| Next changeset 1:c68753eedf72 (2019-10-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit f63413d629e4de3c69984b3a96ad8ccfe0d47ada" |
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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/tn5gaps-sites1.txt test-data/transit-co1-rep1.wig test-data/transit-co1-rep2.wig test-data/transit-co1-rep3.wig test-data/transit-in-tn5.wig test-data/transit-in1-rep1.wig test-data/transit-in1-rep2.wig test-data/transit-in1.prot test-data/transit-in2-tn5.wig test-data/transit_tn5.prot transit_tn5gaps.xml |
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| diff -r 000000000000 -r e4f44f327cf1 gff_to_prot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gff_to_prot.py Tue Oct 08 08:24:46 2019 -0400 |
| [ |
| @@ -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 e4f44f327cf1 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 08 08:24:46 2019 -0400 |
| [ |
| @@ -0,0 +1,82 @@ +<?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> + <requirement type="package" version="3.7">python</requirement> + <yield /> + </requirements> + </xml> + <token name="@VERSION@">3.0.1</token> + <xml name="outputs"> + <yield /> + <data name="sites" from_work_dir="transit_out.txt" format="tabular" label="${tool.name} on ${on_string} Sites" /> + </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="normal"> + <param name="normalization" argument="-n" type="select" label="Normalization method" value="TTR"> + <option value="TTR">TTR</option> + <option value="nonorm">No Normalization</option> + <option value="nzmean">Non-Zero Mean</option> + <option value="totreads">Total read counts</option> + <option value="zinfnb">Zero inflated Negative Binomial model</option> + <option value="quantile">Quantile Normalization</option> + <option value="betageom">Beta-Geometric Correction</option> + </param> + </xml> + <xml name="standard_inputs"> + <expand macro="inputs" /> + <yield /> + <expand macro="ignore_tas" /> + <expand macro="normal" /> + </xml> + <token name="@LINK_INPUTS@"> + <![CDATA[ + #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 + -n $normalization + </token> +</macros> |
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| diff -r 000000000000 -r e4f44f327cf1 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 Tue Oct 08 08:24:46 2019 -0400 |
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| b'@@ -0,0 +1,500 @@\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;pr'..b'xref=GeneID:3919200;Name=SAOUHSC_00258;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00258\n+NC_007795.1\tRefSeq\tCDS\t276308\t279337\t.\t+\t0\tID=cds-YP_498852.1;Parent=gene-SAOUHSC_00258;Dbxref=Genbank:YP_498852.1,GeneID:3919200;Name=YP_498852.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498852.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t279337\t279795\t.\t+\t.\tID=gene-SAOUHSC_00259;Dbxref=GeneID:3919201;Name=SAOUHSC_00259;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00259\n+NC_007795.1\tRefSeq\tCDS\t279337\t279795\t.\t+\t0\tID=cds-YP_498853.1;Parent=gene-SAOUHSC_00259;Dbxref=Genbank:YP_498853.1,GeneID:3919201;Name=YP_498853.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498853.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t279728\t280009\t.\t+\t.\tID=gene-SAOUHSC_00260;Dbxref=GeneID:3919202;Name=SAOUHSC_00260;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00260\n+NC_007795.1\tRefSeq\tCDS\t279728\t280009\t.\t+\t0\tID=cds-YP_498854.1;Parent=gene-SAOUHSC_00260;Dbxref=Genbank:YP_498854.1,GeneID:3919202;Name=YP_498854.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498854.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t280022\t281356\t.\t+\t.\tID=gene-SAOUHSC_00261;Dbxref=GeneID:3919203;Name=SAOUHSC_00261;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00261\n+NC_007795.1\tRefSeq\tCDS\t280022\t281356\t.\t+\t0\tID=cds-YP_498855.1;Parent=gene-SAOUHSC_00261;Dbxref=Genbank:YP_498855.1,GeneID:3919203;Name=YP_498855.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498855.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t281378\t285817\t.\t+\t.\tID=gene-SAOUHSC_00262;Dbxref=GeneID:3919204;Name=SAOUHSC_00262;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00262\n+NC_007795.1\tRefSeq\tCDS\t281378\t285817\t.\t+\t0\tID=cds-YP_498856.1;Parent=gene-SAOUHSC_00262;Dbxref=Genbank:YP_498856.1,GeneID:3919204;Name=YP_498856.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498856.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t285847\t286239\t.\t+\t.\tID=gene-SAOUHSC_00264;Dbxref=GeneID:3919205;Name=SAOUHSC_00264;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00264\n+NC_007795.1\tRefSeq\tCDS\t285847\t286239\t.\t+\t0\tID=cds-YP_498857.1;Parent=gene-SAOUHSC_00264;Dbxref=Genbank:YP_498857.1,GeneID:3919205;Name=YP_498857.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498857.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t286255\t286569\t.\t+\t.\tID=gene-SAOUHSC_00265;Dbxref=GeneID:3919206;Name=SAOUHSC_00265;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00265\n+NC_007795.1\tRefSeq\tCDS\t286255\t286569\t.\t+\t0\tID=cds-YP_498858.1;Parent=gene-SAOUHSC_00265;Dbxref=Genbank:YP_498858.1,GeneID:3919206;Name=YP_498858.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498858.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t286569\t287243\t.\t+\t.\tID=gene-SAOUHSC_00266;Dbxref=GeneID:3919207;Name=SAOUHSC_00266;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00266\n+NC_007795.1\tRefSeq\tCDS\t286569\t287243\t.\t+\t0\tID=cds-YP_498859.1;Parent=gene-SAOUHSC_00266;Dbxref=Genbank:YP_498859.1,GeneID:3919207;Name=YP_498859.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498859.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t287243\t287560\t.\t+\t.\tID=gene-SAOUHSC_00267;Dbxref=GeneID:3919208;Name=SAOUHSC_00267;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00267\n+NC_007795.1\tRefSeq\tCDS\t287243\t287560\t.\t+\t0\tID=cds-YP_498860.1;Parent=gene-SAOUHSC_00267;Dbxref=Genbank:YP_498860.1,GeneID:3919208;Name=YP_498860.1;Note=conserved hypothetical protein;gbkey=CDS;product=hypothetical protein;protein_id=YP_498860.1;transl_table=11\n+NC_007795.1\tRefSeq\tgene\t287570\t289414\t.\t+\t.\tID=gene-SAOUHSC_00268;Dbxref=GeneID:3919209;Name=SAOUHSC_00268;gbkey=Gene;gene_biotype=protein_coding;locus_tag=SAOUHSC_00268\n' |
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| diff -r 000000000000 -r e4f44f327cf1 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 Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,247 @@\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_00'..b'diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate%3B involved in isoprenoid and isopentenyl-PP biosynthesis%3B forms homodimers\t245250\t245966\t+\t238\t-\t-\tispD\tSAOUHSC_00225\t-\r\n+conserved hypothetical protein\t245959\t246984\t+\t341\t-\t-\tSAOUHSC_00226\tSAOUHSC_00226\t-\r\n+conserved hypothetical protein\t247006\t248694\t+\t562\t-\t-\tSAOUHSC_00227\tSAOUHSC_00227\t-\r\n+conserved hypothetical protein\t248727\t250451\t+\t574\t-\t-\tSAOUHSC_00228\tSAOUHSC_00228\t-\r\n+involved in peptidoglycan cross-linking\t250591\t251265\t+\t224\t-\t-\tSAOUHSC_00229\tSAOUHSC_00229\t-\r\n+two-component sensor histidine kinase%2C putative\t251527\t253266\t+\t579\t-\t-\tSAOUHSC_00230\tSAOUHSC_00230\t-\r\n+two-component response regulator%2C putative\t253269\t254009\t+\t246\t-\t-\tSAOUHSC_00231\tSAOUHSC_00231\t-\r\n+negatively regulates murein hydrolase activity\t254122\t254565\t+\t147\t-\t-\tSAOUHSC_00232\tSAOUHSC_00232\t-\r\n+in conjunction with LrgA this protein inhibits the expression or activity of extracellular murein hydrolases\t254558\t255259\t+\t233\t-\t-\tSAOUHSC_00233\tSAOUHSC_00233\t-\r\n+conserved hypothetical protein\t255367\t256071\t-\t234\t-\t-\tSAOUHSC_00234\tSAOUHSC_00234\t-\r\n+conserved hypothetical protein\t256220\t257011\t+\t263\t-\t-\tSAOUHSC_00235\tSAOUHSC_00235\t-\r\n+6-phospho-beta-glucosidase%2C putative\t257027\t258463\t+\t478\t-\t-\tSAOUHSC_00236\tSAOUHSC_00236\t-\r\n+conserved hypothetical protein\t258896\t259657\t-\t253\t-\t-\tSAOUHSC_00237\tSAOUHSC_00237\t-\r\n+-\t259676\t259810\t+\t44\t-\t-\tSAOUHSC_00238\tSAOUHSC_00238\t-\r\n+ribokinase%2C putative\t259908\t260822\t-\t304\t-\t-\tSAOUHSC_00239\tSAOUHSC_00239\t-\r\n+cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose%3B RbsD is required for efficient ribose utilization in E. coli%3B rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source\t260850\t261254\t-\t134\t-\t-\tSAOUHSC_00240\tSAOUHSC_00240\t-\r\n+conserved hypothetical protein\t261269\t262150\t-\t293\t-\t-\tSAOUHSC_00241\tSAOUHSC_00241\t-\r\n+conserved hypothetical protein\t262382\t263380\t-\t332\t-\t-\tSAOUHSC_00242\tSAOUHSC_00242\t-\r\n+NADH dehydrogenase subunit%2C putative\t263531\t263710\t+\t59\t-\t-\tSAOUHSC_00243\tSAOUHSC_00243\t-\r\n+conserved hypothetical protein\t263760\t264152\t+\t130\t-\t-\tSAOUHSC_00244\tSAOUHSC_00244\t-\r\n+drug transporter%2C putative\t264825\t266201\t-\t458\t-\t-\tSAOUHSC_00246\tSAOUHSC_00246\t-\r\n+conserved hypothetical protein\t266435\t267427\t+\t330\t-\t-\tSAOUHSC_00247\tSAOUHSC_00247\t-\r\n+peptidoglycan hydrolase%2C putative\t267753\t268703\t+\t316\t-\t-\tSAOUHSC_00248\tSAOUHSC_00248\t-\r\n+conserved hypothetical protein\t268755\t269414\t-\t219\t-\t-\tSAOUHSC_00249\tSAOUHSC_00249\t-\r\n+conserved hypothetical protein\t269428\t270348\t-\t306\t-\t-\tSAOUHSC_00250\tSAOUHSC_00250\t-\r\n+conserved hypothetical protein\t270345\t271511\t-\t388\t-\t-\tSAOUHSC_00251\tSAOUHSC_00251\t-\r\n+conserved hypothetical protein\t271579\t273102\t-\t507\t-\t-\tSAOUHSC_00253\tSAOUHSC_00253\t-\r\n+conserved hypothetical protein\t273373\t274026\t+\t217\t-\t-\tSAOUHSC_00254\tSAOUHSC_00254\t-\r\n+conserved hypothetical protein\t274060\t274647\t+\t195\t-\t-\tSAOUHSC_00255\tSAOUHSC_00255\t-\r\n+conserved hypothetical protein\t274790\t275683\t-\t297\t-\t-\tSAOUHSC_00256\tSAOUHSC_00256\t-\r\n+conserved hypothetical protein\t275931\t276224\t+\t97\t-\t-\tSAOUHSC_00257\tSAOUHSC_00257\t-\r\n+conserved hypothetical protein\t276308\t279337\t+\t1009\t-\t-\tSAOUHSC_00258\tSAOUHSC_00258\t-\r\n+conserved hypothetical protein\t279337\t279795\t+\t152\t-\t-\tSAOUHSC_00259\tSAOUHSC_00259\t-\r\n+conserved hypothetical protein\t279728\t280009\t+\t93\t-\t-\tSAOUHSC_00260\tSAOUHSC_00260\t-\r\n+conserved hypothetical protein\t280022\t281356\t+\t444\t-\t-\tSAOUHSC_00261\tSAOUHSC_00261\t-\r\n+conserved hypothetical protein\t281378\t285817\t+\t1479\t-\t-\tSAOUHSC_00262\tSAOUHSC_00262\t-\r\n+conserved hypothetical protein\t285847\t286239\t+\t130\t-\t-\tSAOUHSC_00264\tSAOUHSC_00264\t-\r\n+conserved hypothetical protein\t286255\t286569\t+\t104\t-\t-\tSAOUHSC_00265\tSAOUHSC_00265\t-\r\n+conserved hypothetical protein\t286569\t287243\t+\t224\t-\t-\tSAOUHSC_00266\tSAOUHSC_00266\t-\r\n+conserved hypothetical protein\t287243\t287560\t+\t105\t-\t-\tSAOUHSC_00267\tSAOUHSC_00267\t-\r\n+-\t287570\t289414\t+\t614\t-\t-\tSAOUHSC_00268\tSAOUHSC_00268\t-\r\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/gumbel-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gumbel-sites1.txt Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b"@@ -0,0 +1,1011 @@\n+#Gumbel\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit gumbel transit-co1-rep1_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep3_smol.wig transit-in1_smol.prot gumbel-sites1_smol.txt -s 1000 -b 100\n+#Data: b'transit-co1-rep1_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep3_smol.wig'\n+#Annotation path: b'transit-in1_smol.prot'\n+#FDR Corrected thresholds: 0.989000, 0.529000\n+#MH Acceptance-Rate:\t79.07%\n+#Total Iterations Performed:\t1099\n+#Sample Size:\t1000\n+#phi estimate:\t0.407618\n+#Time: 9.027700185775757\n+#Orf\tName\tDesc\tk\tn\tr\ts\tzbar\tCall\n+Rv0001\tdnaA\tchromosomal replication initiation protein \t0\t31\t31\t1365\t1.000000\tE\n+Rv0002\tdnaN\tDNA polymerase III subunit beta \t0\t31\t31\t1167\t1.000000\tE\n+Rv0003\trecF\trecombination protein F \t10\t35\t9\t140\t0.001000\tNE\n+Rv0004\t-\thypothetical protein Rv0004 \t0\t7\t7\t327\t0.975000\tU\n+Rv0005\tgyrB\tDNA gyrase