| Next changeset 1:77d50ec2bcf2 (2024-03-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870" |
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added:
scoary.xml test-data/Gene_presence_absence.csv test-data/Tetracycline_resistance.csv test-data/scoary_output.nwk test-data/scoary_output.tsv test-data/scoary_output_2.nwk test-data/scoary_output_2.tsv |
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| diff -r 000000000000 -r 42a1a5750539 scoary.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scoary.xml Sun Mar 21 12:21:41 2021 +0000 |
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| b'@@ -0,0 +1,218 @@\n+<tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01">\n+ <description>calculates the assocations between all genes in the accessory genome and the traits</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.6.16</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">scoary</requirement>\n+ </requirements>\n+ <version_command>scoary --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+scoary\n+\n+###########\n+## Input ##\n+###########\n+\n+-t \'$input_traits\'\n+-g \'$input_genes\'\n+\n+#if $input_restricts:\n+\t-r \'$input_restricts\'\n+#end if\n+\n+########################\n+## Additional Options ##\n+########################\n+\n+#if len($additional_options.series_pc) != 0\n+ -p #echo " ".join([ "\'%s\'" % $s.pvalue for $i, $s in enumerate($additional_options.series_pc) ])\n+ -c #echo " ".join([ "\'%s\'" % $s.correction for $i, $s in enumerate($additional_options.series_pc) ])\n+#end if\n+\n+#if $additional_options.permute != 0:\n+ -e str($additional_options.permute)\n+#end if\n+\n+#if $additional_options.maxhits != 0:\n+ -m str($additional_options.maxhits)\n+#end if\n+\n+$additional_options.collapse\n+$output_options.upgma\n+\n+#if $input_newicktree:\n+ -n \'$input_newicktree\'\n+#end if\n+\n+#########\n+## END ##\n+#########\n+\n+--no-time\n+&&\n+tail -n +1 *.csv | sed "s/\\,/\\\\t/g" > scoary_output.tsv &&\n+mv *.nwk scoary_output.nwk\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="input_traits" argument="-t" type="data" format="csv" label="Trait table"/>\n+ <param name="input_genes" argument="-g" type="data" format="csv" label="Gene Presence/Absence table from ROARY (default output)"/>\n+ <param name="input_restricts" optional="true" argument="-r" type="data" format="tabular" label="Table to analyze a subset of strains" />\n+\n+ <!-- Additional Options -->\n+ <section name="additional_options" title="Additional Options">\n+ <repeat name="series_pc" title="P-value cutoff(s) and Correction(s)">\n+ <param name="pvalue" argument="-p" type="float" min="0" max="1.0" value="0.05" label="P-value cutoff for one Trait" help="SCOARY will not report genes with higher p-values than this (Default=1.0=All). Provide a single value (applied to all) or exactly as many values as correction criteria and in corresponding order (e.g., 0.05 0.05 for two traits)."/>\n+ <param name="correction" argument="-c" type="select" label="P-value correction" help="Apply the p-value corrections to the p-value cutoffs you have entered (Default = Individual p-value)." >\n+ <option value="I" selected="true">Individual (naive) p-value</option>\n+ <option value="B">Bonferroni adjusted p-value</option>\n+ <option value="BH">Benjamini-Hochberg adjusted p</option>\n+ <option value="PW">Best (lowest) pairwise comparison</option>\n+ <option value="EPW">Entire range of pairwise comparison p-values</option>\n+ <option value="P">Empirical p-value from permutations</option>\n+ </param>\n+ </repeat>\n+ <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" />\n+ <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" />\n+ <param name="collapse" argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>\n+ <param name="input_newicktree" optional="true" argument="-n"'..b' </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+-------------------\n+\n+**Scoary**\n+\n+Scoary is designed to take the csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.\n+\n+-------------------\n+\n+**Inputs**\n+\n+-------------------\n+\n+Scoary requires two input files: csv file from Roary and a list of traits to test associations to.\n+Traits can be anything as long as you can classify it into binary categories (e.g. antibiotic resistance, group membership (yes/no), MIC value higher/lower than 16).