| Next changeset 1:d605800d956c (2019-06-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1 |
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added:
convert_gff.xml gff_to_prot.py 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.gff3 test-data/transit-in1.prot |
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| diff -r 000000000000 -r 99810cf51f2e convert_gff.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert_gff.xml Mon Apr 22 14:42:21 2019 -0400 |
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| @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool id="gff_to_prot" name="Convert GFF3" version="1.0.0"> + <description>to prot_table for TRANSIT</description> + <macros> + <import>macros.xml</import> + </macros> + <command detect_errors="exit_code">$__tool_directory__/gff_to_prot.py '$input' '$output'</command> + <inputs> + <param name="input" type="data" format="gff3" label="GenBank GFF file" /> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input" ftype="gff3" value="gff_to_prot-in1.gff3" /> + <output name="output" file="gff_to_prot-out1.txt" /> + </test> + </tests> + + <help> +<![CDATA[ +.. class:: infomark + + +**What it does** + +------------------- + +Convert Gff3 files coming from Genbank in prot_table file that can be used as an input for TRANSIT tools. + +]]></help> + <expand macro="citations" /> + +</tool> |
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| diff -r 000000000000 -r 99810cf51f2e gff_to_prot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff_to_prot.py Mon Apr 22 14:42:21 2019 -0400 |
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| @@ -0,0 +1,65 @@ +#!/usr/bin/env python +import csv +import os +import sys + + +def get_description(line, parent): + cols = line.split('\t') + labels = {} + for pair in cols[8].split(";"): + k, v = pair.split('=') + labels[k] = v + + if (cols[2]) == "CDS" and labels["Parent"] == parent: + return labels.get("Note", '-') + return '-' + + +def convert_to_prot_table(fname, output_name): + gff_file = open(fname) + output_file = open(output_name, 'w') + writer = csv.writer(output_file, delimiter='\t') + lines = gff_file.readlines() + gff_file.close() + for i, line in enumerate(lines): + line = line.strip() + if line.startswith('#'): + continue + cols = line.split('\t') + if (len(cols) < 9): + print("Ignoring invalid row with entries: {0}".format(cols)) + elif (cols[2]) == "region": + continue + elif (cols[2]) == "CDS": + continue + elif (cols[2]) == "gene": + start = int(cols[3]) + end = int(cols[4]) + strand = cols[6].strip() + labels = {} + diff = int(abs(end - start) / 3) # What is this called? + for pair in cols[8].split(";"): + k, v = pair.split('=') + labels[k.strip()] = v.strip() + + Rv = labels["locus_tag"].strip() # error out if not found + gene = labels.get('Name', '') + desc = get_description(lines[i + 1], labels.get("ID", "")) if (i + 1) < len(lines) else '-' + vals = [desc, start, end, strand, diff, '-', '-', gene, Rv, '-'] + writer.writerow(vals) + output_file.close() + + +if __name__ == "__main__": + usage_string = "Usage: python gff-prot-converter.py <gff filename> <output filename>" + + if len(sys.argv) < 3: + print(usage_string) + sys.exit(0) + file_name = sys.argv[1] + if not os.path.exists(file_name): + print("File not found. Exiting...") + print(usage_string) + sys.exit(0) + convert_to_prot_table(file_name, sys.argv[2]) |
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| diff -r 000000000000 -r 99810cf51f2e macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 22 14:42:21 2019 -0400 |
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| @@ -0,0 +1,68 @@ +<?xml version="1.0"?> +<macros> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1004401</citation> + <yield /> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">transit</requirement> + <yield /> + </requirements> + </xml> + <token name="@VERSION@">2.3.3</token> + <xml name="outputs"> + <yield /> + <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> + </xml> + <xml name="replicates"> + <param name="replicates" type="select" label="How to handle replicates"> + <option value="Mean">Mean</option> + <option value="Sum">Sum</option> + </param> + </xml> + <xml name="inputs"> + <conditional name="mode"> + <param name="replicates" type="select" label="Operation mode" help="If set to 'Batch', transit will run and produce one output for each input file. If set to 'Replicates', transit will run once on all the input files."> + <option value="Batch">Batch</option> + <option value="Replicates">Replicates</option> + </param> + <when value="Batch"> + <param name="inputs" type="data" format="wig,tabular" multiple="false" label="Input .wig files" /> + </when> + <when value="Replicates"> + <param name="inputs" type="data" format="wig,tabular" multiple="true" label="Input .wig files" /> + </when> + </conditional> + <yield /> + <param name="annotation" type="data" format="gff3,tabular" label="Input annotation" /> + </xml> + <xml name="ignore_tas"> + <param name="nterm" argument="-iN" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the N terminus." /> + <param name="cterm" argument="-iC" type="float" value="0" min="0" max="1" label="Ignore TAs occuring at given fraction of the C terminus." /> + </xml> + <xml name="standard_inputs"> + <expand macro="inputs" /> + <yield /> + <expand macro="ignore_tas" /> + </xml> + <token name="@LINK_INPUTS@"> + <![CDATA[ + #if str($mode.replicates) == 'Batch': + #set $input_files = $mode.inputs + #else: + #set $input_files = ','.join(['input_file_%d.wig' % idx for idx, _ in enumerate(str($mode.inputs).split(','))]) + #for idx, filename in enumerate(str($mode.inputs).split(',')): + ln -s '$filename' input_file_${idx}.wig && + #end for + #end if + ln -s '$annotation' annotation.dat && + ]]> + </token> + <token name="@STANDARD_OPTIONS@"> + -iN $nterm + -tC $cterm + </token> +</macros> |
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| diff -r 000000000000 -r 99810cf51f2e test-data/gff_to_prot-in1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff_to_prot-in1.gff3 Mon Apr 22 14:42:21 2019 -0400 |
