n+18708\t5\n+18722\t3\n+18730\t4\n+18760\t1\n+18764\t4\n+18771\t8\n+18772\t12\n+18776\t9\n+18787\t1\n+18795\t13\n+18820\t31\n+18823\t6\n+18828\t2\n+18833\t5\n+18843\t7\n+18849\t11\n+18878\t2\n+18884\t13\n+18886\t10\n+18889\t9\n+18897\t41\n+18917\t3\n+18923\t26\n+18924\t1\n+18925\t26\n+18939\t10\n+18968\t15\n+18970\t6\n+18979\t1\n+18995\t7\n+19011\t3\n+19014\t7\n+19016\t1\n+19019\t11\n+19026\t5\n+19030\t3\n+19040\t10\n+19045\t9\n+19046\t7\n+19047\t8\n+19048\t33\n+19051\t5\n+19052\t16\n+19053\t22\n+19065\t7\n+19067\t3\n+19073\t3\n+19075\t14\n+19081\t1\n+19096\t5\n+19105\t3\n+19108\t5\n+19139\t8\n+19147\t14\n+19151\t2\n+19162\t2\n+19170\t21\n+19176\t12\n+19177\t20\n+19178\t25\n+19185\t11\n+19190\t17\n+19194\t17\n+19197\t11\n+19202\t3\n+19231\t1\n+19235\t7\n+19238\t25\n+19240\t10\n+19265\t12\n+19284\t60\n+19300\t2\n+19312\t12\n+19325\t5\n+19349\t3\n+19350\t4\n+19389\t1\n+19408\t10\n+19419\t13\n+19421\t7\n+19424\t1\n+19427\t7\n+19434\t8\n+19438\t1\n+19441\t2\n+19447\t2\n+19449\t1\n+19455\t23\n+19457\t1\n+19463\t29\n+19472\t2\n+19481\t6\n+19509\t11\n+19513\t4\n+19515\t6\n+19518\t1\n+19519\t8\n+19520\t8\n+19523\t18\n+19537\t8\n+19548\t22\n+19551\t3\n+19553\t22\n+19556\t3\n+19558\t6\n+19561\t5\n+19571\t2\n+19574\t3\n+19579\t27\n+19582\t15\n+19591\t5\n+19603\t4\n+19613\t1\n+19616\t12\n+19621\t1\n+19641\t5\n+19643\t15\n+19645\t2\n+19650\t11\n+19660\t26\n+19663\t1\n+19671\t3\n+19674\t3\n+19681\t12\n+19694\t1\n+19695\t6\n+19699\t1\n+19700\t1\n+19706\t15\n+19711\t3\n+19714\t13\n+19716\t11\n+19720\t12\n+19722\t3\n+19724\t16\n+19738\t14\n+19764\t19\n+19781\t23\n+19786\t26\n+19807\t6\n' |
| b |
| diff -r d605800d956c -r c1751dfb4d94 test-data/transit_tn5.prot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit_tn5.prot Tue Oct 08 08:25:10 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" |