\n+Make sure you your entires are separated by \',\'.\n+The traits file needs to be formatted in a specific way (please take a look into the (documentation)[https://github.com/AdmiralenOla/Scoary]).\n+\n+You can also use as input the pan-genome as called from Jason Sahl\'s program LS-BSR (Large-Scale Blast Score Ratio).\n+The program includes a python script for converting LS-BSR output to the Roary/Scoary format.\n+\n+Trait presence is indicated by 1, trait absence by 0.\n+Assumes strain names in the first column and trait names in the first row.\n+\n+Input gene presence/absence table (comma-separated-values) from ROARY.\n+Strain names must be equal to those in the trait table.\n+\n+-----------\n+\n+**Outputs**\n+\n+-----------\n+\n+Scory outputs a single csv traits file. It uses comma "," as a delimiter.\n+The results consists of genes that were found to be associated with the trait, sorted according to significance.\n+By default, Scoary reports all genes with a naive p-value < 0.05.\n+\n+You can find the description of the columns in the (documentation)[https://github.com/AdmiralenOla/Scoary].\n+\n+--------------------\n+\n+**More Information**\n+\n+--------------------\n+\n+See the excellent `Scoary documentation`_\n+\n+.. _`Scoary documentation`: https://github.com/AdmiralenOla/Scoary\n+\n+\n+**P-value cutoff (-p)**: For Fishers, Bonferronis, and Benjamini-Hochbergs tests, SCOARY will not report genes with higher p-values than this.\n+For empirical p-values, this is treated as an alpha level instead.\n+I.e. 0.02 will filter all genes except the lower and upper percentile from this test.\n+Run with "-p 1.0" to report all genes. Accepts standard form (e.g. 1E-8).\n+Provide a single value (applied to all) or exactly as many values as correction criteria and in corresponding order (e.g., 0.05 0.1 0.05 0.02).\n+\n+**Correction (-c)**: Apply the indicated filtration measure: I=Individual (naive) p-value, B=Bonferroni adjusted p-value, BH=Benjamini-Hochberg adjusted p, PW=Best (lowest) pairwise comparison, EPW=Entire range of pairwise comparison p-values, P=Empirical p-value from permutations.\n+You can enter as many correction criteria as you would like.\n+These will be associated with the p-value cutoffs you enter.\n+For example "-c I EPW -p 0.1 0.05" will apply the following cutoffs: Naive p-value must be lower than 0.1 AND the entire range of pairwise comparison values are below 0.05 for this gene.\n+Note that the empirical p-values should be interpreted at both tails.\n+Therefore, running "-c P -p 0.05" will apply an alpha of 0.05 to the empirical (permuted) p-values, i.e. it will filter everything except the upper and lower 2.5 percent of the distribution.\n+\n+**Permute (-e)**: Perform N number of permutations of the significant results post-analysis.\n+Each permutation will do a label switching of the phenotype and a new p-value is calculated according to this new dataset.\n+After all N permutations are completed, the results are ordered in ascending order, and the percentile of the original result in the permuted p-value distribution is reported.\n+\n+--------------------\n+\n+**Galaxy Wrapper Development**\n+\n+--------------------\n+\n+Author: Florian Heyl\n+\n+\t]]></help>\n+ <citations>\n+\t <citation type="doi">10.1038/s41467-020-15171-6</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 42a1a5750539 test-data/Gene_presence_absence.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Gene_presence_absence.csv Sun Mar 21 12:21:41 2021 +0000 |
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| b'@@ -0,0 +1,9002 @@\n+Gene,Non-unique Gene name,Annotation,No. isolates,No. sequences,Avg sequences per isolate,Genome fragment,Order within fragment,Accessory Fragment,Accessory Order with Fragment,QC,Min group size nuc,Max group size nuc,Avg group size