| Next changeset 1:73a3ea18ec71 (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:
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 transit_resampling.xml |
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| diff -r 000000000000 -r 043a6feaa8bc gff_to_prot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff_to_prot.py Mon Apr 22 14:42:47 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 043a6feaa8bc macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Apr 22 14:42:47 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 043a6feaa8bc 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 14:42:47 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 043a6feaa8bc 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 14:42:47 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 043a6feaa8bc test-data/gumbel-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gumbel-sites1.txt Mon Apr 22 14:42:47 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 043a6feaa8bc test-data/hmm-genes1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmm-genes1.txt Mon Apr 22 14:42:47 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 043a6feaa8bc test-data/hmm-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmm-sites1.txt Mon Apr 22 14:42:47 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 043a6feaa8bc test-data/resampling-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/resampling-sites1.txt Mon Apr 22 14:42:47 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 043a6feaa8bc 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 14:42:47 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 0\n+14938 0\n+14968 0\n+15023 0\n+15084 0\n+15114 0\n+15221 0\n+15245 0\n+15269 0\n+15304 0\n+15327 0\n+15366 0\n+15464 0\n+15515 37\n+15576 0\n+15591 0\n+15657 0\n+15773 0\n+15812 0\n+15927 0\n+16161 0\n+16184 0\n+16273 0\n+16433 0\n+16520 0\n+16535 0\n+16558 0\n+16683 0\n+16794 0\n+16851 0\n+16872 0\n+16926 0\n+17015 0\n+17176 0\n+17190 0\n+17205 0\n+17247 0\n+17313 0\n+17333 0\n+17439 0\n+17476 7\n+17483 0\n+17586 0\n+17862 0\n+17981 0\n+18010 0\n+18123 0\n+18140 0\n+18161 0\n+18215 0\n+18454 0\n+18488 0\n+18527 0\n+18666 0\n+18693 0\n+18725 0\n+18907 0\n+19038 0\n+19043 0\n+19081 0\n+19100 0\n+19107 0\n+19134 0\n+19138 87\n+19151 14\n+19179 0\n+19194 0\n+19226 0\n+19239 0\n+19259 0\n+19310 0\n+19453 0\n+19461 0\n+19582 2\n+19667 0\n+19693 32\n+19760 0\n+19771 0\n+19829 0\n+19838 26\n+19914 0\n+19935 15\n+19951 0\n+19963 0\n+19973 0\n+19984 0\n+20002 0\n+20037 0\n+20044 0\n+20092 0\n+20178 0\n+20211 0\n+20234 82\n+20266 0\n+20278 0\n+20345 185\n+20349 1\n+20376 43\n+20456 0\n+20497 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| b |
| diff -r 000000000000 -r 043a6feaa8bc 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 14:42:47 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). 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| b |
| diff -r 000000000000 -r 043a6feaa8bc 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 14:42:47 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 043a6feaa8bc 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 14:42:47 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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| b |
| diff -r 000000000000 -r 043a6feaa8bc 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 14:42:47 2019 -0400 |
| b |
| b'@@ -0,0 +1,74607 @@\n+# from Griffin et al, (2011). 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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 043a6feaa8bc test-data/transit-in1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1.gff3 Mon Apr 22 14:42:47 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 043a6feaa8bc test-data/transit-in1.prot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1.prot Mon Apr 22 14:42:47 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 043a6feaa8bc transit_resampling.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transit_resampling.xml Mon Apr 22 14:42:47 2019 -0400 |
| [ |
| b'@@ -0,0 +1,146 @@\n+<?xml version="1.0"?>\n+<tool id="transit_resampling" name="Resampling" version="@VERSION@+galaxy1">\n+ <description>- determine per-gene p-values</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ \t@LINK_INPUTS@\n+ #set $control_files = \',\'.join([\'control_file_%d.wig\' % idx for idx, _ in enumerate(str($controls).split(\',\'))])\n+ #for idx, filename in enumerate(str($controls).split(\',\')):\n+ ln -s \'$filename\' control_file_${idx}.wig &&\n+ #end for\n+ transit resampling $input_files $control_files annotation.dat transit_out.txt\n+ @STANDARD_OPTIONS@\n+ -s $samples -n $normalization $histogram $adaptive $exclude_zero $pseudo $loess\n+ ]]>\n+ </command>\n+ <inputs>\n+ <expand macro="standard_inputs">\n+ <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />\n+ <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />\n+ <param name="normalization" argument="-n" type="select" label="Normalization method">\n+ <option value="TTR">TTR</option>\n+ </param>\n+ <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />\n+ <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />\n+ <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />\n+ <param name="pseudo" argument="-pc" type="boolean" truevalue="-pc" falsevalue="" label="Add pseudocounts at each site" />\n+ <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />\n+\n+ </expand>\n+ </inputs>\n+ <outputs>\n+ <expand macro="outputs" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />\n+ <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />\n+ <param name="annotation" ftype="gff3" value="transit-in1.gff3" />\n+ <param name="samples" value="1000" />\n+ <param name="burnin" value="100" />\n+ <param name="replicates" value="Replicates" />\n+ <output name="sites" file="resampling-sites1.txt" ftype="tabular" compare="sim_size" />\n+ </test>\n+ </tests>\n+\n+ <help>\n+<![CDATA[.. class:: infomark\n+\n+**What it does**\n+\n+-------------------\n+\n+\n+The re-sampling method is a comparative analysis the allows that can be used to determine conditional essentiality of genes. It is based on a permutation test, and is capable of determining read-counts that are significantly different across conditions.\n+\n+This technique has yet to be formally published in the context of differential essentiality analysis. Briefly, the read-counts at each genes are determined for each replicate of each condition. The total read-counts in condition A is subtracted from the total read counts at condition B, to obtain an observed difference in read counts. The TA sites are then permuted for a given number of \xe2\x80\x9csamples\xe2\x80\x9d. For each one of these permutations, the difference is read-counts is determined. This forms a null distribution, from which a p-value is calculated for the original, observed difference in read-counts.\n+\n+\n+Note : Can be used for both Himar1 and Tn5 datasets\n+\n+\n+-------------------\n+\n+**Inputs**\n+\n+-------------------\n+\n+Input files for Resampling need to be:\n+\n+- .wig files : Tabulated files containing one column with the TA site coordinate and one column with the read count'..b'r e.g. \'AABB\' Default: empty. Letters used must also be used in --exp_lib. If non-empty, resampling will limit permutations to within-libraries.\n+--exp_lib := String of letters representing library of experimental files in order e.g. \'ABAB\' Default: empty. Letters used must also be used in --ctrl_lib. If non-empty, resampling will limit permutations to within-libraries.\n+\n+\n+The resampling method is non-parametric, and therefore does not require any parameters governing the distributions or the model. The following parameters are available for the method:\n+\n+- Samples: The number of samples (permutations) to perform. The larger the number of samples, the more resolution the p-values calculated will have, at the expense of longer computation time. The re-sampling method runs on 10,000 samples by default.\n+- Output Histograms:Determines whether to output .png images of the histograms obtained from resampling the difference in read-counts.\n+- Adaptive Resampling: An optional \xe2\x80\x9cadaptive\xe2\x80\x9d version of resampling which accelerates the calculation by terminating early for genes which are likely not significant. This dramatically speeds up the computation at the cost of less accurate estimates for those genes that terminate early (i.e. deemed not significant). This option is OFF by default.\n+- Include Zeros: Select to include sites that are zero. This is the preferred behavior, however, unselecting this (thus ignoring sites that) are zero accross all dataset (i.e. completely empty), is useful for decreasing running time (specially for large datasets like Tn5).\n+- Normalization Method: Determines which normalization method to use when comparing datasets. Proper normalization is important as it ensures that other sources of variability are not mistakenly treated as real differences. See the Normalization section for a description of normalization method available in TRANSIT.\n+\n+\n+-------------------\n+\n+**Outputs**\n+\n+-------------------\n+\n+The re-sampling method outputs a tab-delimited file with results for each gene in the genome. P-values are adjusted for multiple comparisons using the Benjamini-Hochberg procedure (called \xe2\x80\x9cq-values\xe2\x80\x9d or \xe2\x80\x9cp-adj.\xe2\x80\x9d). A typical threshold for conditional essentiality on is q-value < 0.05.\n+\n+\n+============================================= ========================================================================================================================\n+**Column Header** **Column Definition**\n+--------------------------------------------- ------------------------------------------------------------------------------------------------------------------------\n+Orf Gene ID\n+Name Gene Name\n+Desc Gene Description\n+N Number of TA sites in the gene.\n+TAs Hit Number of TA sites with at least one insertion.\n+Sum Rd 1 Sum of read counts in condition 1.\n+Sum Rd 2 Sum of read counts in condition 2.\n+Delta Rd Difference in the sum of read counts.\n+p-value P-value calculated by the permutation test.\n+p-adj. Adjusted p-value controlling for the FDR (Benjamini-Hochberg)\n+============================================= ========================================================================================================================\n+\n+\n+\n+-------------------\n+\n+**More Information**\n+\n+-------------------\n+\n+See `TRANSIT documentation`\n+\n+- TRANSIT: https://transit.readthedocs.io/en/latest/index.html\n+- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling\n+]]></help>\n+\n+ <expand macro="citations" />\n+</tool>\n' |