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| b'@@ -0,0 +1,5799 @@\n+##sequence-region NC_007795.1 1 2821361\n+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=93061\n+NC_007795.1\tRefSeq\tregion\t1\t2821361\t.\t+\t.\tID=NC_007795.1:1..2821361;Dbxref=taxon:93061;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=NCTC 8325;sub-species=aureus\n+NC_007795.1\tRefSeq\tgene\t517\t1878\t.\t+\t.\tID=gene-SAOUHSC_00001;Dbxref=GeneID:3919798;Name=dnaA;gbkey=Gene;gene=dnaA;gene_biotype=protein_coding;locus_tag=SAOUHSC_00001\n+NC_007795.1\tRefSeq\tCDS\t517\t1878\t.\t+\t0\tID=cds-YP_498609.1;Parent=gene-SAOUHSC_00001;Dbxref=Genbank:YP_498609.1,GeneID:3919798;Name=YP_498609.1;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.;gbkey=CDS;gene=dnaA;product=chromosomal replication initiation protein;protein_id=YP_498609.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t2156\t3289\t.\t+\t.\tID=gene-SAOUHSC_00002;Dbxref=GeneID:3919799;Name=SAOUHSC_00002;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00002\n+NC_007795.1\tRefSeq\tCDS\t2156\t3289\t.\t+\t0\tID=cds-YP_498610.1;Parent=gene-SAOUHSC_00002;Dbxref=Genbank:YP_498610.1,GeneID:3919799;Name=YP_498610.1;Note=binds the polymerase to DNA and acts as a sliding clamp;gbkey=CDS;product=DNA polymerase III subunit beta;protein_id=YP_498610.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t3670\t3915\t.\t+\t.\tID=gene-SAOUHSC_00003;Dbxref=GeneID:3919176;Name=SAOUHSC_00003;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00003\n+NC_007795.1\tRefSeq\tCDS\t3670\t3915\t.\t+\t0\tID=cds-YP_498611.1;Parent=gene-SAOUHSC_00003;Dbxref=Genbank:YP_498611.1,GeneID:3919176;Name=YP_498611.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498611.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t3912\t5024\t.\t+\t.\tID=gene-SAOUHSC_00004;Dbxref=GeneID:3919177;Name=recF;gbkey=Gene;gene=recF;gene_biotype=protein_coding;locus_tag=SAOUHSC_00004\n+NC_007795.1\tRefSeq\tCDS\t3912\t5024\t.\t+\t0\tID=cds-YP_498612.1;Parent=gene-SAOUHSC_00004;Dbxref=Genbank:YP_498612.1,GeneID:3919177;Name=YP_498612.1;Note=Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA;gbkey=CDS;gene=recF;product=recombination protein F;protein_id=YP_498612.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t5034\t6968\t.\t+\t.\tID=gene-SAOUHSC_00005;Dbxref=GeneID:3919178;Name=SAOUHSC_00005;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00005\n+NC_007795.1\tRefSeq\tCDS\t5034\t6968\t.\t+\t0\tID=cds-YP_498613.1;Parent=gene-SAOUHSC_00005;Dbxref=Genbank:YP_498613.1,GeneID:3919178;Name=YP_498613.1;Note=DNA gyrase%2C B subunit;gbkey=CDS;product=DNA gyrase subunit B;protein_id=YP_498613.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t7005\t9668\t.\t+\t.\tID=gene-SAOUHSC_00006;Dbxref=GeneID:3919179;Name=SAOUHSC_00006;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00006\n+NC_007795.1\tRefSeq\tCDS\t7005\t9668\t.\t+\t0\tID=cds-YP_498614.1;Parent=gene-SAOUHSC_00006;Dbxref=Genbank:YP_498614.1,GeneID:3919179;Name=YP_498614.1;Note=DNA gyrase%2C A subunit;gbkey=CDS;product=DNA gyrase subunit A;protein_id=YP_498614.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t9755\t10456\t.\t-\t.\tID=gene-SAOUHSC_00007;Dbxref=GeneID:3919180;Name=SAOUHSC_00007;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00007\n+NC_007795.1\tRefSeq\tCDS\t9755\t10456\t.\t-\t0\tID=cds-YP_498615.1;Parent=gene-SAOUHSC_00007;Dbxref=Genbank:YP_498615.1,GeneID:3919180;Name=YP_498615.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498615.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t10893\t12407\t.\t+\t.\tID=gene-SAOUHSC_00008;Dbxref=GeneID:3919181;Name=SAOUHSC_00008;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00008\n+NC_007795.1\tRefSeq\tCDS\t10893\t12407\t.\t+\t0\tID=cds-YP_498616.1;Parent=gene-SAOUHSC_00008;Dbxref=Genbank:YP_498616.1,GeneID:3919181;Name=YP_498616.1;Note=catalyzes the degradation of histidine to urocanate and ammmonia;gbkey=CDS;p'..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" |
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| diff -r 000000000000 -r 99810cf51f2e test-data/gff_to_prot-out1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gff_to_prot-out1.txt Mon Apr 22 14:42:21 2019 -0400 |
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| b'@@ -0,0 +1,2842 @@\n+binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication%3B can also affect transcription of multiple genes including itself.\t517\t1878\t+\t453\t-\t-\tdnaA\tSAOUHSC_00001\t-\r\n+binds the polymerase to DNA and acts as a sliding clamp\t2156\t3289\t+\t377\t-\t-\tSAOUHSC_00002\tSAOUHSC_00002\t-\r\n+conserved hypothetical protein\t3670\t3915\t+\t81\t-\t-\tSAOUHSC_00003\tSAOUHSC_00003\t-\r\n+Required for DNA replication%3B binds preferentially to single-stranded%2C linear DNA\t3912\t5024\t+\t370\t-\t-\trecF\tSAOUHSC_00004\t-\r\n+DNA gyrase%2C B subunit\t5034\t6968\t+\t644\t-\t-\tSAOUHSC_00005\tSAOUHSC_00005\t-\r\n+DNA gyrase%2C A subunit\t7005\t9668\t+\t887\t-\t-\tSAOUHSC_00006\tSAOUHSC_00006\t-\r\n+conserved hypothetical protein\t9755\t10456\t-\t233\t-\t-\tSAOUHSC_00007\tSAOUHSC_00007\t-\r\n+catalyzes the degradation of histidine to urocanate and ammmonia\t10893\t12407\t+\t504\t-\t-\tSAOUHSC_00008\tSAOUHSC_00008\t-\r\n+catalyzes a two-step reaction%2C first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP%2C followed by transfer of the aminoacyl-adenylate to its tRNA\t12786\t14072\t+\t428\t-\t-\tSAOUHSC_00009\tSAOUHSC_00009\t-\r\n+conserved hypothetical protein\t14722\t15417\t+\t231\t-\t-\tSAOUHSC_00010\tSAOUHSC_00010\t-\r\n+conserved hypothetical protein\t15414\t15743\t+\t109\t-\t-\tSAOUHSC_00012\tSAOUHSC_00012\t-\r\n+conserved hypothetical protein\t16106\t17074\t+\t322\t-\t-\tSAOUHSC_00013\tSAOUHSC_00013\t-\r\n+conserved hypothetical protein\t17365\t18303\t+\t312\t-\t-\tSAOUHSC_00014\tSAOUHSC_00014\t-\r\n+conserved hypothetical protein\t18318\t20285\t+\t655\t-\t-\tSAOUHSC_00015\tSAOUHSC_00015\t-\r\n+in Escherichia coli this protein is wrapped around the base of the L1 stalk\t20282\t20734\t+\t150\t-\t-\trplI\tSAOUHSC_00017\t-\r\n+replicative DNA helicase\t20766\t22166\t+\t466\t-\t-\tSAOUHSC_00018\tSAOUHSC_00018\t-\r\n+catalyzes the formation of N6-(1%2C2%2C-dicarboxyethyl)-AMP from L-aspartate%2C inosine monophosphate and GTP in AMP