subunit B \t2\t42\t40\t1997\t1.000000\tE\n+Rv0006\tgyrA\tDNA gyrase subunit A \t1\t45\t44\t2243\t1.000000\tE\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t4\t10\t3\t256\t0.001000\tNE\n+Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t3\t4\t1\t2\t0.000000\tNE\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t3\t7\t2\t50\t0.000000\tNE\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t5\t10\t4\t119\t0.000000\tNE\n+Rv0011c\t-\tputative septation inhibitor protein \t0\t3\t3\t133\t-1.000000\tS\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t9\t16\t3\t89\t0.000000\tNE\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t2\t15\t12\t528\t0.989000\tU\n+Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t0\t24\t24\t1784\t1.000000\tE\n+Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t1\t16\t15\t1244\t1.000000\tE\n+Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t9\t37\t8\t240\t0.001000\tNE\n+Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t14\t27\t4\t64\t0.000000\tNE\n+Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t6\t25\t12\t695\t0.965000\tU\n+Rv0019c\t-\thypothetical protein Rv0019c \t7\t13\t2\t20\t0.000000\tNE\n+Rv0020c\tTB39.8\thypothetical protein Rv0020c \t8\t52\t43\t1029\t0.529000\tU\n+Rv0021c\t-\thypothetical protein Rv0021c \t18\t22\t1\t2\t0.000000\tNE\n+Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t8\t0\t0\t0.000000\tNE\n+Rv0023\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN \t0\t12\t12\t582\t0.997000\tE\n+Rv0024\t-\tPUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN \t7\t12\t1\t2\t0.000000\tNE\n+Rv0025\t-\thypothetical protein Rv0025 \t5\t7\t1\t2\t0.000000\tNE\n+Rv0026\t-\thypothetical protein Rv0026 \t8\t14\t3\t188\t0.000000\tNE\n+Rv0027\t-\thypothetical protein Rv0027 \t2\t5\t2\t64\t0.000000\tNE\n+Rv0028\t-\thypothetical protein Rv0028 \t3\t5\t2\t111\t0.000000\tNE\n+Rv0029\t-\thypothetical protein Rv0029 \t13\t18\t2\t30\t0.000000\tNE\n+Rv0030\t-\thypothetical protein Rv0030 \t1\t5\t3\t86\t0.000000\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) \t30\t57\t8\t98\t0.000000\tNE\n+Rv0033\tacpA\tPROBABLE ACYL CARRIER PROTEIN ACPA (ACP) \t3\t3\t0\t0\t-1.000000\tS\n+Rv0034\t-\thypothetical protein Rv0034 \t5\t5\t0\t0\t-1.000000\tS\n+Rv0035\tfadD34\tPROBABLE FATTY-ACID-CoA LIGASE FADD34 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE) \t21\t25\t2\t110\t0.000000\tNE\n+Rv0036c\t-\thypothetical protein Rv0036c \t3\t4\t1\t2\t0.000000\tNE\n+Rv0037c\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t18\t20\t1\t2\t0.000000\tNE\n+Rv0038\t-\thypothetical protein Rv0038 \t6\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) \t6\t9\t2\t22\t0.000000\tNE\n+Rv0041\tleuS\tleucyl-tRNA synthetase \t0\t72\t72\t2800\t0.726000\tU\n+Rv0042c\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY MARR-FAMILY) \t4\t5\t1\t2\t0.000000\tNE\n+Rv0043c\t-\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) \t7\t10\t1\t2\t0.00"..b' PHOSPHATE-BINDING LIPOPROTEIN PSTS1 (PBP-1) (PSTS1) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0935\tpstC1\tPHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTC1 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0936\tpstA2\tPHOSPHATE-TRANSPORT INTEGRAL MEMBRANE ABC TRANSPORTER PSTA2 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0937c\t-\thypothetical protein Rv0937c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0938\t-\tATP-dependent DNA ligase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0939\t-\tPOSSIBLE BIFUNCTIONAL ENZYME: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE (HHDD ISOMERASE) + CYCLASE/DEHYDRASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0940c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0941c\t-\thypothetical protein Rv0941c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0942\t-\thypothetical protein Rv0942 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0943c\t-\tPROBABLE MONOOXYGENASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0944\t-\tPOSSIBLE FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FAPY-DNA GLYCOSYLASE) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0945\t-\tshort chain dehydrogenase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0946c\tpgi\tglucose-6-phosphate isomerase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0948c\t-\thypothetical protein Rv0948c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0949\tuvrD1\tPROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0950c\t-\thypothetical protein Rv0950c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0951\tsucC\tsuccinyl-CoA synthetase subunit beta \t0\t0\t0\t0\t-1.000000\tS\n+Rv0952\tsucD\tsuccinyl-CoA synthetase subunit alpha \t0\t0\t0\t0\t-1.000000\tS\n+Rv0953c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0954\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0955\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0956\tpurN\tphosphoribosylglycinamide formyltransferase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0957\tpurH\tbifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0958\t-\tPOSSIBLE MAGNESIUM CHELATASE \t0\t0\t0\t0\t-1.000000\tS\n+Rv0959\t-\thypothetical protein Rv0959 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0960\t-\thypothetical protein Rv0960 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0961\t-\tPROBABLE INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0962c\tlprP\tPOSSIBLE LIPOPROTEIN LPRP \t0\t0\t0\t0\t-1.000000\tS\n+Rv0963c\t-\thypothetical protein Rv0963c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0964c\t-\thypothetical protein Rv0964c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0965c\t-\thypothetical protein Rv0965c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0966c\t-\thypothetical protein Rv0966c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0967\t-\thypothetical protein Rv0967 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0968\t-\thypothetical protein Rv0968 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0969\tctpV\tPROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t0\t0\t0\t0\t-1.000000\tS\n+Rv0970\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0971c\techA7\tenoyl-CoA hydratase \t0\t0\t0\t0\t-1.000000\tS\n+Rv0972c\tfadE12\tPROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0973c\taccA2\tPROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0974c\taccD2\tPROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0975c\tfadE13\tPROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0976c\t-\thypothetical protein Rv0976c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0977\tPE_PGRS16\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0978c\tPE_PGRS17\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0979A\trpmF\t50S ribosomal protein L32 \t0\t0\t0\t0\t-1.000000\tS\n+Rv0979c\t-\thypothetical protein Rv0979c \t0\t0\t0\t0\t-1.000000\tS\n+Rv0980c\tPE_PGRS18\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t-1.000000\tS\n+Rv0981\tmprA\tMYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0982\tmprB\tPROBABLE TWO COMPONENT SENSOR KINASE MPRB \t0\t0\t0\t0\t-1.000000\tS\n+Rv0983\tpepD\tPROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t0\t0\t0\t0\t-1.000000\tS\n+Rv0984\tmoaB2\tPOSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t0\t0\t0\t0\t-1.000000\tS\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/hmm-genes1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmm-genes1.txt Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,1004 @@\n+#HMM - Genes\n+#genes: ES=14, GD=6, NE=80, GA=0, N/A=900\n+#key: ES=essential, GD=insertions cause growth-defect, NE=non-essential, GA=insertions confer growth-advantage, N/A=not analyzed (genes with 0 TA sites)\n+#ORF\tgene\tannotation\tTAs\tES sites\tGD sites\tNE sites\tGA sites\tsaturation\tmean\tcall\n+Rv0001\tdnaA\tchromosomal replication initiation protein \t32\t31\t0\t1\t0\t0.0312\t110.00\tES\n+Rv0002\tdnaN\tDNA polymerase III subunit beta \t31\t31\t0\t0\t0\t0.0000\t0.00\tES\n+Rv0003\trecF\trecombination protein F \t35\t5\t0\t30\t0\t0.3714\t60.85\tNE\n+Rv0004\t-\thypothetical protein Rv0004 \t8\t6\t0\t2\t0\t0.2500\t78.00\tES\n+Rv0005\tgyrB\tDNA gyrase subunit B \t43\t40\t0\t3\t0\t0.0698\t174.33\tES\n+Rv0006\tgyrA\tDNA gyrase subunit A \t46\t44\t0\t2\t0\t0.0435\t279.00\tES\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t11\t0\t0\t11\t0\t0.3636\t86.50\tNE\n+Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t0\t0\t4\t0\t0.7500\t314.00\tNE\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t0\t0\t7\t0\t1.0000\t175.29\tNE\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t0\t0\t10\t0\t0.6000\t298.83\tNE\n+Rv0011c\t-\tputative septation inhibitor protein \t3\t0\t0\t3\t0\t0.0000\t0.00\tNE\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t0\t0\t16\t0\t0.7500\t330.08\tNE\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t15\t0\t0\t0\t0.0667\t11.00\tES\n+Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t25\t25\t0\t0\t0\t0.0400\t11.00\tES\n+Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t16\t0\t15\t1\t0\t0.0625\t377.00\tGD\n+Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t37\t0\t33\t4\t0\t0.3514\t55.38\tGD\n+Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t27\t0\t0\t27\t0\t0.4815\t104.69\tNE\n+Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t25\t12\t0\t13\t0\t0.3200\t48.62\tNE\n+Rv0019c\t-\thypothetical protein Rv0019c \t13\t1\t0\t12\t0\t0.6154\t289.25\tNE\n+Rv0020c\tTB39.8\thypothetical protein Rv0020c \t52\t43\t0\t9\t0\t0.1346\t94.29\tES\n+Rv0021c\t-\thypothetical protein Rv0021c \t23\t0\t0\t23\t0\t0.8696\t359.65\tNE\n+Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t0\t0\t8\t0\t1.0000\t421.75\tNE\n+Rv0023\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN \t12\t12\t0\t0\t0\t0.0000\t0.00\tES\n+Rv0024\t-\tPUTATIVE SECRETED PROTEIN P60-RELATED PROTEIN \t13\t0\t0\t13\t0\t0.8462\t265.09\tNE\n+Rv0025\t-\thypothetical protein Rv0025 \t8\t0\t0\t8\t0\t1.0000\t79.00\tNE\n+Rv0026\t-\thypothetical protein Rv0026 \t15\t0\t0\t15\t0\t0.7333\t228.64\tNE\n+Rv0027\t-\thypothetical protein Rv0027 \t5\t0\t0\t5\t0\t0.4000\t105.50\tNE\n+Rv0028\t-\thypothetical protein Rv0028 \t5\t0\t0\t5\t0\t0.4000\t136.00\tNE\n+Rv0029\t-\thypothetical protein Rv0029 \t19\t0\t0\t19\t0\t0.7895\t196.33\tNE\n+Rv0030\t-\thypothetical protein Rv0030 \t5\t0\t0\t5\t0\t0.2000\t124.00\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\t298.86\tNE\n+Rv0033\tacpA\tPROBABLE ACYL CARRIER PROTEIN ACPA (ACP) \t3\t0\t0\t3\t0\t1.0000\t186.67\tNE\n+Rv0034\t-\thypothetical protein Rv0034 \t5\t0\t0\t5\t0\t0.8000\t236.25\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\t284.59\tNE\n+Rv0036c\t-\thypothetical protein Rv0036c \t4\t0\t0\t4\t0\t1.0000\t733.00\tNE\n+Rv0037c\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t21\t0\t0\t21\t0\t0.6190\t272.23\tNE\n+Rv0038\t-\thypothetical protein Rv0038 \t8\t0\t0\t8\t0\t0.7500\t420.33\tNE\n+Rv0039c\t-\tPOSSIBLE CONSERVED TRANSMEMBRANE PROTEIN \t4\t0\t0\t4\t0\t0.5000\t625.50\tNE\n+Rv0040c\tmtc28\tSECRETED PROLINE RICH PROTEIN MTC28 (PROLINE RICH 28 KDA ANTIGEN) \t10\t0\t0\t10\t0\t0.5000\t82.80\tNE\n+Rv0041\tleuS\tleucyl-tRNA synthetase \t73\t72\t0\t1\t0\t0.0137\t104.00\tES\n+Rv0042c\t-\tPOSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY MARR-FAMILY) \t5\t0\t0\t5\t0\t0.6000\t100.33\tNE\n+Rv0043c\t-\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY GNTR-FAMILY) \t11\t0\t0\t11\t0\t0.7273\t126.50\tNE\n+Rv0044c\t-\tPOSSIBLE OXIDORED'..b'protein Rv0937c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0938\t-\tATP-dependent DNA ligase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0939\t-\tPOSSIBLE BIFUNCTIONAL ENZYME: 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE (HHDD ISOMERASE) + CYCLASE/DEHYDRASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0940c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0941c\t-\thypothetical protein Rv0941c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0942\t-\thypothetical protein Rv0942 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0943c\t-\tPROBABLE MONOOXYGENASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0944\t-\tPOSSIBLE FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE (FAPY-DNA GLYCOSYLASE) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0945\t-\tshort chain dehydrogenase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0946c\tpgi\tglucose-6-phosphate isomerase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0948c\t-\thypothetical protein Rv0948c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0949\tuvrD1\tPROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0950c\t-\thypothetical protein Rv0950c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0951\tsucC\tsuccinyl-CoA synthetase subunit beta \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0952\tsucD\tsuccinyl-CoA synthetase subunit alpha \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0953c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0954\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0955\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0956\tpurN\tphosphoribosylglycinamide formyltransferase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0957\tpurH\tbifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0958\t-\tPOSSIBLE MAGNESIUM CHELATASE \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0959\t-\thypothetical protein Rv0959 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0960\t-\thypothetical protein Rv0960 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0961\t-\tPROBABLE INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0962c\tlprP\tPOSSIBLE LIPOPROTEIN LPRP \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0963c\t-\thypothetical protein Rv0963c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0964c\t-\thypothetical protein Rv0964c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0965c\t-\thypothetical protein Rv0965c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0966c\t-\thypothetical protein Rv0966c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0967\t-\thypothetical protein Rv0967 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0968\t-\thypothetical protein Rv0968 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0969\tctpV\tPROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0970\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0971c\techA7\tenoyl-CoA hydratase \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0972c\tfadE12\tPROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0973c\taccA2\tPROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0974c\taccD2\tPROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0975c\tfadE13\tPROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0976c\t-\thypothetical protein Rv0976c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0977\tPE_PGRS16\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0978c\tPE_PGRS17\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0979c\t-\thypothetical protein Rv0979c \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0979A\trpmF\t50S ribosomal protein L32 \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0980c\tPE_PGRS18\tPE-PGRS FAMILY PROTEIN \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0981\tmprA\tMYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0982\tmprB\tPROBABLE TWO COMPONENT SENSOR KINASE MPRB \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0983\tpepD\tPROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n+Rv0984\tmoaB2\tPOSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t0\t0\t0\t0\t0\t0.0000\t0.00\tN/A\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/hmm-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hmm-sites1.txt Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,2016 @@\n+#HMM - Sites\n+# Tn-HMM\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit hmm transit-in1-rep1_smol.wig,transit-in1-rep2_smol.wig transit-in1_smol.prot hmm_smol\n+# \n+# Mean:\t257.30\n+# Median:\t132.00\n+# Normalization:\tTTR\n+# LOESS Correction:\tFalse\n+# pins (obs):\t0.473974\n+# pins (est):\t0.633445\n+# Run length (r):\t5\n+# State means:\n+# ES: 1.0101 GD: 3.9520 NE: 195.2002 GA: 976.0011\n+# Self-Transition Prob:\n+# ES: -3.5286e-12 GD: -3.5286e-12 NE: -3.5286e-12 GA: -3.5286e-12\n+# State Emission Parameters (theta):\n+# ES: 0.9900 GD: 0.2530 NE: 0.0051 GA: 0.0010\n+# State Distributions:# ES: 24.47% GD: 4.70% NE: 70.82% GA: 0.00%\n+60\t0\t1.00e+00 \t5.77e-14 \t8.74e-16 \t1.74e-16 \tES\tRv0001_(dnaA)\n+72\t0\t1.00e+00 \t1.47e-14 \t4.52e-18 \t1.80e-19 \tES\tRv0001_(dnaA)\n+102\t0\t1.00e+00 \t3.77e-15 \t2.34e-20 \t1.86e-22 \tES\tRv0001_(dnaA)\n+188\t0\t1.00e+00 \t9.63e-16 \t1.21e-22 \t1.94e-25 \tES\tRv0001_(dnaA)\n+246\t0\t1.00e+00 \t2.46e-16 \t6.34e-25 \t1.64e-27 \tES\tRv0001_(dnaA)\n+333\t0\t1.00e+00 \t6.29e-17 \t1.05e-26 \t1.44e-27 \tES\tRv0001_(dnaA)\n+360\t0\t1.00e+00 \t1.61e-17 \t7.25e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+426\t0\t1.00e+00 \t4.13e-18 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+448\t0\t1.00e+00 \t1.07e-18 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+471\t0\t1.00e+00 \t2.85e-19 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+483\t0\t1.00e+00 \t8.46e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+494\t0\t1.00e+00 \t3.35e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+504\t0\t1.00e+00 \t2.04e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+514\t0\t1.00e+00 \t1.71e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+525\t0\t1.00e+00 \t1.63e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+534\t0\t1.00e+00 \t1.62e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+601\t0\t1.00e+00 \t1.65e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+653\t0\t1.00e+00 \t1.80e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+670\t0\t1.00e+00 \t2.41e-20 \t7.23e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+706\t0\t1.00e+00 \t4.78e-20 \t7.24e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+741\t0\t1.00e+00 \t1.41e-19 \t7.60e-27 \t1.43e-27 \tES\tRv0001_(dnaA)\n+784\t0\t1.00e+00 \t5.04e-19 \t7.85e-26 \t1.43e-27 \tES\tRv0001_(dnaA)\n+794\t0\t1.00e+00 \t1.92e-18 \t1.38e-23 \t1.43e-27 \tES\tRv0001_(dnaA)\n+843\t0\t1.00e+00 \t7.48e-18 \t2.66e-21 \t1.43e-27 \tES\tRv0001_(dnaA)\n+989\t0\t1.00e+00 \t2.92e-17 \t5.14e-19 \t1.45e-27 \tES\tRv0001_(dnaA)\n+1092\t0\t1.00e+00 \t1.14e-16 \t9.94e-17 \t1.35e-26 \tES\tRv0001_(dnaA)\n+1104\t0\t1.00e+00 \t4.47e-16 \t1.92e-14 \t1.16e-23 \tES\tRv0001_(dnaA)\n+1267\t0\t1.00e+00 \t1.75e-15 \t3.71e-12 \t1.12e-20 \tES\tRv0001_(dnaA)\n+1278\t0\t1.00e+00 \t6.85e-15 \t7.17e-10 \t1.08e-17 \tES\tRv0001_(dnaA)\n+1345\t0\t1.00e+00 \t2.68e-14 \t1.39e-07 \t1.05e-14 \tES\tRv0001_(dnaA)\n+1423\t0\t1.00e+00 \t1.05e-13 \t2.68e-05 \t1.01e-11 \tES\tRv0001_(dnaA)\n+1522\t110\t3.38e-218\t1.58e-24 \t1.00e+00 \t2.97e-06 \tNE\tRv0001_(dnaA)\n+1552\t41\t4.33e-104\t1.32e-27 \t1.00e+00 \t2.24e-06 \tNE\t\n+1635\t199\t0.00e+00 \t1.25e-47 \t1.00e+00 \t4.28e-06 \tNE\t\n+1779\t0\t4.55e-13 \t5.03e-16 \t1.00e+00 \t1.89e-06 \tNE\t\n+1782\t0\t4.57e-13 \t5.13e-16 \t1.00e+00 \t1.89e-06 \tNE\t\n+1788\t0\t4.57e-13 \t5.13e-16 \t1.00e+00 \t1.89e-06 \tNE\t\n+1847\t0\t4.57e-13 \t5.13e-16 \t1.00e+00 \t1.89e-06 \tNE\t\n+1858\t342\t0.00e+00 \t1.36e-58 \t1.00e+00 \t7.70e-06 \tNE\t\n+1921\t19\t4.42e-60 \t7.14e-14 \t1.00e+00 \t2.04e-06 \tNE\t\n+2001\t0\t9.95e-01 \t4.87e-13 \t5.17e-03 \t9.77e-09 \tES\t\n+2012\t0\t1.00e+00 \t1.27e-13 \t2.68e-05 \t1.01e-11 \tES\t\n+2063\t0\t1.00e+00 \t3.24e-14 \t1.39e-07 \t1.05e-14 \tES\tRv0002_(dnaN)\n+2104\t0\t1.00e+00 \t8.28e-15 \t7.17e-10 \t1.08e-17 \tES\tRv0002_(dnaN)\n+2141\t0\t1.00e+00 \t2.12e-15 \t3.71e-12 \t1.12e-20 \tES\tRv0002_(dnaN)\n+2232\t0\t1.00e+00 \t5.41e-16 \t1.92e-14 \t1.16e-23 \tES\tRv0002_(dnaN)\n+2290\t0\t1.00e+00 \t1.38e-16 \t9.94e-17 \t1.35e-26 \tES\tRv0002_(dnaN)\n+2315\t0\t1.00e+00 \t3.53e-17 \t5.14e-19 \t1.45e-27 \tES\tRv0002_(dnaN)\n+2318\t0\t1.00e+00 \t9.03e-18 \t2.66e-21 \t1.43e-27 \tES\tRv0002_(dnaN)\n+2333\t0\t1.00e+00 \t2.31e-18 \t1.38e-23 \t1.43e-27 \tES\tRv0002_(dnaN)\n+2344\t0\t1.00e+00 \t5.92e-19 \t7.85e-26 \t1.43e-27 \tES\tRv0002_(dnaN)\n+2363\t0\t1.00e+00 \t1.53e-19 \t7.60e-27 \t1.43e-27 \tES\tRv0002_(dnaN)\n+2387\t0\t1.00e+00 \t4.08e-20 \t7.24e-27 \t1.43e-27 \tES\tRv00'..b'\t6.44e-104\t2.04e-26 \t1.00e+00 \t8.38e-25 \tNE\tRv0097_(-)\n+106858\t125\t5.08e-272\t1.92e-38 \t1.00e+00 \t9.58e-25 \tNE\tRv0097_(-)\n+106906\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t5.25e-25 \tNE\tRv0097_(-)\n+106926\t82\t7.91e-184\t2.14e-31 \t1.00e+00 \t6.94e-25 \tNE\tRv0097_(-)\n+106929\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t5.12e-25 \tNE\tRv0097_(-)\n+106941\t271\t0.00e+00 \t6.39e-55 \t1.00e+00 \t1.92e-24 \tNE\tRv0097_(-)\n+107024\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t6.37e-25 \tNE\tRv0097_(-)\n+107031\t142\t1.08e-303\t7.28e-39 \t1.00e+00 \t1.00e-24 \tNE\tRv0097_(-)\n+107033\t0\t1.00e-17 \t1.70e-19 \t1.00e+00 \t5.59e-25 \tNE\tRv0097_(-)\n+107039\t0\t1.01e-17 \t1.74e-19 \t1.00e+00 \t6.47e-25 \tNE\tRv0097_(-)\n+107106\t593\t0.00e+00 \t2.63e-93 \t1.00e+00 \t1.60e-23 \tNE\tRv0097_(-)\n+107226\t0\t5.19e-20 \t3.44e-21 \t1.00e+00 \t1.41e-24 \tNE\tRv0097_(-)\n+107245\t147\t1.10e-313\t1.74e-39 \t1.00e+00 \t1.41e-24 \tNE\tRv0097_(-)\n+107278\t0\t5.19e-20 \t4.72e-21 \t1.00e+00 \t7.13e-25 \tNE\tRv0097_(-)\n+107288\t17\t5.67e-54 \t3.63e-23 \t1.00e+00 \t1.11e-24 \tNE\tRv0097_(-)\n+107328\t146\t5.66e-314\t9.21e-40 \t1.00e+00 \t5.48e-24 \tNE\tRv0097_(-)\n+107436\t7\t2.77e-36 \t7.02e-23 \t1.00e+00 \t8.55e-24 \tNE\tRv0097_(-)\n+107452\t331\t0.00e+00 \t3.30e-63 \t1.00e+00 \t1.33e-22 \tNE\tRv0097_(-)\n+107456\t1473\t0.00e+00 \t3.09e-206\t1.00e+00 \t2.85e-20 \tNE\tRv0097_(-)\n+107466\t110\t4.70e-242\t1.39e-36 \t1.00e+00 \t1.05e-22 \tNE\tRv0097_(-)\n+107553\t0\t1.94e-15 \t1.15e-17 \t1.00e+00 \t1.92e-23 \tNE\tRv0097_(-)\n+107592\t0\t1.95e-15 \t1.18e-17 \t1.00e+00 \t4.19e-24 \tNE\tRv0097_(-)\n+107696\t0\t1.95e-15 \t1.18e-17 \t1.00e+00 \t1.20e-24 \tNE\tRv0098_(-)\n+107717\t17\t2.12e-49 \t8.87e-20 \t1.00e+00 \t6.65e-25 \tNE\tRv0098_(-)\n+107735\t94\t4.33e-210\t6.34e-30 \t1.00e+00 \t8.59e-25 \tNE\tRv0098_(-)\n+107765\t0\t5.19e-20 \t3.46e-21 \t1.00e+00 \t7.23e-25 \tNE\tRv0098_(-)\n+107795\t47\t6.61e-114\t4.88e-27 \t1.00e+00 \t1.86e-24 \tNE\tRv0098_(-)\n+107797\t0\t5.19e-20 \t3.46e-21 \t1.00e+00 \t4.98e-24 \tNE\tRv0098_(-)\n+107858\t150\t1.12e-319\t7.38e-40 \t1.00e+00 \t4.12e-23 \tNE\tRv0098_(-)\n+107927\t97\t4.40e-216\t1.18e-34 \t1.00e+00 \t1.02e-22 \tNE\tRv0098_(-)\n+107947\t35\t3.29e-92 \t7.51e-17 \t1.00e+00 \t2.59e-22 \tNE\tRv0098_(-)\n+108059\t4\t5.45e-20 \t2.50e-10 \t1.00e+00 \t9.13e-22 \tNE\tRv0098_(-)\n+108129\t0\t2.70e-06 \t8.37e-10 \t1.00e+00 \t4.19e-21 \tNE\tRv0098_(-)\n+108149\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t2.19e-23 \tNE\tRv0098_(-)\n+108179\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t1.04e-24 \tNE\tRv0099_(fadD10)\n+108197\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t2.94e-24 \tNE\tRv0099_(fadD10)\n+108272\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t1.30e-23 \tNE\tRv0099_(fadD10)\n+108285\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t7.94e-23 \tNE\tRv0099_(fadD10)\n+108344\t0\t2.72e-06 \t8.38e-10 \t1.00e+00 \t1.58e-20 \tNE\tRv0099_(fadD10)\n+108356\t156\t6.03e-318\t3.14e-29 \t1.00e+00 \t2.84e-17 \tNE\tRv0099_(fadD10)\n+108393\t0\t2.70e-06 \t5.00e-11 \t1.00e+00 \t1.49e-17 \tNE\tRv0099_(fadD10)\n+108565\t0\t2.72e-06 \t5.10e-11 \t1.00e+00 \t1.68e-20 \tNE\tRv0099_(fadD10)\n+108586\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t1.11e-21 \tNE\tRv0099_(fadD10)\n+108596\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t1.07e-21 \tNE\tRv0099_(fadD10)\n+108692\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t1.20e-21 \tNE\tRv0099_(fadD10)\n+108718\t0\t2.72e-06 \t5.11e-11 \t1.00e+00 \t2.13e-21 \tNE\tRv0099_(fadD10)\n+108807\t0\t2.72e-06 \t5.10e-11 \t1.00e+00 \t2.23e-19 \tNE\tRv0099_(fadD10)\n+108850\t272\t0.00e+00 \t6.97e-45 \t1.00e+00 \t6.42e-16 \tNE\tRv0099_(fadD10)\n+108854\t220\t0.00e+00 \t2.83e-50 \t1.00e+00 \t5.19e-16 \tNE\tRv0099_(fadD10)\n+108899\t0\t5.19e-20 \t8.51e-20 \t1.00e+00 \t2.10e-16 \tNE\tRv0099_(fadD10)\n+108952\t90\t8.24e-200\t5.44e-31 \t1.00e+00 \t3.05e-16 \tNE\tRv0099_(fadD10)\n+108976\t0\t1.49e-08 \t5.33e-12 \t1.00e+00 \t2.11e-16 \tNE\tRv0099_(fadD10)\n+109024\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t2.16e-16 \tNE\tRv0099_(fadD10)\n+109032\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t2.42e-16 \tNE\tRv0099_(fadD10)\n+109070\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t3.67e-16 \tNE\tRv0099_(fadD10)\n+109079\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t9.98e-16 \tNE\tRv0099_(fadD10)\n+109104\t0\t1.50e-08 \t5.44e-12 \t1.00e+00 \t5.15e-15 \tNE\tRv0099_(fadD10)\n+109197\t10\t1.57e-28 \t3.09e-13 \t1.00e+00 \t1.03e-12 \tNE\tRv0099_(fadD10)\n+109215\t115\t6.69e-252\t2.11e-26 \t1.00e+00 \t1.72e-12 \tNE\tRv0099_(fadD10)\n+109226\t0\t2.27e-10 \t5.87e-11 \t1.00e+00 \t1.30e-12 \tNE\tRv0099_(fadD10)\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/resampling-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/resampling-sites1.txt Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b"@@ -0,0 +1,1007 @@\n+#Resampling\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit resampling transit-in1-rep2_smol.wig,transit-in1-rep1_smol.wig transit-co1-rep3_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep1_smol.wig transit-in1_smol.prot resampling-sites1_smol.txt\n+#Control Data: b'transit-in1-rep2_smol.wig,transit-in1-rep1_smol.wig'\n+#Experimental Data: b'transit-co1-rep3_smol.wig,transit-co1-rep2_smol.wig,transit-co1-rep1_smol.wig'\n+#Annotation path: b'transit-in1_smol.prot' \n+#Time: 64.01395511627197\n+#Orf\tName\tDesc\tSites\tMean Ctrl\tMean Exp\tlog2FC\tSum Ctrl\tSum Exp\tDelta Mean\tp-value\tAdj. p-value\n+Rv0001\tdnaA\tchromosomal replication initiation protein \t31\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0002\tdnaN\tDNA polymerase III subunit beta \t31\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0003\trecF\trecombination protein F \t35\t22.6\t27.7\t0.30\t1579.1\t2907.67\t5.1\t0.66630\t1.00000\n+Rv0004\t-\thypothetical protein Rv0004 \t7\t2.9\t0.0\t-1.97\t40.8\t0.00\t-2.9\t0.40810\t1.00000\n+Rv0005\tgyrB\tDNA gyrase subunit B \t42\t11.3\t3.6\t-1.66\t951.9\t450.90\t-7.8\t0.40760\t1.00000\n+Rv0006\tgyrA\tDNA gyrase subunit A \t45\t5.7\t2.4\t-1.22\t511.8\t330.34\t-3.2\t0.50960\t1.00000\n+Rv0007\t-\tPOSSIBLE CONSERVED MEMBRANE PROTEIN \t10\t16.2\t53.7\t1.73\t323.1\t1610.25\t37.5\t0.47710\t1.00000\n+Rv0008c\t-\tPOSSIBLE MEMBRANE PROTEIN \t4\t235.5\t195.4\t-0.27\t1884.3\t2345.17\t-40.1\t0.74730\t1.00000\n+Rv0009\tppiA\tPROBABLE IRON-REGULATED PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A PPIA (PPIase A) (ROTAMASE A) \t7\t175.3\t89.0\t-0.98\t2453.5\t1869.11\t-86.2\t0.24570\t1.00000\n+Rv0010c\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t10\t179.3\t172.9\t-0.05\t3586.6\t5186.87\t-6.4\t0.94490\t1.00000\n+Rv0011c\t-\tputative septation inhibitor protein \t3\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0012\t-\tPROBABLE CONSERVED MEMBRANE PROTEIN \t16\t247.6\t104.1\t-1.25\t7922.3\t4996.36\t-143.5\t0.02820\t1.00000\n+Rv0013\ttrpG\tpara-aminobenzoate synthase component II \t15\t0.7\t2.9\t2.03\t21.1\t129.04\t2.2\t0.90500\t1.00000\n+Rv0014c\tpknB\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE B PKNB (PROTEIN KINASE B) (STPK B) \t24\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0015c\tpknA\tTRANSMEMBRANE SERINE/THREONINE-PROTEIN KINASE A PKNA (PROTEIN KINASE A) (STPK A) \t16\t23.6\t12.4\t-0.92\t753.9\t596.59\t-11.1\t0.70820\t1.00000\n+Rv0016c\tpbpA\tPROBABLE PENICILLIN-BINDING PROTEIN PBPA \t37\t19.4\t12.9\t-0.58\t1436.0\t1436.86\t-6.5\t0.43400\t1.00000\n+Rv0017c\trodA\tPROBABLE CELL DIVISION PROTEIN RODA \t27\t50.3\t50.0\t-0.01\t2718.6\t4051.86\t-0.3\t0.98690\t1.00000\n+Rv0018c\tppp\tPOSSIBLE SERINE/THREONINE PHOSPHATASE PPP \t25\t15.5\t12.4\t-0.32\t777.2\t933.35\t-3.1\t0.72310\t1.00000\n+Rv0019c\t-\thypothetical protein Rv0019c \t13\t178.0\t36.5\t-2.29\t4628.3\t1421.57\t-141.6\t0.00390\t1.00000\n+Rv0020c\tTB39.8\thypothetical protein Rv0020c \t52\t12.7\t17.5\t0.47\t1317.9\t2736.79\t4.9\t0.63120\t1.00000\n+Rv0021c\t-\thypothetical protein Rv0021c \t22\t301.9\t542.8\t0.85\t13281.7\t35827.15\t241.0\t0.24080\t1.00000\n+Rv0022c\twhiB5\tPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB5 \t8\t421.8\t527.6\t0.32\t6749.0\t12661.35\t105.7\t0.74770\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\t225.5\t222.8\t-0.02\t5410.9\t8019.31\t-2.7\t0.97750\t1.00000\n+Rv0025\t-\thypothetical protein Rv0025 \t7\t90.1\t275.8\t1.61\t1261.4\t5790.99\t185.7\t0.03210\t1.00000\n+Rv0026\t-\thypothetical protein Rv0026 \t14\t154.7\t166.7\t0.11\t4332.5\t7000.58\t11.9\t0.83090\t1.00000\n+Rv0027\t-\thypothetical protein Rv0027 \t5\t42.4\t9.2\t-2.21\t423.7\t137.74\t-33.2\t0.17520\t1.00000\n+Rv0028\t-\thypothetical protein Rv0028 \t5\t54.5\t68.7\t0.33\t544.9\t1030.50\t14.2\t0.79850\t1.00000\n+Rv0029\t-\thypothetical protein Rv0029 \t18\t163.6\t682.7\t2.06\t5889.3\t36863.16\t519.1\t0.23780\t1.00000\n+Rv0030\t-\thypothetical protein Rv0030 \t5\t24.8\t13.7\t-0.86\t247.9\t205.46\t-11.1\t0.62930\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 SYNTHE"..b'hosphate isomerase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0948c\t-\thypothetical protein Rv0948c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0949\tuvrD1\tPROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0950c\t-\thypothetical protein Rv0950c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0951\tsucC\tsuccinyl-CoA synthetase subunit beta \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0952\tsucD\tsuccinyl-CoA synthetase subunit alpha \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0953c\t-\tPOSSIBLE OXIDOREDUCTASE \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0954\t-\tPROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0955\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0956\tpurN\tphosphoribosylglycinamide formyltransferase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0957\tpurH\tbifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0958\t-\tPOSSIBLE MAGNESIUM CHELATASE \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0959\t-\thypothetical protein Rv0959 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0960\t-\thypothetical protein Rv0960 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0961\t-\tPROBABLE INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0962c\tlprP\tPOSSIBLE LIPOPROTEIN LPRP \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0963c\t-\thypothetical protein Rv0963c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0964c\t-\thypothetical protein Rv0964c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0965c\t-\thypothetical protein Rv0965c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0966c\t-\thypothetical protein Rv0966c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0967\t-\thypothetical protein Rv0967 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0968\t-\thypothetical protein Rv0968 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0969\tctpV\tPROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0970\t-\tPROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0971c\techA7\tenoyl-CoA hydratase \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0972c\tfadE12\tPROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0973c\taccA2\tPROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0974c\taccD2\tPROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0975c\tfadE13\tPROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0976c\t-\thypothetical protein Rv0976c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0977\tPE_PGRS16\tPE-PGRS FAMILY PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0978c\tPE_PGRS17\tPE-PGRS FAMILY PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0979A\trpmF\t50S ribosomal protein L32 \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0979c\t-\thypothetical protein Rv0979c \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0980c\tPE_PGRS18\tPE-PGRS FAMILY PROTEIN \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0981\tmprA\tMYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0982\tmprB\tPROBABLE TWO COMPONENT SENSOR KINASE MPRB \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0983\tpepD\tPROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n+Rv0984\tmoaB2\tPOSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t0\t0.0\t0.0\t0.00\t0.0\t0.00\t0.0\t1.00000\t1.00000\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/tn5gaps-sites1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tn5gaps-sites1.txt Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b"@@ -0,0 +1,512 @@\n+#Tn5 Gaps\n+#Console: python /Users/delphinel/miniconda3/envs/transit_test/bin/transit tn5gaps transit-in-tn5_smoll.wig,transit-in2-tn5_smol.wig transit_tn5_smol.prot tn5gaps-sites1_smol.txt\n+#Data: b'transit-in-tn5_smoll.wig,transit-in2-tn5_smol.wig'\n+#Annotation path: b'transit_tn5_smol.prot'\n+#Time: 1.1462020874023438\n+#Essential gene count: 1\n+#Minimum reads: 1\n+#Replicate combination method: Sum\n+#Minimum significant run length: 216\n+#Expected run length: 6.88000\n+#Expected max run length: 52.61348258987123\n+#Orf\tName\tDesc\tk\tn\tr\tovr\tlenovr\tpval\tpadj\tcall\n+BW25113_0001\tthrL\t-\t14\t63\t10\t8\t8\t1.00000\t1.00000\tNon-essential\n+BW25113_0002\tthrA\tbifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal)\t356\t2460\t48\t48\t48\t0.72170\t1.00000\tNon-essential\n+BW25113_0003\tthrB\t-\t160\t930\t32\t32\t32\t1.00000\t1.00000\tNon-essential\n+BW25113_0004\tthrC\t-\t194\t1284\t54\t54\t54\t0.38483\t1.00000\tNon-essential\n+BW25113_0005\tyaaX\t-\t48\t294\t32\t32\t32\t1.00000\t1.00000\tNon-essential\n+BW25113_0006\tyaaA\t-\t115\t774\t41\t41\t41\t0.98087\t1.00000\tNon-essential\n+BW25113_0007\tyaaJ\tinner membrane transport protein\t214\t1428\t46\t46\t46\t0.82900\t1.00000\tNon-essential\n+BW25113_0008\ttalB\t-\t181\t951\t54\t54\t54\t0.38483\t1.00000\tNon-essential\n+BW25113_0009\tmog\tputative molybdochetalase in molybdopterine biosynthesis\t95\t585\t45\t24\t24\t1.00000\t1.00000\tNon-essential\n+BW25113_0010\tsatP\t-\t108\t564\t37\t37\t37\t0.99947\t1.00000\tNon-essential\n+BW25113_0011\tyaaW\t-\t113\t711\t34\t34\t34\t1.00000\t1.00000\tNon-essential\n+BW25113_0013\tyaaI\t-\t77\t402\t26\t26\t26\t1.00000\t1.00000\tNon-essential\n+BW25113_0014\tdnaK\tchaperone Hsp70%3B DNA biosynthesis%3B autoregulated heat shock proteins\t34\t1914\t835\t216\t216\t0.00000\t0.00000\tEssential\n+BW25113_0015\tdnaJ\tchaperone with DnaK%3B heat shock protein\t169\t1128\t67\t67\t67\t0.05791\t1.00000\tNon-essential\n+BW25113_0016\tinsL1\t-\t235\t1110\t36\t36\t36\t0.99986\t1.00000\tNon-essential\n+BW25113_0018\tmokC\tregulatory peptide whose translation enables hokC (gef) expression%3B completely contained in another CDS\t68\t207\t12\t12\t12\t1.00000\t1.00000\tNon-essential\n+BW25113_0019\tnhaA\tNa+/H antiporter%2C pH dependent\t171\t1164\t36\t36\t36\t0.99986\t1.00000\tNon-essential\n+BW25113_0020\tnhaR\t-\t116\t903\t38\t38\t38\t0.99837\t1.00000\tNon-essential\n+BW25113_0021\tinsB1\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0022\tinsA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0023\trpsT\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0024\tyaaY\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0025\tribF\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0026\tileS\tisoleucine tRNA synthetase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0027\tlspA\tprolipoprotein signal peptidase (SPase II)\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0028\tfkpB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0029\tispH\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0030\trihC\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0031\tdapB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0032\tcarA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0033\tcarB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0034\tcaiF\ttranscriptional regulator of cai operon\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0035\tcaiE\tpossible synthesis of cofactor for carnitine racemase and dehydratase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0036\tcaiD\tcarnitine racemase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0037\tcaiC\tprobable crotonobetaine/carnitine-CoA ligase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0038\tcaiB\tl-carnitine dehydratase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0039\tcaiA\tprobable carnitine operon oxidoreductase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0040\tcaiT\tprobable carnitine transporter\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0041\tfixA\tprobable flavoprotein subunit%2C carnitine metabolism\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0042\tfixB\tprobable flavoprotein subunit%2C carnitine metabolism\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_"..b'\t1.00000\tNon-essential\n+BW25113_0489\tqmcA\tputative protease\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0490\tfetA\tputative ATP-binding component of a transport system\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0491\tfetB\tputative metal resistance protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0492\tybbN\tputative thioredoxin-like protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0493\tybbO\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0494\ttesA\tacyl-CoA thioesterase I%3B also functions as protease I\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0495\tybbA\tputative ATP-binding component of a transport system\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0496\tybbP\tputative oxidoreductase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0497\trhsD\trhsD protein in rhs element\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0498\tybbC\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0503\tmnmH\tputative capsule anchoring protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0504\tallS\tputative transcriptional regulator LYSR-type\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0505\tallA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0506\tallR\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0507\tgcl\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0508\thyi\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0509\tglxR\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0511\tybbW\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0512\tallB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0513\tybbY\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0514\tglxK\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0515\tallE\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0516\tallC\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0517\tallD\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0518\tfdrA\tinvolved in protein transport%3B multicopy suppressor of dominant negative ftsH mutants\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0520\tylbF\tputative carboxylase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0521\tybcF\tputative carbamate kinase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0522\tpurK\tphosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C CO(2)-fixing subunit\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0523\tpurE\tphosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C catalytic subunit\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0524\tlpxH\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0525\tppiB\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0526\tcysS\tcysteine tRNA synthetase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0527\tybcI\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0528\tybcJ\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0529\tfolD\t5%2C10-methylene-tetrahydrofolate dehydrogenase%3B 5%2C10-methylene-tetrahydrofolate cyclohydrolase\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0530\tsfmA\tputative fimbrial-like protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_0531\tsfmC\tputative chaperone\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4406\tyaeP\tconserved hypothetical protein\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4412\thokC\tsmall toxic membrane polypeptide%3B completely contained in another CDS\t36\t150\t12\t12\t12\t1.00000\t1.00000\tNon-essential\n+BW25113_4413\tsokC\t-\t20\t52\t12\t12\t12\t1.00000\t1.00000\tNon-essential\n+BW25113_4414\ttff\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4504\tykfH\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4506\tykgO\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4572\tylbE\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4577\tsgrS\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4585\tchiX\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4586\tykfM\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4662\tsgrT\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4671\tykgR\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n+BW25113_4690\teyeA\t-\t0\t0\t0\t0\t0\t1.00000\t1.00000\tNon-essential\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-co1-rep1.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-co1-rep1.wig Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\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 42\n+20547 2\n+20650 0\n+20671 0\n+20680 0\n+20712 0\n+20756 26\n+20787 0\n+20859 0\n+20883 218\n+21041 0\n+21204 0\n+21210 0\n+21266 2\n+21359 0\n+21414 1\n+21477 0\n+21481 22\n+21548 0\n+21608 0\n+21777 0\n+22070 0\n+22092 0\n+22118 85\n+22144 0\n+22187 0\n+22195 0\n+22199 77\n+22202 0\n+22279 0\n+22314 0\n+22338 0\n+22454 0\n+22460 0\n+22578 0\n+22590 0\n+22625 0\n+22817 0\n+22836 0\n+22887 0\n+22932 0\n+230'..b'9\n+84872 165\n+84918 19\n+84930 0\n+84952 160\n+84956 134\n+85010 15\n+85113 0\n+85135 0\n+85166 0\n+85178 124\n+85223 95\n+85276 56\n+85300 3\n+85575 74\n+85637 130\n+85720 40\n+85873 0\n+85915 0\n+85976 0\n+85986 0\n+86103 129\n+86135 0\n+86272 77\n+86280 31\n+86359 14\n+86378 4\n+86429 336\n+86436 0\n+86448 84\n+86486 0\n+86492 0\n+86509 0\n+86514 0\n+86527 0\n+86613 0\n+86621 0\n+86681 0\n+86698 0\n+86709 0\n+86835 0\n+86924 0\n+87124 0\n+87131 62\n+87276 0\n+87288 92\n+87309 0\n+87343 19\n+87433 0\n+87586 0\n+87605 0\n+87615 182\n+87631 0\n+87774 92\n+87875 0\n+87955 11\n+88015 0\n+88076 0\n+88232 241\n+88280 73\n+88299 0\n+88427 5\n+88439 0\n+88454 0\n+88604 5\n+88631 258\n+88665 4\n+88681 249\n+88732 1\n+88778 487\n+88954 90\n+88963 27\n+89271 128\n+89370 0\n+89383 339\n+89471 1\n+89478 0\n+89516 0\n+89523 0\n+89549 55\n+89593 109\n+89747 227\n+89797 248\n+89817 0\n+89885 13\n+89917 31\n+89982 0\n+89994 0\n+90015 0\n+90101 0\n+90240 0\n+90290 109\n+90321 222\n+90497 30\n+90587 0\n+90607 98\n+90619 4\n+90811 0\n+90935 89\n+90939 99\n+91072 175\n+91165 170\n+91216 0\n+91281 0\n+91291 36\n+91353 13\n+91937 0\n+92035 165\n+92134 51\n+92136 10\n+92155 0\n+92194 35\n+92196 27\n+92269 0\n+92278 0\n+92294 45\n+92334 0\n+92338 14\n+92393 0\n+92407 0\n+92638 0\n+92816 92\n+92857 35\n+92973 1\n+93199 0\n+93294 74\n+93434 0\n+93603 0\n+93773 63\n+94215 0\n+94244 1\n+94256 0\n+94269 0\n+94345 0\n+94428 153\n+94472 0\n+94485 18\n+94538 0\n+94564 66\n+94611 0\n+94776 56\n+94872 0\n+95042 0\n+95410 37\n+95445 0\n+95463 0\n+95549 0\n+95567 0\n+95594 0\n+95611 0\n+95636 0\n+95684 0\n+95727 0\n+95797 0\n+95840 0\n+96143 0\n+96188 0\n+96267 0\n+96319 0\n+96392 0\n+96458 33\n+96513 0\n+96566 0\n+96642 83\n+96647 13\n+96655 0\n+96688 0\n+96718 0\n+96872 0\n+96890 0\n+96912 0\n+96920 0\n+96936 0\n+96974 0\n+96980 164\n+97071 87\n+97102 0\n+97273 0\n+97285 0\n+97330 0\n+97335 0\n+97399 0\n+97470 0\n+97509 0\n+97581 66\n+97592 0\n+97623 0\n+97668 23\n+97688 0\n+97707 25\n+97718 0\n+97788 0\n+97823 0\n+97888 0\n+97893 53\n+98092 38\n+98152 11\n+98260 345\n+98297 28\n+98313 69\n+98330 60\n+98349 115\n+98379 98\n+98396 1\n+98437 0\n+98468 166\n+98552 59\n+98613 104\n+98692 7\n+98709 66\n+98751 0\n+98818 22\n+98836 0\n+98963 43\n+99023 0\n+99137 30\n+99151 0\n+99188 49\n+99322 14\n+99343 0\n+99444 0\n+99546 5\n+99609 0\n+99638 0\n+99732 207\n+99791 0\n+99848 128\n+99940 512\n+100020 117\n+100068 0\n+100176 143\n+100179 90\n+100206 34\n+100256 23\n+100310 0\n+100459 0\n+100505 133\n+100517 369\n+100629 43\n+100805 31\n+100887 0\n+100983 97\n+101082 150\n+101095 22\n+101123 1\n+101166 5\n+101194 75\n+101198 1\n+101246 0\n+101319 3\n+101331 0\n+101409 20\n+101643 86\n+101686 46\n+101697 1\n+101715 12\n+101850 3\n+101864 13\n+102093 0\n+102135 0\n+102231 0\n+102385 0\n+102456 35\n+102531 265\n+102612 92\n+102683 21\n+102809 0\n+102816 0\n+102889 0\n+103041 0\n+103052 0\n+103106 2\n+103214 0\n+103405 0\n+103534 2\n+103630 31\n+103809 2\n+103957 39\n+104034 18\n+104050 88\n+104092 36\n+104113 125\n+104157 50\n+104424 6\n+104464 3\n+104472 31\n+104491 104\n+104562 31\n+104587 2\n+104611 54\n+104806 14\n+104952 0\n+105089 0\n+105096 0\n+105112 0\n+105146 0\n+105177 0\n+105188 166\n+105198 12\n+105208 53\n+105249 0\n+105259 37\n+105288 0\n+105319 9\n+105329 64\n+105331 181\n+105416 281\n+105426 54\n+105507 47\n+105528 0\n+105586 0\n+105603 0\n+105732 22\n+105774 44\n+105808 23\n+105863 0\n+105871 0\n+105877 1\n+105908 0\n+105933 0\n+105939 0\n+105982 0\n+106017 194\n+106032 0\n+106038 1\n+106041 33\n+106050 0\n+106105 4\n+106154 0\n+106323 178\n+106355 31\n+106367 0\n+106483 1\n+106491 39\n+106535 35\n+106601 0\n+106667 282\n+106688 10\n+106742 0\n+106805 0\n+106807 1\n+106829 0\n+106836 0\n+106858 1\n+106906 0\n+106926 4\n+106929 0\n+106941 198\n+107024 0\n+107031 9\n+107033 0\n+107039 0\n+107106 58\n+107226 0\n+107245 56\n+107278 0\n+107288 0\n+107328 4\n+107436 1\n+107452 19\n+107456 211\n+107466 0\n+107553 0\n+107592 0\n+107696 0\n+107717 199\n+107735 61\n+107765 0\n+107795 1\n+107797 3\n+107858 176\n+107927 97\n+107947 35\n+108059 0\n+108129 0\n+108149 0\n+108179 33\n+108197 0\n+108272 0\n+108285 0\n+108344 0\n+108356 126\n+108393 0\n+108565 0\n+108586 0\n+108596 0\n+108692 0\n+108718 0\n+108807 0\n+108850 8\n+108854 123\n+108899 0\n+108952 6\n+108976 18\n+109024 0\n+109032 0\n+109070 0\n+109079 0\n+109104 0\n+109197 0\n+109215 126\n+109226 0\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-co1-rep2.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-co1-rep2.wig Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\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 9\n+1635 7\n+1779 0\n+1782 0\n+1788 0\n+1847 0\n+1858 21\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 0\n+3513 0\n+3591 0\n+3682 0\n+3708 0\n+3728 42\n+3739 0\n+3770 22\n+3782 99\n+3796 0\n+3833 0\n+3925 0\n+3960 0\n+3967 0\n+3986 1\n+4011 0\n+4028 0\n+4094 0\n+4118 0\n+4121 34\n+4130 0\n+4158 0\n+4207 0\n+4217 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93\n+87774 38\n+87875 32\n+87955 48\n+88015 0\n+88076 0\n+88232 340\n+88280 13\n+88299 0\n+88427 3\n+88439 69\n+88454 0\n+88604 0\n+88631 6\n+88665 10\n+88681 202\n+88732 104\n+88778 432\n+88954 88\n+88963 35\n+89271 26\n+89370 23\n+89383 777\n+89471 35\n+89478 0\n+89516 0\n+89523 0\n+89549 41\n+89593 7\n+89747 90\n+89797 126\n+89817 0\n+89885 207\n+89917 52\n+89982 0\n+89994 0\n+90015 0\n+90101 29\n+90240 35\n+90290 82\n+90321 115\n+90497 66\n+90587 0\n+90607 109\n+90619 44\n+90811 114\n+90935 42\n+90939 80\n+91072 48\n+91165 97\n+91216 0\n+91281 0\n+91291 8\n+91353 43\n+91937 0\n+92035 62\n+92134 30\n+92136 8\n+92155 0\n+92194 3\n+92196 34\n+92269 13\n+92278 1\n+92294 4\n+92334 18\n+92338 50\n+92393 0\n+92407 0\n+92638 0\n+92816 87\n+92857 38\n+92973 1\n+93199 0\n+93294 52\n+93434 0\n+93603 0\n+93773 2\n+94215 6\n+94244 109\n+94256 0\n+94269 7\n+94345 0\n+94428 4\n+94472 0\n+94485 0\n+94538 0\n+94564 10\n+94611 0\n+94776 2\n+94872 14\n+95042 0\n+95410 5\n+95445 0\n+95463 5\n+95549 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29\n+101082 37\n+101095 0\n+101123 11\n+101166 12\n+101194 99\n+101198 0\n+101246 0\n+101319 0\n+101331 0\n+101409 150\n+101643 76\n+101686 1\n+101697 0\n+101715 0\n+101850 1\n+101864 2\n+102093 0\n+102135 0\n+102231 5\n+102385 0\n+102456 21\n+102531 171\n+102612 0\n+102683 39\n+102809 0\n+102816 0\n+102889 0\n+103041 0\n+103052 0\n+103106 41\n+103214 0\n+103405 23\n+103534 98\n+103630 93\n+103809 0\n+103957 10\n+104034 3\n+104050 85\n+104092 56\n+104113 44\n+104157 47\n+104424 15\n+104464 0\n+104472 2\n+104491 93\n+104562 8\n+104587 7\n+104611 3\n+104806 44\n+104952 0\n+105089 0\n+105096 0\n+105112 0\n+105146 0\n+105177 0\n+105188 135\n+105198 0\n+105208 3\n+105249 0\n+105259 0\n+105288 6\n+105319 23\n+105329 307\n+105331 43\n+105416 554\n+105426 43\n+105507 23\n+105528 0\n+105586 4\n+105603 0\n+105732 34\n+105774 4\n+105808 2\n+105863 0\n+105871 0\n+105877 35\n+105908 0\n+105933 0\n+105939 0\n+105982 0\n+106017 2\n+106032 0\n+106038 257\n+106041 71\n+106050 34\n+106105 0\n+106154 5\n+106323 113\n+106355 77\n+106367 1\n+106483 16\n+106491 5\n+106535 0\n+106601 0\n+106667 330\n+106688 19\n+106742 43\n+106805 28\n+106807 7\n+106829 0\n+106836 0\n+106858 0\n+106906 0\n+106926 3\n+106929 0\n+106941 62\n+107024 0\n+107031 0\n+107033 11\n+107039 0\n+107106 30\n+107226 0\n+107245 17\n+107278 0\n+107288 10\n+107328 69\n+107436 3\n+107452 6\n+107456 357\n+107466 0\n+107553 0\n+107592 64\n+107696 0\n+107717 0\n+107735 0\n+107765 0\n+107795 0\n+107797 0\n+107858 37\n+107927 0\n+107947 0\n+108059 50\n+108129 0\n+108149 0\n+108179 28\n+108197 0\n+108272 0\n+108285 0\n+108344 0\n+108356 25\n+108393 0\n+108565 0\n+108586 0\n+108596 0\n+108692 0\n+108718 0\n+108807 0\n+108850 89\n+108854 34\n+108899 0\n+108952 93\n+108976 0\n+109024 0\n+109032 0\n+109070 0\n+109079 0\n+109104 0\n+109197 0\n+109215 0\n+109226 0\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-co1-rep3.