biosynthesis\t22444\t23727\t+\t427\t-\t-\tSAOUHSC_00019\tSAOUHSC_00019\t-\r\n+-\t24157\t24231\t+\t24\t-\t-\tSAOUHSC_T00018\tSAOUHSC_T00018\t-\r\n+-\t24239\t24311\t+\t24\t-\t-\tSAOUHSC_T00011\tSAOUHSC_T00011\t-\r\n+two-component response regulator%2C putative\t24931\t25632\t+\t233\t-\t-\tSAOUHSC_00020\tSAOUHSC_00020\t-\r\n+sensory box histidine kinase VicK%2C putative\t25645\t27471\t+\t608\t-\t-\tSAOUHSC_00021\tSAOUHSC_00021\t-\r\n+conserved hypothetical protein\t27515\t28798\t+\t427\t-\t-\tSAOUHSC_00022\tSAOUHSC_00022\t-\r\n+conserved hypothetical protein\t28799\t29587\t+\t262\t-\t-\tSAOUHSC_00023\tSAOUHSC_00023\t-\r\n+conserved hypothetical protein\t29977\t30777\t+\t266\t-\t-\tSAOUHSC_00024\tSAOUHSC_00024\t-\r\n+conserved hypothetical protein\t31005\t33323\t+\t772\t-\t-\tSAOUHSC_00025\tSAOUHSC_00025\t-\r\n+conserved hypothetical protein\t33555\t34034\t-\t159\t-\t-\tSAOUHSC_00026\tSAOUHSC_00026\t-\r\n+SPOUT methyltransferase family protein%3B crystal structure shows homodimer%3B in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA\t33691\t34170\t+\t159\t-\t-\tSAOUHSC_00027\tSAOUHSC_00027\t-\r\n+-\t34375\t34509\t-\t44\t-\t-\tSAOUHSC_00028\tSAOUHSC_00028\t-\r\n+conserved hypothetical protein\t34473\t34565\t+\t30\t-\t-\tSAOUHSC_00029\tSAOUHSC_00029\t-\r\n+conserved hypothetical protein\t34712\t36457\t+\t581\t-\t-\tSAOUHSC_00030\tSAOUHSC_00030\t-\r\n+conserved hypothetical protein\t36551\t37003\t-\t150\t-\t-\tSAOUHSC_00031\tSAOUHSC_00031\t-\r\n+conserved hypothetical protein\t37019\t37120\t-\t33\t-\t-\tSAOUHSC_00032\tSAOUHSC_00032\t-\r\n+conserved hypothetical protein\t37218\t37973\t-\t251\t-\t-\tSAOUHSC_00033\tSAOUHSC_00033\t-\r\n+conserved hypothetical protein\t37973\t38233\t-\t86\t-\t-\tSAOUHSC_00034\tSAOUHSC_00034\t-\r\n+conserved hypothetical protein\t38370\t39437\t+\t355\t-\t-\tSAOUHSC_00035\tSAOUHSC_00035\t-\r\n+conserved hypothetical protein\t39468\t40802\t+\t444\t-\t-\tSAOUHSC_00036\tSAOUHSC_00036\t-\r\n+conserved hypothetical protein\t40821\t42014\t+\t397\t-\t-\tSAOUHSC_00037\tSAOUHSC_00037\t-\r\n+conserved hypothetical protein\t42281\t42382\t-\t33\t-\t-\tSAOUHSC_00038\tSAOUHSC_00038\t-\r\n+conserved hypothetical protein\t42681\t43613\t-\t310\t-\t-\tSAOUHSC_00039\tSAOUHSC_00039\t-\r\n+conserved hypothetical protein\t43976\t44179\t+\t67\t-\t-\tSAOUHSC_0'..b"Z\tSAOUHSC_03015\t-\r\n+conserved hypothetical protein\t2789402\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" |
| b |
| diff -r 000000000000 -r 99810cf51f2e test-data/gumbel-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gumbel-sites1.txt Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,4001 @@\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+#Total Iterations Performed:\t1099\n+#Sample Size:\t1000\n+#phi estimate:\t0.337057\n+#Time: 24.356441021\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+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+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+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+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+Rv0024\t-\tPUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN \t10\t12\t1\t2\t0.000000\tNE\n+Rv0025\t-\thypothetical protein Rv0025 \t7\t7\t0\t0\t0.000000\tNE\n+Rv0026\t-\thypothetical protein Rv0026 \t10\t14\t1\t2\t0.000000\tNE\n+Rv0027\t-\thypothetical protein Rv0027 \t2\t5\t2\t31\t0.000000\tNE\n+Rv0028\t-\thypothetical protein Rv0028 \t2\t5\t3\t128\t0.000000\tNE\n+Rv0029\t-\thypothetical protein Rv0029 \t15\t18\t1\t2\t0.000000\tNE\n+Rv0030\t-\thypothetical protein Rv0030 \t1\t5\t3\t86\t0.002000\tNE\n+Rv0031\t-\tPOSSIBLE REMNANT OF A TRANSPOSASE \t0\t1\t1\t2\t-1.000000\tS\n+Rv0032\tbioF2\tPOSSIBLE 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) \t29\t57\t12\t231\t0.053000\tU\n+Rv0033\tacpA\tPROBABLE ACYL CARRIER PROTEIN ACPA (ACP) \t3\t3\t0\t0\t-1.000000\tS\n+Rv0034\t-\thypothetical protein Rv0034 \t4\t5\t1\t2\t-1.000000\tS\n+Rv0035\tfadD34\tPROBABLE FATTY-ACID-CoA LIGASE FADD34 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) \t22\t25\t1\t2\t0.000000\tNE\n+Rv0036c\t-\thypothetical protein Rv0036c \t4\t4\t0\t0\t0.000000\tNE\n+Rv0037c\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t12\t20\t4\t335\t0.108000\tU\n+Rv0038\t-\thypothetical protein Rv0038 \t5\t7\t1\t2\t0.000000\tNE\n+Rv0039c\t-\tPOSSIBLE CONSERVED TRANSMEMBRANE PROTEIN \t2\t4\t2\t25\t0.000000\tNE\n+Rv0040c\tmtc28\tSECRETED PROLINE RICH PROTEIN MTC28 (PROLINE RICH 28 KDA ANTIGEN) \t5\t9\t2\t22\t0.000000\tNE\n+Rv0041\tleuS\tleucyl-tRNA synthetase \t0\t72\t72\t2800\t0.490000\tU\n+Rv0042c\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY MARR-FAMILY) \t3\t5\t1\t2\t0.000000\tNE\n+Rv0043c\t-\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) \t7\t10\t1\t2\t0.000000\tNE\n+Rv0044c\t-\tPOSSIBLE OXIDOREDUCTASE \t17\t20\t1\t2\t0.000000\tNE\n+Rv0045c\t-\tPOSSIBLE HYDROLAS'..b'NE\n+Rv3875\tesxA\t6 KDA EARLY SECRETORY ANTIGENIC TARGET ESXA (ESAT-6) \t0\t4\t4\t158\t0.965000\tU\n+Rv3876\t-\tCONSERVED HYPOTHETICAL PROLINE AND ALANINE RICH PROTEIN \t24\t25\t1\t2\t0.000000\tNE\n+Rv3877\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t23\t28\t3\t120\t0.000000\tNE\n+Rv3878\t-\tCONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t3\t5\t2\t410\t0.227000\tU\n+Rv3879c\t-\tHYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t28\t38\t3\t41\t0.000000\tNE\n+Rv3880c\t-\thypothetical protein Rv3880c \t3\t4\t1\t2\t0.000000\tNE\n+Rv3881c\t-\tCONSERVED HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN \t15\t24\t2\t68\t0.000000\tNE\n+Rv3882c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t21\t23\t1\t2\t0.000000\tNE\n+Rv3883c\tmycP1\tMEMBRANE-ANCHORED MYCOSIN MYCP1 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-1) \t15\t17\t1\t2\t0.000000\tNE\n+Rv3884c\t-\tPROBABLE CBXX/CFQX FAMILY PROTEIN \t21\t33\t4\t121\t0.000000\tNE\n+Rv3885c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t16\t27\t3\t164\t0.000000\tNE\n+Rv3886c\tmycP2\tPROBABLE ALANINE AND PROLINE RICH MEMBRANE-ANCHORED MYCOSIN MYCP2 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-2) \t18\t27\t3\t87\t0.000000\tNE\n+Rv3887c\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t21\t32\t4\t48\t0.000000\tNE\n+Rv3888c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t13\t29\t10\t213\t0.008000\tNE\n+Rv3889c\t-\thypothetical protein Rv3889c \t12\t19\t4\t203\t0.000000\tNE\n+Rv3890c\tesxC\tESAT-6 LIKE PROTEIN ESXC (ESAT-6 like protein 11) \t4\t5\t1\t2\t0.000000\tNE\n+Rv3891c\tesxD\tPOSSIBLE ESAT-6 LIKE PROTEIN ESXD \t3\t9\t3\t48\t0.000000\tNE\n+Rv3892c\tPPE69\tPPE FAMILY PROTEIN \t8\t10\t1\t2\t0.000000\tNE\n+Rv3893c\tPE36\tPE FAMILY PROTEIN \t2\t2\t0\t0\t-1.000000\tS\n+Rv3894c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t39\t51\t2\t22\t0.000000\tNE\n+Rv3895c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t12\t13\t1\t2\t0.000000\tNE\n+Rv3896c\t-\thypothetical protein Rv3896c \t13\t15\t1\t2\t0.000000\tNE\n+Rv3897c\t-\thypothetical protein Rv3897c \t6\t7\t1\t2\t0.000000\tNE\n+Rv3898c\t-\thypothetical protein Rv3898c \t6\t6\t0\t0\t0.000000\tNE\n+Rv3899c\t-\thypothetical protein Rv3899c \t12\t18\t3\t190\t0.000000\tNE\n+Rv3900c\t-\tCONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t9\t17\t4\t72\t0.000000\tNE\n+Rv3901c\t-\tPOSSIBLE MEMBRANE PROTEIN \t10\t14\t2\t11\t0.000000\tNE\n+Rv3902c\t-\thypothetical protein Rv3902c \t0\t26\t26\t516\t0.540000\tU\n+Rv3903c\t-\tHYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t29\t51\t5\t73\t0.000000\tNE\n+Rv3904c\tesxE\tPUTATIVE ESAT-6 LIKE PROTEIN ESXE (HYPOTHETICAL ALANINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 12) \t2\t3\t1\t2\t0.000000\tNE\n+Rv3905c\tesxF\tPUTATIVE ESAT-6 LIKE PROTEIN ESXF (HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 13) \t5\t5\t0\t0\t0.000000\tNE\n+Rv3906c\t-\thypothetical protein Rv3906c \t9\t10\t1\t2\t0.000000\tNE\n+Rv3907c\tpcnA\tPROBABLE POLY(A) POLYMERASE PCNA (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) (NTP POLYMERASE) (RNA ADENYLATING ENZYME) (POLY(A) POLYMERASE) \t0\t19\t19\t1337\t1.000000\tE\n+Rv3908\t-\thypothetical protein Rv3908 \t4\t11\t5\t137\t0.000000\tNE\n+Rv3909\t-\thypothetical protein Rv3909 \t0\t41\t41\t2318\t1.000000\tE\n+Rv3910\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t11\t54\t34\t1439\t0.760000\tU\n+Rv3911\tsigM\tRNA polymerase sigma factor SigM \t9\t12\t1\t2\t0.000000\tNE\n+Rv3912\t-\tHYPOTHETICAL ALANINE RICH PROTEIN \t6\t11\t2\t17\t0.000000\tNE\n+Rv3913\ttrxB2\tPROBABLE THIOREDOXIN REDUCTASE TRXB2 (TRXR) (TR) \t2\t18\t16\t869\t1.000000\tE\n+Rv3914\ttrxC\tTHIOREDOXIN TRXC (TRX) (MPT46) \t0\t5\t5\t266\t0.992000\tE\n+Rv3915\t-\tPROBABLE HYDROLASE \t0\t24\t24\t1113\t0.999000\tE\n+Rv3916c\t-\thypothetical protein Rv3916c \t1\t11\t5\t281\t0.160000\tU\n+Rv3917c\tparB\tPROBABLE CHROMOSOME PARTITIONING PROTEIN PARB \t0\t18\t18\t876\t1.000000\tE\n+Rv3918c\tparA\tPROBABLE CHROMOSOME PARTITIONING PROTEIN PARA \t1\t19\t18\t912\t1.000000\tE\n+Rv3919c\tgidB\tglucose-inhibited division protein B \t8\t13\t2\t8\t0.000000\tNE\n+Rv3920c\t-\tHYPOTHETICAL PROTEIN SIMILAR TO JAG PROTEIN \t3\t3\t0\t0\t0.000000\tNE\n+Rv3921c\t-\tputative inner membrane protein translocase component YidC \t1\t23\t22\t865\t0.999000\tE\n+Rv3922c\t-\thypothetical protein Rv3922c \t3\t12\t7\t105\t0.001000\tNE\n+Rv3923c\trnpA\tribonuclease P \t1\t4\t3\t71\t0.000000\tNE\n+Rv3924c\trpmH\t50S ribosomal protein L34 \t0\t2\t2\t12\t-1.000000\tS\n+Rvnr01\trrs\t16S rRNA\t0\t62\t62\t1455\t0.485000\tU\n' |
| b |
| diff -r 000000000000 -r 99810cf51f2e test-data/hmm-genes1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmm-genes1.txt Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,3991 @@\n+#HMM - Genes\n+Rv0001\tdnaA\tchromosomal replication initiation protein \t32\t31\t0\t1\t0\t0.0312\t89.00\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+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+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 Rv0025 \t8\t0\t0\t8\t0\t1.0000\t62.38\tNE\n+Rv0026\t-\thypothetical protein Rv0026 \t15\t0\t0\t15\t0\t0.7333\t180.45\tNE\n+Rv0027\t-\thypothetical protein Rv0027 \t5\t0\t0\t5\t0\t0.4000\t84.50\tNE\n+Rv0028\t-\thypothetical protein Rv0028 \t5\t0\t0\t5\t0\t0.4000\t110.50\tNE\n+Rv0029\t-\thypothetical protein Rv0029 \t19\t0\t0\t19\t0\t0.7895\t155.27\tNE\n+Rv0030\t-\thypothetical protein Rv0030 \t5\t0\t0\t5\t0\t0.2000\t99.00\tNE\n+Rv0031\t-\tPOSSIBLE REMNANT OF A TRANSPOSASE \t1\t0\t0\t1\t0\t0.0000\t0.00\tNE\n+Rv0032\tbioF2\tPOSSIBLE 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) \t57\t12\t0\t45\t0\t0.5088\t234.62\tES\n+Rv0033\tacpA\tPROBABLE ACYL CARRIER PROTEIN ACPA (ACP) \t3\t0\t0\t3\t0\t1.0000\t146.33\tNE\n+Rv0034\t-\thypothetical protein Rv0034 \t5\t0\t0\t5\t0\t0.8000\t189.00\tNE\n+Rv0035\tfadD34\tPROBABLE FATTY-ACID-CoA LIGASE FADD34 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) \t25\t0\t0\t25\t0\t0.8800\t223.86\tNE\n+Rv0036c\t-\thypothetical protein Rv0036c \t4\t0\t0\t4\t0\t1.0000\t574.50\tNE\n+Rv0037c\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t21\t0\t0\t21\t0\t0.6190\t211.15\tNE\n+Rv0038\t-\thypothetical protein Rv0038 \t8\t0\t0\t8\t0\t0.7500\t329.17\tNE\n+Rv0039c\t-\tPOSSIBLE CONSERVED TRANSMEMBRANE PROTEIN \t4\t0\t0\t4\t0\t0.5000\t490.00\tNE\n+Rv0040c\tmtc28\tSECRETED PROLINE RICH PROTEIN MTC28 (PROLINE RICH 28 KDA ANTIGEN) \t10\t0\t0\t10\t0\t0.5000\t64.60\tNE\n+Rv0041\tleuS\tleucyl-tRNA synthetase \t73\t72\t0\t1\t0\t0.0137\t83.00\tES\n+Rv0042c\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY MARR-FAMILY) \t5\t0\t0\t5\t0\t0.6000\t80.33\tNE\n+Rv0043c\t-\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) \t11\t0\t0\t11\t0\t0.7273\t101.12\tNE\n+Rv0044c\t-\tPOSSIBLE OXIDOREDUCTASE \t20\t0\t0\t20\t0\t0.8500\t216.65\tNE\n+Rv0045c\t-\tPOSSIBLE HYDROLASE \t7\t0\t0\t7\t0\t1.0000\t244.29\tNE\n+Rv0046c\tino1\tMYO-INOSITOL-1-PHOSPHATE SYNTHASE INO1 (Inositol 1-phosphate synthetase) (D-glucose 6-phosphate cycloaldolase) (Glucose 6-phosphate cyclase) (Glucocycloaldolase) \t17\t17\t0\t0\t0\t0.00'..b'\t0\t28\t0\t0.8214\t285.35\tNE\n+Rv3878\t-\tCONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t6\t0\t0\t6\t0\t0.6667\t212.75\tNE\n+Rv3879c\t-\tHYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t38\t0\t0\t38\t0\t0.7368\t468.71\tNE\n+Rv3880c\t-\thypothetical protein Rv3880c \t5\t0\t0\t5\t0\t0.8000\t61.00\tNE\n+Rv3881c\t-\tCONSERVED HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN \t24\t0\t0\t24\t0\t0.6250\t352.20\tNE\n+Rv3882c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t24\t0\t0\t24\t0\t0.9167\t436.27\tNE\n+Rv3883c\tmycP1\tMEMBRANE-ANCHORED MYCOSIN MYCP1 