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-co1-rep3.wig Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\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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| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-in-tn5.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in-tn5.wig Tue Oct 08 08:24:46 2019 -0400 |
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|
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-in1-rep1.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1-rep1.wig Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\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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60\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 0\n+15576 0\n+15591 7\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 76\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 8\n+19043 0\n+19081 0\n+19100 48\n+19107 0\n+19134 0\n+19138 38\n+19151 0\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 0\n+19667 0\n+19693 3\n+19760 0\n+19771 0\n+19829 0\n+19838 0\n+19914 0\n+19935 0\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 131\n+20266 0\n+20278 0\n+20345 0\n+20349 0\n+20376 0\n+20456 0\n+20497 23\n+20547 119\n+20650 0\n+20671 0\n+20680 0\n+20712 0\n+20756 0\n+20787 0\n+20859 0\n+20883 79\n+21041 0\n+21204 0\n+21210 16\n+21266 0\n+21359 0\n+21414 0\n+21477 0\n+21481 36\n+21548 0\n+21608 0\n+21777 0\n+22070 0\n+22092 0\n+22118 20\n+22144 53\n+22187 0\n+22195 0\n+22199 16\n+22202 46\n+22279 0\n+22314 0\n+22338 0\n+22454 8\n+22460 0\n+22578 0\n+22590 0\n+22625 0\n+22817 0\n+22836 0\n+22887 0\n+22'..b'84930 0\n+84952 68\n+84956 218\n+85010 211\n+85113 0\n+85135 62\n+85166 42\n+85178 134\n+85223 147\n+85276 33\n+85300 0\n+85575 136\n+85637 105\n+85720 0\n+85873 0\n+85915 0\n+85976 24\n+85986 0\n+86103 249\n+86135 4\n+86272 5\n+86280 92\n+86359 14\n+86378 113\n+86429 309\n+86436 20\n+86448 99\n+86486 0\n+86492 0\n+86509 0\n+86514 0\n+86527 0\n+86613 0\n+86621 11\n+86681 0\n+86698 0\n+86709 70\n+86835 0\n+86924 0\n+87124 0\n+87131 18\n+87276 0\n+87288 215\n+87309 0\n+87343 25\n+87433 0\n+87586 0\n+87605 286\n+87615 96\n+87631 121\n+87774 66\n+87875 33\n+87955 349\n+88015 0\n+88076 0\n+88232 544\n+88280 36\n+88299 0\n+88427 0\n+88439 0\n+88454 0\n+88604 14\n+88631 139\n+88665 0\n+88681 306\n+88732 71\n+88778 764\n+88954 63\n+88963 0\n+89271 64\n+89370 0\n+89383 520\n+89471 0\n+89478 0\n+89516 0\n+89523 0\n+89549 0\n+89593 64\n+89747 251\n+89797 183\n+89817 0\n+89885 134\n+89917 82\n+89982 0\n+89994 0\n+90015 0\n+90101 216\n+90240 230\n+90290 111\n+90321 7\n+90497 173\n+90587 0\n+90607 100\n+90619 0\n+90811 13\n+90935 29\n+90939 14\n+91072 4\n+91165 137\n+91216 0\n+91281 0\n+91291 0\n+91353 1\n+91937 0\n+92035 254\n+92134 97\n+92136 0\n+92155 131\n+92194 0\n+92196 181\n+92269 0\n+92278 25\n+92294 103\n+92334 0\n+92338 223\n+92393 0\n+92407 0\n+92638 0\n+92816 150\n+92857 40\n+92973 189\n+93199 0\n+93294 1\n+93434 0\n+93603 0\n+93773 84\n+94215 42\n+94244 0\n+94256 0\n+94269 6\n+94345 0\n+94428 97\n+94472 0\n+94485 11\n+94538 0\n+94564 0\n+94611 0\n+94776 0\n+94872 0\n+95042 0\n+95410 7\n+95445 0\n+95463 0\n+95549 0\n+95567 0\n+95594 0\n+95611 0\n+95636 0\n+95684 0\n+95727 0\n+95797 0\n+95840 0\n+96143 0\n+96188 0\n+96267 0\n+96319 0\n+96392 38\n+96458 2\n+96513 136\n+96566 0\n+96642 88\n+96647 0\n+96655 0\n+96688 0\n+96718 0\n+96872 0\n+96890 0\n+96912 0\n+96920 0\n+96936 0\n+96974 0\n+96980 83\n+97071 29\n+97102 0\n+97273 0\n+97285 0\n+97330 0\n+97335 0\n+97399 0\n+97470 0\n+97509 0\n+97581 75\n+97592 0\n+97623 0\n+97668 32\n+97688 30\n+97707 67\n+97718 0\n+97788 0\n+97823 0\n+97888 46\n+97893 18\n+98092 0\n+98152 96\n+98260 28\n+98297 0\n+98313 75\n+98330 12\n+98349 8\n+98379 0\n+98396 153\n+98437 0\n+98468 225\n+98552 77\n+98613 274\n+98692 0\n+98709 0\n+98751 0\n+98818 28\n+98836 0\n+98963 127\n+99023 3\n+99137 48\n+99151 0\n+99188 4\n+99322 19\n+99343 2\n+99444 24\n+99546 0\n+99609 0\n+99638 0\n+99732 119\n+99791 0\n+99848 41\n+99940 554\n+100020 109\n+100068 0\n+100176 157\n+100179 363\n+100206 94\n+100256 0\n+100310 0\n+100459 0\n+100505 8\n+100517 772\n+100629 55\n+100805 115\n+100887 0\n+100983 33\n+101082 345\n+101095 0\n+101123 147\n+101166 33\n+101194 153\n+101198 36\n+101246 0\n+101319 200\n+101331 0\n+101409 85\n+101643 106\n+101686 19\n+101697 0\n+101715 49\n+101850 126\n+101864 4\n+102093 0\n+102135 0\n+102231 0\n+102385 109\n+102456 40\n+102531 223\n+102612 4\n+102683 33\n+102809 0\n+102816 0\n+102889 0\n+103041 6\n+103052 0\n+103106 0\n+103214 15\n+103405 0\n+103534 44\n+103630 211\n+103809 28\n+103957 21\n+104034 10\n+104050 8\n+104092 42\n+104113 39\n+104157 19\n+104424 87\n+104464 0\n+104472 10\n+104491 141\n+104562 84\n+104587 22\n+104611 49\n+104806 28\n+104952 0\n+105089 4\n+105096 0\n+105112 0\n+105146 0\n+105177 0\n+105188 259\n+105198 113\n+105208 0\n+105249 0\n+105259 126\n+105288 13\n+105319 0\n+105329 137\n+105331 48\n+105416 477\n+105426 71\n+105507 0\n+105528 0\n+105586 0\n+105603 0\n+105732 82\n+105774 0\n+105808 1\n+105863 0\n+105871 0\n+105877 62\n+105908 0\n+105933 0\n+105939 0\n+105982 0\n+106017 0\n+106032 0\n+106038 139\n+106041 15\n+106050 0\n+106105 0\n+106154 0\n+106323 233\n+106355 9\n+106367 0\n+106483 38\n+106491 0\n+106535 31\n+106601 0\n+106667 447\n+106688 0\n+106742 400\n+106805 0\n+106807 41\n+106829 0\n+106836 0\n+106858 83\n+106906 0\n+106926 54\n+106929 0\n+106941 138\n+107024 0\n+107031 72\n+107033 0\n+107039 0\n+107106 302\n+107226 0\n+107245 0\n+107278 0\n+107288 1\n+107328 53\n+107436 0\n+107452 130\n+107456 459\n+107466 0\n+107553 0\n+107592 0\n+107696 0\n+107717 0\n+107735 29\n+107765 0\n+107795 7\n+107797 0\n+107858 88\n+107927 0\n+107947 0\n+108059 0\n+108129 0\n+108149 0\n+108179 0\n+108197 0\n+108272 0\n+108285 0\n+108344 0\n+108356 53\n+108393 0\n+108565 0\n+108586 0\n+108596 0\n+108692 0\n+108718 0\n+108807 0\n+108850 121\n+108854 124\n+108899 0\n+108952 0\n+108976 0\n+109024 0\n+109032 0\n+109070 0\n+109079 0\n+109104 0\n+109197 0\n+109215 0\n+109226 0\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-in1-rep2.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1-rep2.wig Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\n+# from Griffin et al, (2011). PLOS Pathogens, e1002251.\n+variableStep chrom=H37Rv\n+60 0\n+72 0\n+102 0\n+188 0\n+246 0\n+333 0\n+360 0\n+426 0\n+448 0\n+471 0\n+483 0\n+494 0\n+504 0\n+514 0\n+525 0\n+534 0\n+601 0\n+653 0\n+670 0\n+706 0\n+741 0\n+784 0\n+794 0\n+843 0\n+989 0\n+1092 0\n+1104 0\n+1267 0\n+1278 0\n+1345 0\n+1423 0\n+1522 124\n+1552 0\n+1635 201\n+1779 0\n+1782 0\n+1788 0\n+1847 0\n+1858 342\n+1921 21\n+2001 0\n+2012 0\n+2063 0\n+2104 0\n+2141 0\n+2232 0\n+2290 0\n+2315 0\n+2318 0\n+2333 0\n+2344 0\n+2363 0\n+2387 0\n+2404 0\n+2427 0\n+2479 0\n+2507 0\n+2537 0\n+2591 0\n+2648 0\n+2738 0\n+2774 0\n+2845 0\n+2920 0\n+3027 0\n+3056 0\n+3066 0\n+3070 0\n+3119 0\n+3131 0\n+3145 0\n+3222 0\n+3228 0\n+3277 0\n+3283 5\n+3329 107\n+3372 0\n+3379 0\n+3384 0\n+3396 0\n+3412 0\n+3425 0\n+3441 0\n+3467 56\n+3471 0\n+3513 0\n+3591 0\n+3682 0\n+3708 49\n+3728 0\n+3739 161\n+3770 0\n+3782 37\n+3796 0\n+3833 27\n+3925 13\n+3960 0\n+3967 0\n+3986 4\n+4011 6\n+4028 1\n+4094 0\n+4118 0\n+4121 110\n+4130 0\n+4158 0\n+4207 0\n+4217 0\n+4353 0\n+4664 0\n+4721 0\n+4789 0\n+4912 0\n+4961 0\n+4970 0\n+4989 23\n+4995 63\n+5066 58\n+5120 69\n+5128 40\n+5170 90\n+5230 0\n+5273 0\n+5287 0\n+5336 0\n+5364 0\n+5420 0\n+5439 0\n+5517 0\n+5547 0\n+5579 0\n+5586 0\n+5623 0\n+5631 0\n+5669 0\n+5687 0\n+5792 0\n+5977 0\n+5996 0\n+6055 0\n+6128 0\n+6230 0\n+6249 0\n+6286 0\n+6403 0\n+6490 0\n+6502 0\n+6526 0\n+6605 0\n+6612 0\n+6672 0\n+6729 0\n+6793 0\n+6809 0\n+6856 0\n+6944 0\n+6983 0\n+7067 0\n+7077 0\n+7093 0\n+7225 0\n+7265 0\n+7299 101\n+7383 0\n+7392 0\n+7470 0\n+7551 0\n+7578 0\n+7620 0\n+7686 0\n+7763 0\n+7767 0\n+7798 0\n+7865 0\n+7970 0\n+8031 0\n+8077 0\n+8099 0\n+8127 0\n+8219 0\n+8236 0\n+8288 0\n+8295 0\n+8338 0\n+8391 0\n+8394 0\n+8436 0\n+8486 0\n+8546 0\n+8786 0\n+8858 0\n+8874 0\n+8901 0\n+9030 0\n+9045 0\n+9100 0\n+9150 0\n+9165 0\n+9419 0\n+9465 0\n+9492 0\n+9503 0\n+9519 0\n+9526 0\n+9542 0\n+9564 0\n+9624 0\n+9776 127\n+9816 325\n+9850 0\n+9877 115\n+9894 21\n+9903 49\n+10023 0\n+10104 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3\n+20345 54\n+20349 10\n+20376 10\n+20456 0\n+20497 41\n+20547 206\n+20650 0\n+20671 0\n+20680 2\n+20712 0\n+20756 0\n+20787 0\n+20859 0\n+20883 160\n+21041 0\n+21204 0\n+21210 1\n+21266 0\n+21359 53\n+21414 63\n+21477 0\n+21481 199\n+21548 0\n+21608 0\n+21777 0\n+22070 31\n+22092 0\n+22118 22\n+22144 0\n+22187 0\n+22195 1\n+22199 4\n+22202 23\n+22279 0\n+22314 0\n+22338 69\n+22454 45\n+22460 0\n+22578 0\n+22'..b'76\n+85276 24\n+85300 92\n+85575 583\n+85637 133\n+85720 0\n+85873 0\n+85915 0\n+85976 13\n+85986 0\n+86103 127\n+86135 16\n+86272 49\n+86280 62\n+86359 155\n+86378 57\n+86429 375\n+86436 49\n+86448 451\n+86486 0\n+86492 0\n+86509 0\n+86514 0\n+86527 0\n+86613 0\n+86621 4\n+86681 0\n+86698 0\n+86709 33\n+86835 0\n+86924 0\n+87124 3\n+87131 9\n+87276 0\n+87288 35\n+87309 11\n+87343 1\n+87433 6\n+87586 136\n+87605 271\n+87615 65\n+87631 128\n+87774 44\n+87875 214\n+87955 252\n+88015 70\n+88076 19\n+88232 524\n+88280 14\n+88299 0\n+88427 5\n+88439 18\n+88454 0\n+88604 35\n+88631 126\n+88665 133\n+88681 783\n+88732 65\n+88778 734\n+88954 208\n+88963 0\n+89271 277\n+89370 0\n+89383 765\n+89471 15\n+89478 0\n+89516 0\n+89523 0\n+89549 186\n+89593 179\n+89747 302\n+89797 516\n+89817 0\n+89885 41\n+89917 270\n+89982 0\n+89994 0\n+90015 0\n+90101 45\n+90240 114\n+90290 245\n+90321 63\n+90497 677\n+90587 0\n+90607 182\n+90619 53\n+90811 137\n+90935 110\n+90939 230\n+91072 201\n+91165 139\n+91216 0\n+91281 0\n+91291 0\n+91353 20\n+91937 0\n+92035 324\n+92134 368\n+92136 43\n+92155 14\n+92194 73\n+92196 370\n+92269 0\n+92278 97\n+92294 72\n+92334 117\n+92338 193\n+92393 7\n+92407 22\n+92638 17\n+92816 302\n+92857 126\n+92973 55\n+93199 0\n+93294 48\n+93434 0\n+93603 0\n+93773 140\n+94215 13\n+94244 0\n+94256 14\n+94269 34\n+94345 0\n+94428 45\n+94472 0\n+94485 79\n+94538 0\n+94564 20\n+94611 0\n+94776 28\n+94872 0\n+95042 58\n+95410 0\n+95445 0\n+95463 0\n+95549 0\n+95567 0\n+95594 42\n+95611 0\n+95636 0\n+95684 0\n+95727 0\n+95797 0\n+95840 0\n+96143 32\n+96188 0\n+96267 0\n+96319 0\n+96392 13\n+96458 100\n+96513 108\n+96566 0\n+96642 194\n+96647 0\n+96655 75\n+96688 0\n+96718 0\n+96872 0\n+96890 0\n+96912 0\n+96920 0\n+96936 0\n+96974 0\n+96980 139\n+97071 30\n+97102 1\n+97273 0\n+97285 0\n+97330 0\n+97335 0\n+97399 0\n+97470 0\n+97509 0\n+97581 