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-1) \t17\t0\t0\t17\t0\t0.8824\t353.27\tNE\n+Rv3884c\t-\tPROBABLE CBXX/CFQX FAMILY PROTEIN \t34\t0\t0\t34\t0\t0.6471\t172.36\tNE\n+Rv3885c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t28\t0\t0\t28\t0\t0.6071\t90.06\tNE\n+Rv3886c\tmycP2\tPROBABLE ALANINE AND PROLINE RICH MEMBRANE-ANCHORED MYCOSIN MYCP2 (SERINE PROTEASE) (SUBTILISIN-LIKE PROTEASE) (SUBTILASE-LIKE) (MYCOSIN-2) \t27\t0\t0\t27\t0\t0.6667\t173.33\tNE\n+Rv3887c\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t33\t0\t0\t33\t0\t0.6364\t299.33\tNE\n+Rv3888c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t29\t0\t0\t29\t0\t0.4483\t113.62\tNE\n+Rv3889c\t-\thypothetical protein Rv3889c \t19\t0\t0\t19\t0\t0.6316\t369.00\tNE\n+Rv3890c\tesxC\tESAT-6 LIKE PROTEIN ESXC (ESAT-6 like protein 11) \t6\t0\t0\t6\t0\t0.8333\t192.00\tNE\n+Rv3891c\tesxD\tPOSSIBLE ESAT-6 LIKE PROTEIN ESXD \t9\t0\t0\t9\t0\t0.3333\t335.33\tNE\n+Rv3892c\tPPE69\tPPE FAMILY PROTEIN \t11\t0\t0\t11\t0\t0.8182\t172.67\tNE\n+Rv3893c\tPE36\tPE FAMILY PROTEIN \t3\t0\t0\t3\t0\t1.0000\t307.67\tNE\n+Rv3894c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t52\t0\t0\t52\t0\t0.7692\t119.35\tNE\n+Rv3895c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t14\t0\t0\t14\t0\t0.9286\t225.00\tNE\n+Rv3896c\t-\thypothetical protein Rv3896c \t15\t0\t0\t15\t0\t0.8667\t165.31\tNE\n+Rv3897c\t-\thypothetical protein Rv3897c \t8\t0\t0\t8\t0\t0.8750\t230.86\tNE\n+Rv3898c\t-\thypothetical protein Rv3898c \t7\t0\t0\t7\t0\t1.0000\t256.57\tNE\n+Rv3899c\t-\thypothetical protein Rv3899c \t18\t0\t0\t18\t0\t0.6667\t217.33\tNE\n+Rv3900c\t-\tCONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t17\t0\t0\t17\t0\t0.5294\t185.89\tNE\n+Rv3901c\t-\tPOSSIBLE MEMBRANE PROTEIN \t14\t0\t0\t14\t0\t0.7143\t500.10\tNE\n+Rv3902c\t-\thypothetical protein Rv3902c \t27\t27\t0\t0\t0\t0.0000\t0.00\tES\n+Rv3903c\t-\tHYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t51\t3\t0\t48\t0\t0.5686\t200.62\tNE\n+Rv3904c\tesxE\tPUTATIVE ESAT-6 LIKE PROTEIN ESXE (HYPOTHETICAL ALANINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 12) \t3\t0\t0\t3\t0\t0.6667\t44.50\tNE\n+Rv3905c\tesxF\tPUTATIVE ESAT-6 LIKE PROTEIN ESXF (HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 13) \t5\t0\t0\t5\t0\t1.0000\t195.60\tNE\n+Rv3906c\t-\thypothetical protein Rv3906c \t11\t0\t0\t11\t0\t0.9091\t163.60\tNE\n+Rv3907c\tpcnA\tPROBABLE POLY(A) POLYMERASE PCNA (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) (NTP POLYMERASE) (RNA ADENYLATING ENZYME) (POLY(A) POLYMERASE) \t20\t19\t0\t1\t0\t0.0500\t124.00\tES\n+Rv3908\t-\thypothetical protein Rv3908 \t11\t5\t0\t6\t0\t0.3636\t298.00\tNE\n+Rv3909\t-\thypothetical protein Rv3909 \t41\t41\t0\t0\t0\t0.0000\t0.00\tES\n+Rv3910\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t54\t34\t0\t20\t0\t0.2037\t105.82\tES\n+Rv3911\tsigM\tRNA polymerase sigma factor SigM \t12\t0\t0\t12\t0\t0.7500\t215.67\tNE\n+Rv3912\t-\tHYPOTHETICAL ALANINE RICH PROTEIN \t11\t0\t0\t11\t0\t0.5455\t179.33\tNE\n+Rv3913\ttrxB2\tPROBABLE THIOREDOXIN REDUCTASE TRXB2 (TRXR) (TR) \t18\t17\t0\t1\t0\t0.1111\t47.00\tES\n+Rv3914\ttrxC\tTHIOREDOXIN TRXC (TRX) (MPT46) \t6\t0\t0\t6\t0\t0.1667\t331.00\tNE\n+Rv3915\t-\tPROBABLE HYDROLASE \t25\t24\t0\t1\t0\t0.0400\t152.00\tES\n+Rv3916c\t-\thypothetical protein Rv3916c \t12\t0\t0\t12\t0\t0.1667\t20.50\tNE\n+Rv3917c\tparB\tPROBABLE CHROMOSOME PARTITIONING PROTEIN PARB \t19\t18\t0\t1\t0\t0.0526\t32.00\tES\n+Rv3918c\tparA\tPROBABLE CHROMOSOME PARTITIONING PROTEIN PARA \t19\t18\t0\t1\t0\t0.0526\t27.00\tES\n+Rv3919c\tgidB\tglucose-inhibited division protein B \t13\t0\t0\t13\t0\t0.6154\t103.50\tNE\n+Rv3920c\t-\tHYPOTHETICAL PROTEIN SIMILAR TO JAG PROTEIN \t4\t0\t0\t4\t0\t1.0000\t146.75\tNE\n+Rv3921c\t-\tputative inner membrane protein translocase component YidC \t23\t0\t23\t0\t0\t0.0435\t1.00\tGD\n+Rv3922c\t-\thypothetical protein Rv3922c \t12\t0\t12\t0\t0\t0.2500\t29.33\tGD\n+Rv3923c\trnpA\tribonuclease P \t4\t0\t4\t0\t0\t0.2500\t9.00\tGD\n+Rv3924c\trpmH\t50S ribosomal protein L34 \t2\t0\t2\t0\t0\t0.0000\t0.00\tGD\n' |
| b |
| diff -r 000000000000 -r 99810cf51f2e test-data/hmm-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmm-sites1.txt Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,74621 @@\n+#HMM - Sites\n+# Tn-HMM\n+#Console: python /home/inithello/miniconda3/envs/__transit@2.3.3/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+# 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-27 \tES\tRv0002_(dnaN)\n+2404\t0\t1.00e+00 \t9.02e-20 \t3.4'..b' \tNE\tRv3920c_(-)\n+4408553\t22\t1.18e-65 \t3.33e-25 \t1.00e+00 \t2.29e-11 \tNE\tRv3920c_(-)\n+4408742\t86\t2.22e-193\t1.05e-33 \t1.00e+00 \t3.12e-11 \tNE\tRv3920c_(-)\n+4408755\t437\t0.00e+00 \t1.08e-80 \t1.00e+00 \t1.70e-10 \tNE\tRv3920c_(-)\n+4409010\t1\t2.21e-02 \t9.29e-01 \t4.93e-02 \t1.08e-12 \tGD\tRv3921c_(-)\n+4409166\t0\t7.28e-01 \t2.71e-01 \t1.80e-03 \t9.96e-15 \tGD\tRv3921c_(-)\n+4409255\t0\t7.29e-01 \t2.71e-01 \t1.34e-05 \t2.12e-17 \tGD\tRv3921c_(-)\n+4409280\t0\t7.29e-01 \t2.71e-01 \t1.40e-07 \t1.10e-19 \tGD\tRv3921c_(-)\n+4409297\t0\t7.29e-01 \t2.71e-01 \t2.14e-09 \t1.34e-21 \tGD\tRv3921c_(-)\n+4409338\t0\t7.29e-01 \t2.71e-01 \t4.13e-11 \t2.45e-23 \tGD\tRv3921c_(-)\n+4409353\t0\t7.29e-01 \t2.71e-01 \t8.67e-13 \t8.61e-25 \tGD\tRv3921c_(-)\n+4409357\t0\t7.29e-01 \t2.71e-01 \t1.87e-14 \t1.27e-24 \tGD\tRv3921c_(-)\n+4409424\t0\t7.29e-01 \t2.71e-01 \t4.07e-16 \t4.58e-24 \tGD\tRv3921c_(-)\n+4409444\t0\t7.29e-01 \t2.71e-01 \t8.85e-18 \t1.67e-23 \tGD\tRv3921c_(-)\n+4409546\t0\t7.29e-01 \t2.71e-01 \t1.93e-19 \t6.12e-23 \tGD\tRv3921c_(-)\n+4409581\t0\t7.29e-01 \t2.71e-01 \t5.35e-21 \t2.24e-22 \tGD\tRv3921c_(-)\n+4409607\t0\t7.29e-01 \t2.71e-01 \t4.28e-21 \t8.19e-22 \tGD\tRv3921c_(-)\n+4409615\t0\t7.29e-01 \t2.71e-01 \t1.53e-20 \t3.00e-21 \tGD\tRv3921c_(-)\n+4409676\t0\t7.29e-01 \t2.71e-01 \t5.61e-20 \t1.10e-20 \tGD\tRv3921c_(-)\n+4409682\t0\t7.29e-01 \t2.71e-01 \t2.05e-19 \t4.01e-20 \tGD\tRv3921c_(-)\n+4409702\t0\t7.29e-01 \t2.71e-01 \t7.51e-19 \t1.47e-19 \tGD\tRv3921c_(-)\n+4409822\t0\t7.29e-01 \t2.71e-01 \t2.75e-18 \t5.37e-19 \tGD\tRv3921c_(-)\n+4409903\t0\t7.29e-01 \t2.71e-01 \t1.01e-17 \t1.97e-18 \tGD\tRv3921c_(-)\n+4409974\t0\t7.28e-01 \t2.72e-01 \t3.94e-17 \t7.19e-18 \tGD\tRv3921c_(-)\n+4409996\t0\t7.26e-01 \t2.74e-01 \t5.77e-16 \t2.63e-17 \tGD\tRv3921c_(-)\n+4410026\t0\t7.16e-01 \t2.84e-01 \t7.48e-14 \t1.03e-16 \tGD\tRv3921c_(-)\n+4410029\t0\t6.83e-01 \t3.17e-01 \t1.25e-11 \t6.00e-15 \tGD\tRv3921c_(-)\n+4410146\t1\t1.71e-02 \t9.83e-01 \t6.36e-09 \t1.45e-11 \tGD\tRv3922c_(-)\n+4410158\t0\t1.92e-01 \t8.08e-01 \t1.01e-08 \t8.05e-11 \tGD\tRv3922c_(-)\n+4410240\t77\t2.04e-149\t3.24e-05 \t9.25e-01 \t7.48e-02 \tGD\tRv3922c_(-)\n+4410264\t0\t7.68e-12 \t1.00e+00 \t1.27e-06 \t7.12e-08 \tGD\tRv3922c_(-)\n+4410271\t0\t7.72e-12 \t1.00e+00 \t2.76e-08 \t3.10e-10 \tGD\tRv3922c_(-)\n+4410277\t0\t7.72e-12 \t1.00e+00 \t6.02e-10 \t1.35e-12 \tGD\tRv3922c_(-)\n+4410305\t0\t7.71e-12 \t1.00e+00 \t1.32e-11 \t5.89e-15 \tGD\tRv3922c_(-)\n+4410327\t0\t7.68e-12 \t1.00e+00 \t3.47e-13 \t2.57e-17 \tGD\tRv3922c_(-)\n+4410337\t0\t7.57e-12 \t1.00e+00 \t6.76e-14 \t1.12e-19 \tGD\tRv3922c_(-)\n+4410367\t0\t7.15e-12 \t1.00e+00 \t6.15e-14 \t4.89e-22 \tGD\tRv3922c_(-)\n+4410373\t10\t1.32e-30 \t1.00e+00 \t1.36e-12 \t6.45e-23 \tGD\tRv3922c_(-)\n+4410403\t0\t1.08e-22 \t1.00e+00 \t6.14e-14 \t6.97e-25 \tGD\tRv3922c_(-)\n+4410423\t9\t1.90e-39 \t1.00e+00 \t9.96e-13 \t1.87e-22 \tGD\tRv3923c_(rnpA)\n+4410624\t0\t5.04e-08 \t1.00e+00 \t6.14e-14 \t1.54e-22 \tGD\tRv3923c_(rnpA)\n+4410668\t0\t6.42e-08 \t1.00e+00 \t6.13e-14 \t3.93e-23 \tGD\tRv3923c_(rnpA)\n+4410693\t0\t6.80e-08 \t1.00e+00 \t6.28e-14 \t1.08e-23 \tGD\tRv3923c_(rnpA)\n+4410769\t1\t9.46e-10 \t1.00e+00 \t1.78e-13 \t4.58e-24 \tGD\t\n+4410851\t0\t8.96e-08 \t1.00e+00 \t2.41e-12 \t6.04e-23 \tGD\tRv3924c_(rpmH)\n+4410861\t0\t9.52e-08 \t1.00e+00 \t1.07e-10 \t1.92e-22 \tGD\tRv3924c_(rpmH)\n+4410944\t0\t9.67e-08 \t1.00e+00 \t4.92e-09 \t2.88e-20 \tGD\t\n+4411049\t0\t9.71e-08 \t1.00e+00 \t2.26e-07 \t6.09e-18 \tGD\t\n+4411098\t0\t9.72e-08 \t1.00e+00 \t1.04e-05 \t1.37e-15 \tGD\t\n+4411102\t0\t9.73e-08 \t1.00e+00 \t4.75e-04 \t3.14e-13 \tGD\t\n+4411164\t90\t7.56e-186\t3.56e-11 \t1.00e+00 \t5.05e-09 \tNE\t\n+4411182\t185\t0.00e+00 \t2.19e-34 \t1.00e+00 \t7.92e-09 \tNE\t\n+4411245\t0\t3.08e-17 \t6.38e-19 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411258\t0\t3.09e-17 \t6.51e-19 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411273\t52\t4.18e-121\t6.50e-26 \t1.00e+00 \t4.22e-09 \tNE\t\n+4411277\t176\t0.00e+00 \t5.70e-46 \t1.00e+00 \t7.59e-09 \tNE\t\n+4411337\t0\t4.53e-15 \t7.40e-17 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411397\t0\t4.56e-15 \t7.56e-17 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411412\t0\t4.56e-15 \t7.56e-17 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411421\t14\t4.92e-43 \t9.85e-19 \t1.00e+00 \t3.53e-09 \tNE\t\n+4411440\t121\t1.97e-263\t2.66e-33 \t1.00e+00 \t5.85e-09 \tNE\t\n+4411479\t0\t1.12e-05 \t2.30e-07 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411508\t0\t1.13e-05 \t2.35e-07 \t1.00e+00 \t3.30e-09 \tNE\t\n+4411526\t0\t1.13e-05 \t2.35e-07 \t1.00e+00 \t3.30e-09 \tNE\t\n' |
| b |
| diff -r 000000000000 -r 99810cf51f2e test-data/resampling-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/resampling-sites1.txt Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,3997 @@\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+#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+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+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\t1.00000\n+Rv0019c\t-\thypothetical protein Rv0019c \t13\t137.3\t28.2\t-2.28\t3568.6\t1100.18\t-109.0\t0.00300\t0.12091\n+Rv0020c\tTB39.8\thypothetical protein Rv0020c \t52\t9.9\t13.6\t0.46\t1027.7\t2115.58\t3.7\t0.65200\t1.00000\n+Rv0021c\t-\thypothetical protein Rv0021c \t22\t235.7\t428.8\t0.86\t10372.4\t28300.20\t193.1\t0.24000\t1.00000\n+Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t334.6\t421.9\t0.33\t5353.0\t10124.72\t87.3\t0.76700\t1.00000\n+Rv0023\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN \t12\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0024\t-\tPUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN \t12\t177.5\t175.6\t-0.02\t4259.9\t6321.26\t-1.9\t0.98000\t1.00000\n+Rv0025\t-\thypothetical protein Rv0025 \t7\t70.9\t217.4\t1.62\t992.9\t4565.47\t146.5\t0.03300\t0.68578\n+Rv0026\t-\thypothetical protein Rv0026 \t14\t122.2\t130.2\t0.09\t3421.5\t5468.18\t8.0\t0.85300\t1.00000\n+Rv0027\t-\thypothetical protein Rv0027 \t5\t33.9\t7.1\t-2.26\t338.8\t105.86\t-26.8\t0.18000\t1.00000\n+Rv0028\t-\thypothetical protein Rv0028 \t5\t44.1\t53.1\t0.27\t441.1\t796.30\t9.0\t0.85100\t1.00000\n+Rv0029\t-\thypothetical protein Rv0029 \t18\t129.4\t548.1\t2.08\t4659.5\t29597.48\t418.7\t0.23400\t1.00000\n+Rv0030\t-\thypothetical protein Rv0030 \t5\t19.7\t10.6\t-0.90\t197.1\t158.38\t-9.2\t0.63600\t1.00000\n+Rv0031\t-\tPOSSIBLE REMNANT OF A TRANSPOSASE \t1\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0032\tbioF2\tPOSSIBLE 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) \t57\t119.3\t169.7\t0.51\t13605.5\t29020.52\t5'..b'.2\t0.66600\t1.00000\n+Rv3888c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t29\t51.0\t42.1\t-0.28\t2957.8\t3661.31\t-8.9\t0.71400\t1.00000\n+Rv3889c\t-\thypothetical protein Rv3889c \t19\t233.1\t232.6\t-0.00\t8856.3\t13259.01\t-0.4\t0.99600\t1.00000\n+Rv3890c\tesxC\tESAT-6 LIKE PROTEIN ESXC (ESAT-6 like protein 11) \t5\t191.3\t181.3\t-0.08\t1913.2\t2719.69\t-10.0\t0.92100\t1.00000\n+Rv3891c\tesxD\tPOSSIBLE ESAT-6 LIKE PROTEIN ESXD \t9\t111.8\t92.8\t-0.27\t2012.1\t2506.44\t-19.0\t0.72400\t1.00000\n+Rv3892c\tPPE69\tPPE FAMILY PROTEIN \t10\t147.1\t176.0\t0.26\t2942.1\t5281.34\t28.9\t0.65800\t1.00000\n+Rv3893c\tPE36\tPE FAMILY PROTEIN \t2\t324.3\t321.2\t-0.01\t1297.4\t1926.99\t-3.2\t0.97500\t1.00000\n+Rv3894c\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t51\t93.1\t275.2\t1.56\t9500.1\t42111.70\t182.1\t0.20200\t1.00000\n+Rv3895c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t13\t191.6\t129.8\t-0.56\t4982.4\t5064.13\t-61.8\t0.37200\t1.00000\n+Rv3896c\t-\thypothetical protein Rv3896c \t15\t143.1\t105.2\t-0.44\t4293.9\t4732.06\t-38.0\t0.51000\t1.00000\n+Rv3897c\t-\thypothetical protein Rv3897c \t7\t209.1\t183.5\t-0.19\t2927.4\t3854.07\t-25.6\t0.69800\t1.00000\n+Rv3898c\t-\thypothetical protein Rv3898c \t6\t267.6\t258.3\t-0.05\t3211.0\t4649.74\t-9.3\t0.91000\t1.00000\n+Rv3899c\t-\thypothetical protein Rv3899c \t18\t144.9\t184.0\t0.34\t5217.9\t9934.43\t39.0\t0.55700\t1.00000\n+Rv3900c\t-\tCONSERVED HYPOTHETICAL ALANINE RICH PROTEIN \t17\t98.5\t93.1\t-0.08\t3348.1\t4746.85\t-5.4\t0.88200\t1.00000\n+Rv3901c\t-\tPOSSIBLE MEMBRANE PROTEIN \t14\t357.2\t358.1\t0.00\t10002.7\t15041.40\t0.9\t0.99100\t1.00000\n+Rv3902c\t-\thypothetical protein Rv3902c \t26\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv3903c\t-\tHYPOTHETICAL ALANINE AND PROLINE RICH PROTEIN \t51\t114.1\t81.8\t-0.48\t11637.4\t12519.73\t-32.3\t0.16500\t1.00000\n+Rv3904c\tesxE\tPUTATIVE ESAT-6 LIKE PROTEIN ESXE (HYPOTHETICAL ALANINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 12) \t3\t29.6\t54.2\t0.87\t177.6\t487.59\t24.6\t0.88700\t1.00000\n+Rv3905c\tesxF\tPUTATIVE ESAT-6 LIKE PROTEIN ESXF (HYPOTHETICAL ALANINE AND GLYCINE RICH PROTEIN) (ESAT-6 LIKE PROTEIN 13) \t5\t195.8\t261.2\t0.42\t1958.0\t3917.65\t65.4\t0.43000\t1.00000\n+Rv3906c\t-\thypothetical protein Rv3906c \t10\t163.4\t125.9\t-0.38\t3268.1\t3778.32\t-37.5\t0.59100\t1.00000\n+Rv3907c\tpcnA\tPROBABLE POLY(A) POLYMERASE PCNA (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) (NTP POLYMERASE) (RNA ADENYLATING ENZYME) (POLY(A) POLYMERASE) \t19\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv3908\t-\thypothetical protein Rv3908 \t11\t108.4\t233.2\t1.11\t2385.0\t7696.26\t124.8\t0.54500\t1.00000\n+Rv3909\t-\thypothetical protein Rv3909 \t41\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv3910\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t54\t21.6\t44.3\t1.04\t2329.9\t7174.23\t22.7\t0.14900\t1.00000\n+Rv3911\tsigM\tRNA polymerase sigma factor SigM \t12\t161.8\t112.7\t-0.52\t3884.2\t4058.32\t-49.1\t0.39800\t1.00000\n+Rv3912\t-\tHYPOTHETICAL ALANINE RICH PROTEIN \t11\t98.0\t79.2\t-0.31\t2155.1\t2612.15\t-18.8\t0.63400\t1.00000\n+Rv3913\ttrxB2\tPROBABLE THIOREDOXIN REDUCTASE TRXB2 (TRXR) (TR) \t18\t5.2\t3.4\t-0.65\t189.0\t180.93\t-1.9\t0.71600\t1.00000\n+Rv3914\ttrxC\tTHIOREDOXIN TRXC (TRX) (MPT46) \t5\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv3915\t-\tPROBABLE HYDROLASE \t24\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv3916c\t-\thypothetical protein Rv3916c \t11\t0.3\t0.0\t-0.41\t7.2\t0.00\t-0.3\t0.40700\t1.00000\n+Rv3917c\tparB\tPROBABLE CHROMOSOME PARTITIONING PROTEIN PARB \t18\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv3918c\tparA\tPROBABLE CHROMOSOME PARTITIONING PROTEIN PARA \t19\t1.4\t0.0\t-1.26\t53.2\t0.00\t-1.4\t0.40700\t1.00000\n+Rv3919c\tgidB\tglucose-inhibited division protein B \t13\t63.6\t18.8\t-1.76\t1654.2\t733.76\t-44.8\t0.01800\t0.46038\n+Rv3920c\t-\tHYPOTHETICAL PROTEIN SIMILAR TO JAG PROTEIN \t3\t181.3\t172.3\t-0.07\t1088.0\t1551.08\t-9.0\t0.93000\t1.00000\n+Rv3921c\t-\tputative inner membrane protein translocase component YidC \t23\t0.1\t0.0\t-0.09\t2.9\t0.00\t-0.1\t0.40400\t1.00000\n+Rv3922c\t-\thypothetical protein Rv3922c \t12\t7.4\t3.9\t-0.93\t177.9\t139.68\t-3.5\t0.49500\t1.00000\n+Rv3923c\trnpA\tribonuclease P \t4\t2.2\t5.1\t1.25\t17.2\t61.43\t3.0\t1.00000\t1.00000\n+Rv3924c\trpmH\t50S ribosomal protein L34 \t2\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rvnr01\trrs\t16S rRNA\t62\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n' |
| b |
| diff -r 000000000000 -r 99810cf51f2e test-data/transit-co1-rep1.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-co1-rep1.wig Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). PLOS Pathogens, e1002251.\n+variableStep chrom=H37Rv\n+60 0\n+72 0\n+102 0\n+188 0\n+246 0\n+333 0\n+360 0\n+426 0\n+448 0\n+471 0\n+483 0\n+494 0\n+504 0\n+514 0\n+525 0\n+534 0\n+601 0\n+653 0\n+670 0\n+706 0\n+741 0\n+784 0\n+794 0\n+843 0\n+989 0\n+1092 0\n+1104 0\n+1267 0\n+1278 0\n+1345 0\n+1423 0\n+1522 0\n+1552 0\n+1635 54\n+1779 0\n+1782 0\n+1788 0\n+1847 0\n+1858 80\n+1921 0\n+2001 0\n+2012 0\n+2063 0\n+2104 0\n+2141 0\n+2232 0\n+2290 0\n+2315 0\n+2318 0\n+2333 0\n+2344 0\n+2363 0\n+2387 0\n+2404 0\n+2427 0\n+2479 0\n+2507 0\n+2537 0\n+2591 0\n+2648 0\n+2738 0\n+2774 0\n+2845 0\n+2920 0\n+3027 0\n+3056 0\n+3066 0\n+3070 0\n+3119 0\n+3131 0\n+3145 0\n+3222 0\n+3228 0\n+3277 0\n+3283 74\n+3329 0\n+3372 0\n+3379 0\n+3384 0\n+3396 0\n+3412 0\n+3425 0\n+3441 0\n+3467 0\n+3471 0\n+3513 0\n+3591 0\n+3682 0\n+3708 113\n+3728 66\n+3739 0\n+3770 7\n+3782 0\n+3796 0\n+3833 0\n+3925 38\n+3960 0\n+3967 0\n+3986 0\n+4011 0\n+4028 0\n+4094 0\n+4118 0\n+4121 117\n+4130 0\n+4158 0\n+4207 0\n+4217 0\n+4353 0\n+4664 0\n+4721 0\n+4789 0\n+4912 0\n+4961 0\n+4970 0\n+4989 0\n+4995 101\n+5066 44\n+5120 90\n+5128 64\n+5170 28\n+5230 0\n+5273 0\n+5287 0\n+5336 0\n+5364 0\n+5420 0\n+5439 0\n+5517 0\n+5547 0\n+5579 0\n+5586 0\n+5623 0\n+5631 0\n+5669 0\n+5687 0\n+5792 0\n+5977 0\n+5996 0\n+6055 0\n+6128 0\n+6230 0\n+6249 0\n+6286 0\n+6403 0\n+6490 0\n+6502 0\n+6526 0\n+6605 0\n+6612 0\n+6672 0\n+6729 0\n+6793 0\n+6809 0\n+6856 0\n+6944 0\n+6983 0\n+7067 0\n+7077 0\n+7093 0\n+7225 0\n+7265 1\n+7299 66\n+7383 0\n+7392 0\n+7470 0\n+7551 0\n+7578 0\n+7620 0\n+7686 0\n+7763 0\n+7767 0\n+7798 0\n+7865 0\n+7970 0\n+8031 0\n+8077 0\n+8099 0\n+8127 0\n+8219 0\n+8236 0\n+8288 0\n+8295 0\n+8338 0\n+8391 0\n+8394 0\n+8436 0\n+8486 0\n+8546 0\n+8786 0\n+8858 0\n+8874 0\n+8901 0\n+9030 0\n+9045 0\n+9100 0\n+9150 0\n+9165 0\n+9419 0\n+9465 0\n+9492 0\n+9503 0\n+9519 0\n+9526 0\n+9542 0\n+9564 0\n+9624 0\n+9776 69\n+9816 8\n+9850 0\n+9877 41\n+9894 0\n+9903 43\n+10023 0\n+10104 0\n+10277 0\n+10299 1\n+10414 0\n+10426 273\n+10583 15\n+10600 0\n+10608 0\n+10769 48\n+10826 68\n+10857 0\n+10876 0\n+10884 0\n+10892 0\n+10894 0\n+10907 0\n+10923 0\n+10953 0\n+11096 6\n+11119 0\n+11131 0\n+11176 0\n+11198 0\n+11207 88\n+11289 50\n+11301 0\n+11422 27\n+11444 0\n+11530 33\n+11556 60\n+11618 3\n+11659 0\n+11675 363\n+11679 359\n+11733 233\n+11739 207\n+11743 621\n+11749 0\n+11787 89\n+11848 2\n+12042 54\n+12054 0\n+12145 0\n+12250 147\n+12352 304\n+12466 1\n+12491 35\n+12512 0\n+12530 0\n+12621 25\n+12663 5\n+12750 0\n+12798 0\n+13025 305\n+13046 51\n+13079 0\n+13155 0\n+13168 0\n+13275 0\n+13309 69\n+13322 8\n+13325 341\n+13369 0\n+13459 0\n+13469 0\n+13486 0\n+13560 5\n+13567 27\n+13595 0\n+13608 0\n+13669 0\n+13686 0\n+13699 0\n+13772 0\n+13852 0\n+13903 0\n+14021 61\n+14059 35\n+14080 80\n+14088 11\n+14096 249\n+14177 3\n+14367 0\n+14421 0\n+14454 0\n+14621 50\n+14661 52\n+14665 244\n+14667 0\n+14677 0\n+14749 0\n+14758 76\n+14782 0\n+14813 2\n+14821 2\n+14872 0\n+14902 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| b |