47\n+97592 0\n+97623 0\n+97668 0\n+97688 1\n+97707 38\n+97718 0\n+97788 75\n+97823 0\n+97888 3\n+97893 64\n+98092 43\n+98152 139\n+98260 125\n+98297 0\n+98313 310\n+98330 34\n+98349 71\n+98379 43\n+98396 343\n+98437 0\n+98468 374\n+98552 47\n+98613 122\n+98692 0\n+98709 116\n+98751 0\n+98818 64\n+98836 0\n+98963 201\n+99023 207\n+99137 128\n+99151 0\n+99188 72\n+99322 186\n+99343 45\n+99444 70\n+99546 0\n+99609 0\n+99638 0\n+99732 86\n+99791 118\n+99848 26\n+99940 1185\n+100020 23\n+100068 0\n+100176 347\n+100179 316\n+100206 76\n+100256 0\n+100310 0\n+100459 12\n+100505 131\n+100517 854\n+100629 53\n+100805 124\n+100887 0\n+100983 207\n+101082 147\n+101095 48\n+101123 81\n+101166 76\n+101194 141\n+101198 1\n+101246 17\n+101319 313\n+101331 0\n+101409 373\n+101643 304\n+101686 47\n+101697 0\n+101715 10\n+101850 12\n+101864 16\n+102093 0\n+102135 0\n+102231 0\n+102385 0\n+102456 75\n+102531 360\n+102612 28\n+102683 126\n+102809 0\n+102816 0\n+102889 0\n+103041 29\n+103052 0\n+103106 1\n+103214 0\n+103405 0\n+103534 152\n+103630 57\n+103809 40\n+103957 10\n+104034 27\n+104050 120\n+104092 43\n+104113 160\n+104157 102\n+104424 61\n+104464 47\n+104472 30\n+104491 124\n+104562 67\n+104587 51\n+104611 71\n+104806 10\n+104952 0\n+105089 0\n+105096 0\n+105112 0\n+105146 0\n+105177 0\n+105188 159\n+105198 19\n+105208 0\n+105249 0\n+105259 69\n+105288 132\n+105319 0\n+105329 196\n+105331 209\n+105416 1060\n+105426 232\n+105507 38\n+105528 106\n+105586 0\n+105603 4\n+105732 176\n+105774 1\n+105808 29\n+105863 0\n+105871 0\n+105877 139\n+105908 0\n+105933 10\n+105939 0\n+105982 0\n+106017 61\n+106032 9\n+106038 109\n+106041 63\n+106050 0\n+106105 0\n+106154 0\n+106323 388\n+106355 100\n+106367 0\n+106483 147\n+106491 119\n+106535 0\n+106601 0\n+106667 860\n+106688 0\n+106742 73\n+106805 0\n+106807 0\n+106829 0\n+106836 47\n+106858 0\n+106906 0\n+106926 0\n+106929 0\n+106941 71\n+107024 0\n+107031 38\n+107033 0\n+107039 0\n+107106 155\n+107226 0\n+107245 166\n+107278 0\n+107288 18\n+107328 74\n+107436 8\n+107452 152\n+107456 881\n+107466 124\n+107553 0\n+107592 0\n+107696 0\n+107717 19\n+107735 57\n+107765 0\n+107795 41\n+107797 0\n+107858 19\n+107927 109\n+107947 40\n+108059 4\n+108129 0\n+108149 0\n+108179 0\n+108197 0\n+108272 0\n+108285 0\n+108344 0\n+108356 86\n+108393 0\n+108565 0\n+108586 0\n+108596 0\n+108692 0\n+108718 0\n+108807 0\n+108850 101\n+108854 37\n+108899 0\n+108952 102\n+108976 0\n+109024 0\n+109032 0\n+109070 0\n+109079 0\n+109104 0\n+109197 11\n+109215 130\n+109226 0\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-in1.prot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in1.prot Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,1000 @@\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'5485\t-\tRv0948c\tCOG1605E\t\r\n+PROBABLE ATP-DEPENDENT DNA HELICASE II UVRD1 \t1058260\t1060575\t+\t771\t57116803\t885442\tuvrD1\tRv0949\tCOG0210L\t\r\n+hypothetical protein Rv0950c \t1060656\t1061654\t-\t332\t15608090\t885438\t-\tRv0950c\tCOG0739M\t\r\n+succinyl-CoA synthetase subunit beta \t1061964\t1063127\t+\t387\t15608091\t885434\tsucC\tRv0951\tCOG0045C\t\r\n+succinyl-CoA synthetase subunit alpha \t1063140\t1064051\t+\t303\t15608092\t885426\tsucD\tRv0952\tCOG0074C\t\r\n+POSSIBLE OXIDOREDUCTASE \t1064114\t1064962\t-\t282\t15608093\t885419\t-\tRv0953c\tCOG2141C\t\r\n+PROBABLE CONSERVED TRANSMEMBRANE PROTEIN \t1065127\t1066038\t+\t303\t15608094\t885411\t-\tRv0954\t-\t\r\n+PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t1066078\t1067445\t+\t455\t15608095\t885408\t-\tRv0955\t-\t\r\n+phosphoribosylglycinamide formyltransferase \t1067561\t1068208\t+\t215\t15608096\t885407\tpurN\tRv0956\tCOG0299F\t\r\n+bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase \t1068205\t1069776\t+\t523\t15608097\t885406\tpurH\tRv0957\tCOG0138F\t\r\n+POSSIBLE MAGNESIUM CHELATASE \t1069883\t1071262\t+\t459\t15608098\t885405\t-\tRv0958\tCOG1239H\t\r\n+hypothetical protein Rv0959 \t1071255\t1073273\t+\t672\t15608099\t885329\t-\tRv0959\tCOG4867R\t\r\n+hypothetical protein Rv0960 \t1073545\t1073928\t+\t127\t15608100\t885158\t-\tRv0960\tCOG4113R\t\r\n+PROBABLE INTEGRAL MEMBRANE PROTEIN \t1074074\t1074421\t+\t115\t15608101\t885173\t-\tRv0961\t-\t\r\n+POSSIBLE LIPOPROTEIN LPRP \t1074440\t1075114\t-\t224\t15608102\t885177\tlprP\tRv0962c\tCOG1902C, COG4608E\t\r\n+hypothetical protein Rv0963c \t1075297\t1076097\t-\t266\t15608103\t885184\t-\tRv0963c\t-\t\r\n+hypothetical protein Rv0964c \t1076196\t1076678\t-\t160\t15608104\t885186\t-\tRv0964c\t-\t\r\n+hypothetical protein Rv0965c \t1076778\t1077197\t-\t139\t15608105\t885230\t-\tRv0965c\t-\t\r\n+hypothetical protein Rv0966c \t1077233\t1077835\t-\t200\t57116804\t885043\t-\tRv0966c\t-\t\r\n+hypothetical protein Rv0967 \t1077975\t1078334\t+\t119\t15608107\t885312\t-\tRv0967\tCOG1937S\t\r\n+hypothetical protein Rv0968 \t1078391\t1078687\t+\t98\t15608108\t885052\t-\tRv0968\t-\t\r\n+PROBABLE METAL CATION TRANSPORTER P-TYPE ATPASE CTPV \t1078743\t1081055\t+\t770\t15608109\t885254\tctpV\tRv0969\tCOG2217P\t\r\n+PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN \t1081052\t1081684\t+\t210\t15608110\t885242\t-\tRv0970\t-\t\r\n+enoyl-CoA hydratase \t1081775\t1082584\t-\t269\t15608111\t885308\techA7\tRv0971c\tCOG1024I\t\r\n+PROBABLE ACYL-CoA DEHYDROGENASE FADE12 \t1082584\t1083750\t-\t388\t15608112\t885237\tfadE12\tRv0972c\tCOG1960I\t\r\n+PROBABLE ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN (ALPHA SUBUNIT) ACCA2: BIOTIN CARBOXYLASE + BIOTIN CARBOXYL CARRIER PROTEIN (BCCP) \t1083747\t1085750\t-\t667\t15608113\t885922\taccA2\tRv0973c\tCOG0439I, COG0511I, COG4770I\t\r\n+PROBABLE ACETYL-/PROPIONYL-CoA CARBOXYLASE (BETA SUBUNIT) ACCD2 \t1085756\t1087345\t-\t529\t15608114\t886064\taccD2\tRv0974c\tCOG4799I\t\r\n+PROBABLE ACYL-CoA DEHYDROGENASE FADE13 \t1087348\t1088496\t-\t382\t15608115\t885856\tfadE13\tRv0975c\tCOG1960I\t\r\n+hypothetical protein Rv0976c \t1088493\t1090175\t-\t560\t15608116\t885860\t-\tRv0976c\t-\t\r\n+PE-PGRS FAMILY PROTEIN \t1090373\t1093144\t+\t923\t57116805\t885264\tPE_PGRS16\tRv0977\t-\t\r\n+PE-PGRS FAMILY PROTEIN \t1093361\t1094356\t-\t331\t57116806\t885077\tPE_PGRS17\tRv0978c\tCOG3391S\t\r\n+hypothetical protein Rv0979c \t1094670\t1094864\t-\t64\t57116807\t885063\t-\tRv0979c\t-\t\r\n+50S ribosomal protein L32 \t1094886\t1095059\t+\t57\t57116808\t3205057\trpmF\tRv0979A\t-\t\r\n+PE-PGRS FAMILY PROTEIN \t1095078\t1096451\t-\t457\t57116809\t885327\tPE_PGRS18\tRv0980c\tCOG3391S\t\r\n+MYCOBACTERIAL PERSISTENCE REGULATOR MRPA (TWO COMPONENT RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN) \t1096816\t1097508\t+\t230\t15608121\t885038\tmprA\tRv0981\tCOG0745TK\t\r\n+PROBABLE TWO COMPONENT SENSOR KINASE MPRB \t1097508\t1099022\t+\t504\t15608122\t885062\tmprB\tRv0982\tCOG0642T\t\r\n+PROBABLE SERINE PROTEASE PEPD (SERINE PROTEINASE) (MTB32B) \t1099066\t1100460\t+\t464\t15608123\t885382\tpepD\tRv0983\tCOG0265O\t\r\n+POSSIBLE PTERIN-4-ALPHA-CARBINOLAMINE DEHYDRATASE MOAB2 (PHS) (4-ALPHA-HYDROXY-TETRAHYDROPTERIN DEHYDRATASE) (PTERIN-4-A-CARBINOLAMINE DEHYDRATASE) (PHENYLALANINE HYDROXYLASE-STIMULATING PROTEIN) (PHS) (PTERIN CARBINOLAMINE DEHYDRATASE) (PCD) \t1100460\t1101005\t+\t181\t15608124\t885378\tmoaB2\tRv0984\tCOG0521H\t\r\n' |
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit-in2-tn5.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit-in2-tn5.wig Tue Oct 08 08:24:46 2019 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r e4f44f327cf1 test-data/transit_tn5.prot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transit_tn5.prot Tue Oct 08 08:24:46 2019 -0400 |
| b |
| b'@@ -0,0 +1,500 @@\n+-\t190\t255\t+\t21\t-\t-\tthrL\tBW25113_0001\t-\r\n+bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal)\t337\t2799\t+\t820\t-\t-\tthrA\tBW25113_0002\t-\r\n+-\t2801\t3733\t+\t310\t-\t-\tthrB\tBW25113_0003\t-\r\n+-\t3734\t5020\t+\t428\t-\t-\tthrC\tBW25113_0004\t-\r\n+-\t5234\t5530\t+\t98\t-\t-\tyaaX\tBW25113_0005\t-\r\n+-\t5683\t6459\t-\t258\t-\t-\tyaaA\tBW25113_0006\t-\r\n+inner membrane transport protein\t6529\t7959\t-\t476\t-\t-\tyaaJ\tBW25113_0007\t-\r\n+-\t8238\t9191\t+\t317\t-\t-\ttalB\tBW25113_0008\t-\r\n+putative molybdochetalase in molybdopterine biosynthesis\t9306\t9893\t+\t195\t-\t-\tmog\tBW25113_0009\t-\r\n+-\t9928\t10494\t-\t188\t-\t-\tsatP\tBW25113_0010\t-\r\n+-\t10643\t11356\t-\t237\t-\t-\tyaaW\tBW25113_0011\t-\r\n+-\t11382\t11786\t-\t134\t-\t-\tyaaI\tBW25113_0013\t-\r\n+chaperone Hsp70%3B DNA biosynthesis%3B autoregulated heat shock proteins\t12163\t14079\t+\t638\t-\t-\tdnaK\tBW25113_0014\t-\r\n+chaperone with DnaK%3B heat shock protein\t14168\t15298\t+\t376\t-\t-\tdnaJ\tBW25113_0015\t-\r\n+-\t15445\t16557\t+\t370\t-\t-\tinsL1\tBW25113_0016\t-\r\n+regulatory peptide whose translation enables hokC (gef) expression%3B completely contained in another CDS\t16751\t16960\t-\t69\t-\t-\tmokC\tBW25113_0018\t-\r\n+small toxic membrane polypeptide%3B completely contained in another CDS\t16751\t16903\t-\t50\t-\t-\thokC\tBW25113_4412\t-\r\n+-\t16952\t17006\t+\t18\t-\t-\tsokC\tBW25113_4413\t-\r\n+Na+/H antiporter%2C pH dependent\t17489\t18655\t+\t388\t-\t-\tnhaA\tBW25113_0019\t-\r\n+-\t18715\t19620\t+\t301\t-\t-\tnhaR\tBW25113_0020\t-\r\n+-\t19811\t20314\t-\t167\t-\t-\tinsB1\tBW25113_0021\t-\r\n+-\t20233\t20508\t-\t91\t-\t-\tinsA\tBW25113_0022\t-\r\n+-\t20815\t21078\t-\t87\t-\t-\trpsT\tBW25113_0023\t-\r\n+-\t21181\t21399\t+\t72\t-\t-\tyaaY\tBW25113_0024\t-\r\n+-\t21407\t22348\t+\t313\t-\t-\tribF\tBW25113_0025\t-\r\n+isoleucine tRNA synthetase\t22391\t25207\t+\t938\t-\t-\tileS\tBW25113_0026\t-\r\n+prolipoprotein signal peptidase (SPase II)\t25207\t25701\t+\t164\t-\t-\tlspA\tBW25113_0027\t-\r\n+-\t25826\t26275\t+\t149\t-\t-\tfkpB\tBW25113_0028\t-\r\n+-\t26277\t27227\t+\t316\t-\t-\tispH\tBW25113_0029\t-\r\n+-\t27293\t28207\t+\t304\t-\t-\trihC\tBW25113_0030\t-\r\n+-\t28374\t29195\t+\t273\t-\t-\tdapB\tBW25113_0031\t-\r\n+-\t29651\t30799\t+\t382\t-\t-\tcarA\tBW25113_0032\t-\r\n+-\t30817\t34038\t+\t1073\t-\t-\tcarB\tBW25113_0033\t-\r\n+transcriptional regulator of cai operon\t34300\t34695\t+\t131\t-\t-\tcaiF\tBW25113_0034\t-\r\n+possible synthesis of cofactor for carnitine racemase and dehydratase\t34781\t35371\t-\t196\t-\t-\tcaiE\tBW25113_0035\t-\r\n+carnitine racemase\t35377\t36162\t-\t261\t-\t-\tcaiD\tBW25113_0036\t-\r\n+probable crotonobetaine/carnitine-CoA ligase\t36271\t37824\t-\t517\t-\t-\tcaiC\tBW25113_0037\t-\r\n+l-carnitine dehydratase\t37898\t39115\t-\t405\t-\t-\tcaiB\tBW25113_0038\t-\r\n+probable carnitine operon oxidoreductase\t39244\t40386\t-\t380\t-\t-\tcaiA\tBW25113_0039\t-\r\n+probable carnitine transporter\t40417\t41931\t-\t504\t-\t-\tcaiT\tBW25113_0040\t-\r\n+probable flavoprotein subunit%2C carnitine metabolism\t42403\t43173\t+\t256\t-\t-\tfixA\tBW25113_0041\t-\r\n+probable flavoprotein subunit%2C carnitine metabolism\t43188\t44129\t+\t313\t-\t-\tfixB\tBW25113_0042\t-\r\n+flavoprotein%3B electron transport\t44180\t45466\t+\t428\t-\t-\tfixC\tBW25113_0043\t-\r\n+putative ferredoxin\t45463\t45750\t+\t95\t-\t-\tfixX\tBW25113_0044\t-\r\n+putative transport protein\t45807\t47138\t+\t443\t-\t-\tyaaU\tBW25113_0045\t-\r\n+putative NAD(P)H oxidoreductase\t47246\t47776\t+\t176\t-\t-\tkefF\tBW25113_0046\t-\r\n+K+ efflux antiporter%2C glutathione-regulated\t47769\t49631\t+\t620\t-\t-\tkefC\tBW25113_0047\t-\r\n+dihydrofolate reductase type I%3B trimethoprim resistance\t49823\t50302\t+\t159\t-\t-\tfolA\tBW25113_0048\t-\r\n+-\t50380\t51222\t-\t280\t-\t-\tapaH\tBW25113_0049\t-\r\n+-\t51229\t51606\t-\t125\t-\t-\tapaG\tBW25113_0050\t-\r\n+-\t51609\t52430\t-\t273\t-\t-\trsmA\tBW25113_0051\t-\r\n+pyridoxine biosynthesis\t52427\t53416\t-\t329\t-\t-\tpdxA\tBW25113_0052\t-\r\n+survival protein\t53416\t54702\t-\t428\t-\t-\tsurA\tBW25113_0053\t-\r\n+organic solvent tolerance\t54755\t57109\t-\t784\t-\t-\tlptD\tBW25113_0054\t-\r\n+-\t57364\t58179\t+\t271\t-\t-\tdjlA\tBW25113_0055\t-\r\n+-\t59687\t60346\t-\t219\t-\t-\trluA\tBW25113_0058\t-\r\n+probable ATP-dependent RNA helicase\t60358\t63264\t-\t968\t-\t-\trapA\tBW25113_0059\t-\r\n+-\t63429\t65780\t-\t783\t-\t-\tpolB\tBW25113_0060\t-\r\n+transcriptional regulator for ara