| diff -r 000000000000 -r 99810cf51f2e test-data/transit-co1-rep2.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-co1-rep2.wig Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). 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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 000000000000 -r 99810cf51f2e test-data/transit-co1-rep3.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-co1-rep3.wig Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). PLOS Pathogens, e1002251.\n+variableStep chrom=H37Rv\n+60 0\n+72 0\n+102 0\n+188 0\n+246 0\n+333 0\n+360 0\n+426 0\n+448 0\n+471 0\n+483 0\n+494 0\n+504 0\n+514 0\n+525 0\n+534 0\n+601 0\n+653 0\n+670 0\n+706 0\n+741 0\n+784 0\n+794 0\n+843 0\n+989 0\n+1092 0\n+1104 0\n+1267 0\n+1278 0\n+1345 0\n+1423 0\n+1522 0\n+1552 0\n+1635 0\n+1779 0\n+1782 0\n+1788 0\n+1847 0\n+1858 20\n+1921 0\n+2001 0\n+2012 0\n+2063 0\n+2104 0\n+2141 0\n+2232 0\n+2290 0\n+2315 0\n+2318 0\n+2333 0\n+2344 0\n+2363 0\n+2387 0\n+2404 0\n+2427 0\n+2479 0\n+2507 0\n+2537 0\n+2591 0\n+2648 0\n+2738 0\n+2774 0\n+2845 0\n+2920 0\n+3027 0\n+3056 0\n+3066 0\n+3070 0\n+3119 0\n+3131 0\n+3145 0\n+3222 0\n+3228 0\n+3277 0\n+3283 0\n+3329 0\n+3372 0\n+3379 0\n+3384 0\n+3396 0\n+3412 0\n+3425 0\n+3441 0\n+3467 0\n+3471 104\n+3513 0\n+3591 0\n+3682 0\n+3708 46\n+3728 0\n+3739 0\n+3770 0\n+3782 1\n+3796 0\n+3833 0\n+3925 0\n+3960 0\n+3967 0\n+3986 35\n+4011 0\n+4028 0\n+4094 0\n+4118 3\n+4121 1\n+4130 0\n+4158 0\n+4207 0\n+4217 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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 000000000000 -r 99810cf51f2e test-data/transit-in1-rep1.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1-rep1.wig Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). PLOS Pathogens, e1002251.\n+variableStep chrom=H37Rv\n+60 0\n+72 0\n+102 0\n+188 0\n+246 0\n+333 0\n+360 0\n+426 0\n+448 0\n+471 0\n+483 0\n+494 0\n+504 0\n+514 0\n+525 0\n+534 0\n+601 0\n+653 0\n+670 0\n+706 0\n+741 0\n+784 0\n+794 0\n+843 0\n+989 0\n+1092 0\n+1104 0\n+1267 0\n+1278 0\n+1345 0\n+1423 0\n+1522 0\n+1552 27\n+1635 14\n+1779 0\n+1782 0\n+1788 0\n+1847 0\n+1858 26\n+1921 0\n+2001 0\n+2012 0\n+2063 0\n+2104 0\n+2141 0\n+2232 0\n+2290 0\n+2315 0\n+2318 0\n+2333 0\n+2344 0\n+2363 0\n+2387 0\n+2404 0\n+2427 0\n+2479 0\n+2507 0\n+2537 0\n+2591 0\n+2648 0\n+2738 0\n+2774 0\n+2845 0\n+2920 0\n+3027 0\n+3056 0\n+3066 0\n+3070 0\n+3119 0\n+3131 0\n+3145 0\n+3222 0\n+3228 0\n+3277 0\n+3283 62\n+3329 0\n+3372 0\n+3379 0\n+3384 0\n+3396 0\n+3412 0\n+3425 0\n+3441 0\n+3467 0\n+3471 0\n+3513 0\n+3591 0\n+3682 0\n+3708 63\n+3728 0\n+3739 0\n+3770 13\n+3782 46\n+3796 0\n+3833 1\n+3925 0\n+3960 0\n+3967 0\n+3986 0\n+4011 0\n+4028 0\n+4094 0\n+4118 0\n+4121 0\n+4130 0\n+4158 0\n+4207 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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 000000000000 -r 99810cf51f2e test-data/transit-in1-rep2.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1-rep2.wig Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). PLOS Pathogens, e1002251.\n+variableStep chrom=H37Rv\n+60 0\n+72 0\n+102 0\n+188 0\n+246 0\n+333 0\n+360 0\n+426 0\n+448 0\n+471 0\n+483 0\n+494 0\n+504 0\n+514 0\n+525 0\n+534 0\n+601 0\n+653 0\n+670 0\n+706 0\n+741 0\n+784 0\n+794 0\n+843 0\n+989 0\n+1092 0\n+1104 0\n+1267 0\n+1278 0\n+1345 0\n+1423 0\n+1522 124\n+1552 0\n+1635 201\n+1779 0\n+1782 0\n+1788 0\n+1847 0\n+1858 342\n+1921 21\n+2001 0\n+2012 0\n+2063 0\n+2104 0\n+2141 0\n+2232 0\n+2290 0\n+2315 0\n+2318 0\n+2333 0\n+2344 0\n+2363 0\n+2387 0\n+2404 0\n+2427 0\n+2479 0\n+2507 0\n+2537 0\n+2591 0\n+2648 0\n+2738 0\n+2774 0\n+2845 0\n+2920 0\n+3027 0\n+3056 0\n+3066 0\n+3070 0\n+3119 0\n+3131 0\n+3145 0\n+3222 0\n+3228 0\n+3277 0\n+3283 5\n+3329 107\n+3372 0\n+3379 0\n+3384 0\n+3396 0\n+3412 0\n+3425 0\n+3441 0\n+3467 56\n+3471 0\n+3513 0\n+3591 0\n+3682 0\n+3708 49\n+3728 0\n+3739 161\n+3770 0\n+3782 37\n+3796 0\n+3833 27\n+3925 13\n+3960 0\n+3967 0\n+3986 4\n+4011 6\n+4028 1\n+4094 0\n+4118 0\n+4121 110\n+4130 0\n+4158 0\n+4207 0\n+4217 0\n+4353 0\n+4664 0\n+4721 0\n+4789 0\n+4912 0\n+4961 0\n+4970 0\n+4989 23\n+4995 63\n+5066 58\n+5120 69\n+5128 40\n+5170 90\n+5230 0\n+5273 0\n+5287 0\n+5336 0\n+5364 0\n+5420 0\n+5439 0\n+5517 0\n+5547 0\n+5579 0\n+5586 0\n+5623 0\n+5631 0\n+5669 0\n+5687 0\n+5792 0\n+5977 0\n+5996 0\n+6055 0\n+6128 0\n+6230 0\n+6249 0\n+6286 0\n+6403 0\n+6490 0\n+6502 0\n+6526 0\n+6605 0\n+6612 0\n+6672 0\n+6729 0\n+6793 0\n+6809 0\n+6856 0\n+6944 0\n+6983 0\n+7067 0\n+7077 0\n+7093 0\n+7225 0\n+7265 0\n+7299 101\n+7383 0\n+7392 0\n+7470 0\n+7551 0\n+7578 0\n+7620 0\n+7686 0\n+7763 0\n+7767 0\n+7798 0\n+7865 0\n+7970 0\n+8031 0\n+8077 0\n+8099 0\n+8127 0\n+8219 0\n+8236 0\n+8288 0\n+8295 0\n+8338 0\n+8391 0\n+8394 0\n+8436 0\n+8486 0\n+8546 0\n+8786 0\n+8858 0\n+8874 0\n+8901 0\n+9030 0\n+9045 0\n+9100 0\n+9150 0\n+9165 0\n+9419 0\n+9465 0\n+9492 0\n+9503 0\n+9519 0\n+9526 0\n+9542 0\n+9564 0\n+9624 0\n+9776 127\n+9816 325\n+9850 0\n+9877 115\n+9894 21\n+9903 49\n+10023 0\n+10104 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3\n+20345 54\n+20349 10\n+20376 10\n+20456 0\n+20497 41\n+20547 206\n+20650 0\n+20671 0\n+20680 2\n+20712 0\n+20756 0\n+20787 0\n+20859 0\n+20883 160\n+21041 0\n+21204 0\n+21210 1\n+21266 0\n+21359 53\n+21414 63\n+21477 0\n+21481 199\n+21548 0\n+21608 0\n+21777 0\n+22070 31\n+22092 0\n+22118 22\n+22144 0\n+22187 0\n+22195 1\n+22199 4\n+22202 23\n+22279 0\n+22314 0\n+22338 69\n+22454 45\n+22460 0\n+22578 0\n+2'..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 000000000000 -r 99810cf51f2e test-data/transit-in1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1.gff3 Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,3990 @@\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 000000000000 -r 99810cf51f2e test-data/transit-in1.prot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1.prot Mon Apr 22 14:42:21 2019 -0400 |
| b |
| b'@@ -0,0 +1,3990 @@\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' |