operon\t66874\t67752\t+\t292\t-\t-\taraC\tBW25113_0064\t-\r\n+-\t67838\t68602\t+\t254\t-\t-\tyabI\tBW25113_0065\t-'..b"or III\t487548\t489479\t+\t643\t-\t-\tdnaX\tBW25113_0470\t-\r\n+-\t489532\t489861\t+\t109\t-\t-\tybaB\tBW25113_0471\t-\r\n+recombination and repair\t489861\t490466\t+\t201\t-\t-\trecR\tBW25113_0472\t-\r\n+chaperone Hsp90%2C heat shock protein C 62.5\t490576\t492450\t+\t624\t-\t-\thtpG\tBW25113_0473\t-\r\n+adenylate kinase activity%3B pleiotropic effects on glycerol-3-phosphate acyltransferase activity\t492631\t493275\t+\t214\t-\t-\tadk\tBW25113_0474\t-\r\n+ferrochelatase: final enzyme of heme biosynthesis\t493511\t494473\t+\t320\t-\t-\themH\tBW25113_0475\t-\r\n+-\t494470\t495429\t-\t319\t-\t-\taes\tBW25113_0476\t-\r\n+inosine-guanosine kinase\t495581\t496885\t+\t434\t-\t-\tgsk\tBW25113_0477\t-\r\n+putative transport protein\t497018\t498694\t-\t558\t-\t-\tybaL\tBW25113_0478\t-\r\n+fosmidomycin resistance protein\t498932\t500152\t-\t406\t-\t-\tfsr\tBW25113_0479\t-\r\n+UDP-sugar hydrolase (5'-nucleotidase)\t500370\t502022\t+\t550\t-\t-\tushA\tBW25113_0480\t-\r\n+-\t502059\t502538\t-\t159\t-\t-\tybaK\tBW25113_0481\t-\r\n+-\t502660\t502743\t+\t27\t-\t-\tchiX\tBW25113_4585\t-\r\n+putative ligase\t502742\t503536\t-\t264\t-\t-\tybaP\tBW25113_0482\t-\r\n+-\t503674\t504015\t+\t113\t-\t-\tybaQ\tBW25113_0483\t-\r\n+-\t504331\t506835\t-\t834\t-\t-\tcopA\tBW25113_0484\t-\r\n+putative glutaminase\t507097\t508029\t+\t310\t-\t-\tglsA\tBW25113_0485\t-\r\n+putative amino acid/amine transport protein\t508032\t509324\t+\t430\t-\t-\tybaT\tBW25113_0486\t-\r\n+-\t509449\t509856\t+\t135\t-\t-\tcueR\tBW25113_0487\t-\r\n+-\t509857\t510315\t-\t152\t-\t-\tybbJ\tBW25113_0488\t-\r\n+putative protease\t510312\t511229\t-\t305\t-\t-\tqmcA\tBW25113_0489\t-\r\n+putative ATP-binding component of a transport system\t511375\t512052\t+\t225\t-\t-\tfetA\tBW25113_0490\t-\r\n+putative metal resistance protein\t512039\t512818\t+\t259\t-\t-\tfetB\tBW25113_0491\t-\r\n+putative thioredoxin-like protein\t512881\t513735\t-\t284\t-\t-\tybbN\tBW25113_0492\t-\r\n+-\t513796\t514605\t-\t269\t-\t-\tybbO\tBW25113_0493\t-\r\n+acyl-CoA thioesterase I%3B also functions as protease I\t514595\t515221\t-\t208\t-\t-\ttesA\tBW25113_0494\t-\r\n+putative ATP-binding component of a transport system\t515189\t515875\t+\t228\t-\t-\tybbA\tBW25113_0495\t-\r\n+putative oxidoreductase\t515872\t518286\t+\t804\t-\t-\tybbP\tBW25113_0496\t-\r\n+rhsD protein in rhs element\t518717\t522997\t+\t1426\t-\t-\trhsD\tBW25113_0497\t-\r\n+-\t523037\t523405\t+\t122\t-\t-\tybbC\tBW25113_0498\t-\r\n+putative capsule anchoring protein\t525588\t526682\t-\t364\t-\t-\tmnmH\tBW25113_0503\t-\r\n+putative transcriptional regulator LYSR-type\t526751\t527677\t-\t308\t-\t-\tallS\tBW25113_0504\t-\r\n+-\t527907\t528389\t+\t160\t-\t-\tallA\tBW25113_0505\t-\r\n+-\t528467\t529282\t+\t271\t-\t-\tallR\tBW25113_0506\t-\r\n+-\t529372\t531153\t+\t593\t-\t-\tgcl\tBW25113_0507\t-\r\n+-\t531166\t531942\t+\t258\t-\t-\thyi\tBW25113_0508\t-\r\n+-\t532042\t532920\t+\t292\t-\t-\tglxR\tBW25113_0509\t-\r\n+-\t533089\t534543\t+\t484\t-\t-\tybbW\tBW25113_0511\t-\r\n+-\t534603\t535964\t+\t453\t-\t-\tallB\tBW25113_0512\t-\r\n+-\t536021\t537322\t+\t433\t-\t-\tybbY\tBW25113_0513\t-\r\n+-\t537344\t538489\t+\t381\t-\t-\tglxK\tBW25113_0514\t-\r\n+-\t538717\t539502\t-\t261\t-\t-\tallE\tBW25113_0515\t-\r\n+-\t539513\t540748\t-\t411\t-\t-\tallC\tBW25113_0516\t-\r\n+-\t540770\t541819\t-\t349\t-\t-\tallD\tBW25113_0517\t-\r\n+involved in protein transport%3B multicopy suppressor of dominant negative ftsH mutants\t542136\t543803\t+\t555\t-\t-\tfdrA\tBW25113_0518\t-\r\n+-\t543813\t545072\t+\t419\t-\t-\tylbE\tBW25113_4572\t-\r\n+putative carboxylase\t545083\t545898\t+\t271\t-\t-\tylbF\tBW25113_0520\t-\r\n+putative carbamate kinase\t545895\t546788\t+\t297\t-\t-\tybcF\tBW25113_0521\t-\r\n+phosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C CO(2)-fixing subunit\t546983\t548050\t-\t355\t-\t-\tpurK\tBW25113_0522\t-\r\n+phosphoribosylaminoimidazole carboxylase %3D AIR carboxylase%2C catalytic subunit\t548047\t548556\t-\t169\t-\t-\tpurE\tBW25113_0523\t-\r\n+-\t548674\t549396\t-\t240\t-\t-\tlpxH\tBW25113_0524\t-\r\n+-\t549399\t549893\t-\t164\t-\t-\tppiB\tBW25113_0525\t-\r\n+cysteine tRNA synthetase\t550067\t551452\t+\t461\t-\t-\tcysS\tBW25113_0526\t-\r\n+-\t551488\t552009\t-\t173\t-\t-\tybcI\tBW25113_0527\t-\r\n+-\t552117\t552329\t-\t70\t-\t-\tybcJ\tBW25113_0528\t-\r\n+5%2C10-methylene-tetrahydrofolate dehydrogenase%3B 5%2C10-methylene-tetrahydrofolate cyclohydrolase\t552331\t553197\t-\t288\t-\t-\tfolD\tBW25113_0529\t-\r\n+putative fimbrial-like protein\t553668\t554210\t+\t180\t-\t-\tsfmA\tBW25113_0530\t-\r\n+putative chaperone\t554430\t555122\t+\t230\t-\t-\tsfmC\tBW25113_0531\t-\r\n" |
| b |
| diff -r 000000000000 -r e4f44f327cf1 transit_tn5gaps.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/transit_tn5gaps.xml Tue Oct 08 08:24:46 2019 -0400 |
| [ |
| b'@@ -0,0 +1,119 @@\n+<?xml version="1.0"?>\n+<tool id="transit_tn5gaps" name="Tn5Gaps" version="@VERSION@+galaxy1">\n+ <description>- determine essential genes</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+ transit tn5gaps $input_files annotation.dat transit_out.txt\n+ @STANDARD_OPTIONS@\n+ -m $smallest\n+ ]]>\n+ </command>\n+ <inputs>\n+ <expand macro="standard_inputs">\n+ <param name="smallest" argument="-m" type="integer" value="1" label="Smallest read-count to consider" />\n+ </expand>\n+ </inputs>\n+ <outputs>\n+ <expand macro="outputs" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="inputs" ftype="wig" value="transit-in-tn5.wig,transit-in2-tn5.wig" />\n+ <param name="annotation" ftype="tabular" value="transit_tn5.prot" />\n+ <param name="replicates" value="Replicates" />\n+ <output name="sites" file="tn5gaps-sites1.txt" ftype="tabular" compare="sim_size" />\n+ </test>\n+ </tests>\n+\n+<help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+-------------------\n+\n+This method is loosely is based on the original **Gumbel** analysis method. The **Gumbel** method can be used to determine which genes are essential in a single condition. It does a gene-by-gene analysis of the insertions at TA sites with each gene, makes a call based on the longest consecutive sequence of TA sites without insertion in the genes, calculates the probability of this using a Bayesian model.\n+The Tn5Gaps method modifies the original method in order to work on Tn5 datasets, which have significantly lower saturation of insertion sites than Himar1 datasets. The main difference comes from the fact that the runs of non-insertion (or \xe2\x80\x9cgaps\xe2\x80\x9d) are analyzed throughout the whole genome, including non-coding regions, instead of within single genes. In doing so, the expected maximum run length is calculated and a p-value can be derived for every run. A gene is then classified by using the p-value of the run with the largest number of nucleotides overlapping with the gene.\n+\n+-------------------\n+\n+**Inputs**\n+\n+-------------------\n+\n+Input files for Tn5Gaps need to be:\n+\n+- .wig files: Tabulated files containing one column with the TA site coordinate and one column with the read count at this site.\n+- annotation .prot_table: Annotation file generated by the `Convert Gff3 to prot_table for TRANSIT` tool.\n+\n+\n+-------------------\n+\n+**Parameters**\n+\n+-------------------\n+\n+Optional Arguments:\n+ -m <integer> := Smallest read-count to consider. Default: -m 1\n+ -r <string> := How to handle replicates. Sum or Mean. Default: -r Sum\n+ --iN <float> := Ignore TAs occuring at given fraction of the N terminus. Default: -iN 0.0\n+ --iC <float> := Ignore TAs occuring at given fraction of the C terminus. Default: -iC 0.0\n+ -n <string> := Determines which normalization method to use. Default -n TTR\n+\n+- Minimum Read: The minimum read count that is considered a true read. Because the Gumbel method depends on determining gaps of TA sites lacking insertions, it may be susceptible to spurious reads (e.g. errors). The default value of 1 will consider all reads as true reads. A value of 2, for example, will ignore read counts of 1.\n+- Replicates: Determines how to deal with replicates by averaging the read-counts or summing read counts across datasets. This should not have an affect for the Gumbel method, aside from potentially affecting spurious reads.\n+- Normalisation :\n+ - TTR (Default) : Trimmed Total Reads (TTR), normalized by the total read-counts (like totreads), but trims top and bottom 5% of read-counts. This is the recommended normalization method for most cases as it has the beneffit of normalizing for difference in saturation in the context of resa'..b's.\n+ - zinfnb : Fits a zero-inflated negative binomial model, and then divides read-counts by the mean. The zero-inflated negative binomial model will treat some empty sites as belonging to the \xe2\x80\x9ctrue\xe2\x80\x9d negative binomial distribution responsible for read-counts while treating the others as \xe2\x80\x9cessential\xe2\x80\x9d (and thus not influencing its parameters).\n+ - quantile : Normalizes datasets using the quantile normalization method described by Bolstad et al. (2003). In this normalization procedure, datasets are sorted, an empirical distribution is estimated as the mean across the sorted datasets at each site, and then the original (unsorted) datasets are assigned values from the empirical distribution based on their quantiles.\n+ - betageom : Normalizes the datasets to fit an \xe2\x80\x9cideal\xe2\x80\x9d Geometric distribution with a variable probability parameter p. Specially useful for datasets that contain a large skew. See Beta-Geometric Correction .\n+ - nonorm : No normalization is performed.\n+\n+\n+-------------------\n+\n+ **Outputs**\n+\n+-------------------\n+\n+============================================= ========================================================================================================================\n+**Column Header** **Column Definition**\n+--------------------------------------------- ------------------------------------------------------------------------------------------------------------------------\n+Orf Gene ID\n+Name Gene Name\n+Desc Gene Description\n+k Number of Transposon Insertions Observed within the ORF.\n+n Total Number of TA dinucleotides within the ORF.\n+r Span of nucleotides for the Maximum Run of Non-Insertions.\n+ovr The number of nucleotides in the overlap with the longest run partially covering the gene.\n+lenovr The length of the above run with the largest overlap with the gene.\n+pval P-value calculated by the permutation test.\n+padj Adjusted p-value controlling for the FDR (Benjamini-Hochberg).\n+State Call Essentiality call for the gene. Depends on FDR corrected thresholds. E=Essential U=Uncertain, NE=Non-Essential, S=too short\n+============================================= ========================================================================================================================\n+\n+\n+\n+Note: Technically, Bayesian models are used to calculate posterior probabilities, not p-values (which is a concept associated with the frequentist framework). However, we have implemented a method for computing the approximate false-discovery rate (FDR) that serves a similar purpose. This determines a threshold for significance on the posterior probabilities that is corrected for multiple tests. The actual thresholds used are reported in the headers of the output file (and are near 1 for essentials and near 0 for non-essentials). There can be many genes that score between the two thresholds (t1 < zbar < t2). This reflects intrinsic uncertainty associated with either low read counts, sparse insertion density, or small genes. If the insertion_density is too low (< ~30%), the method may not work as well, and might indicate an unusually large number of Uncertain or Essential genes.\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 Tn5Gaps`: https://transit.readthedocs.io/en/latest/transit_methods.html#tn5gaps\n+ ]]></help>\n+\n+ <expand macro="citations" />\n+\n+</tool>\n' |