nuc,Isolate_1,Isolate_10,Isolate_11,Isolate_12,Isolate_13,Isolate_14,Isolate_15,Isolate_16,Isolate_17,Isolate_18,Isolate_19,Isolate_2,Isolate_20,Isolate_21,Isolate_22,Isolate_23,Isolate_24,Isolate_25,Isolate_26,Isolate_27,Isolate_28,Isolate_29,Isolate_3,Isolate_30,Isolate_31,Isolate_32,Isolate_33,Isolate_34,Isolate_35,Isolate_36,Isolate_37,Isolate_38,Isolate_39,Isolate_4,Isolate_40,Isolate_41,Isolate_42,Isolate_43,Isolate_44,Isolate_45,Isolate_46,Isolate_47,Isolate_48,Isolate_49,Isolate_5,Isolate_50,Isolate_51,Isolate_52,Isolate_53,Isolate_54,Isolate_55,Isolate_56,Isolate_57,Isolate_58,Isolate_59,Isolate_6,Isolate_60,Isolate_61,Isolate_62,Isolate_63,Isolate_64,Isolate_65,Isolate_66,Isolate_67,Isolate_68,Isolate_69,Isolate_7,Isolate_70,Isolate_71,Isolate_72,Isolate_73,Isolate_74,Isolate_75,Isolate_76,Isolate_77,Isolate_78,Isolate_79,Isolate_8,Isolate_80,Isolate_81,Isolate_82,Isolate_83,Isolate_84,Isolate_85,Isolate_86,Isolate_87,Isolate_88,Isolate_89,Isolate_9,Isolate_90,Isolate_91,Isolate_92,Isolate_93,Isolate_94,Isolate_95,Isolate_96,Isolate_97,Isolate_98,Isolate_99,Isolate_100\n+gene_0,,A core gene,100,100,1,1,1,,,,1113,1113,1113,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1,,A core gene,100,100,1,1,2,,,,843,843,843,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_10,,A core gene,100,100,1,1,3,,,,685,685,685,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_100,,A core gene,100,100,1,1,4,,,,917,917,917,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1000,,A core gene,100,100,1,1,5,,,,1084,1084,1084,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1001,,A core gene,100,100,1,1,6,,,,1015,1015,1015,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1002,,A core gene,100,100,1,1,7,,,,1060,1060,1060,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1003,,A core gene,100,100,1,1,8,,,,1112,1112,1112,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1004,,A core gene,100,100,1,1,9,,,,1124,1124,1124,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1005,,A core gene,100,100,1,1,10,,,,1105,1105,1105,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1\n+gene_1006,,A core gene,100,100,1,1,11,,,,1271,1271,1271,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,'..b'0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_7773,,A gene with no relevance to tetracycline resistance,0,0,1,1,7528,,,,961,961,961,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_7791,,A gene with no relevance to tetracycline resistance,0,0,1,1,7548,,,,1238,1238,1238,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_7985,,A gene with no relevance to tetracycline resistance,0,0,1,1,7763,,,,864,864,864,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8044,,A gene with no relevance to tetracycline resistance,0,0,1,1,7830,,,,1044,1044,1044,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8121,,A gene with no relevance to tetracycline resistance,0,0,1,1,7916,,,,1239,1239,1239,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8213,,A gene with no relevance to tetracycline resistance,0,0,1,1,8018,,,,1182,1182,1182,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8228,,A gene with no relevance to tetracycline resistance,0,0,1,1,8034,,,,694,694,694,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8332,,A gene with no relevance to tetracycline resistance,0,0,1,1,8150,,,,1252,1252,1252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8421,,A gene with no relevance to tetracycline resistance,0,0,1,1,8249,,,,1288,1288,1288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8725,,A gene with no relevance to tetracycline resistance,0,0,1,1,8586,,,,650,650,650,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8806,,A gene with no relevance to tetracycline resistance,0,0,1,1,8676,,,,794,794,794,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8901,,A gene with no relevance to tetracycline resistance,0,0,1,1,8782,,,,616,616,616,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+gene_8988,,A gene with no relevance to tetracycline resistance,0,0,1,1,8877,,,,1138,1138,1138,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n' |
| b |
| diff -r 000000000000 -r 42a1a5750539 test-data/Tetracycline_resistance.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Tetracycline_resistance.csv Sun Mar 21 12:21:41 2021 +0000 |
| b |
| @@ -0,0 +1,101 @@ +,Tetracycline_resistance,Bogus_trait +Isolate_1,0,0 +Isolate_10,0,1 +Isolate_11,0,1 +Isolate_12,1,0 +Isolate_13,0,NA +Isolate_14,0,1 +Isolate_15,0,0 +Isolate_16,0,0 +Isolate_17,0,1 +Isolate_18,0,0 +Isolate_19,0,0 +Isolate_2,0,1 +Isolate_20,0,1 +Isolate_21,0,1 +Isolate_22,1,1 +Isolate_23,1,0 +Isolate_24,0,0 +Isolate_25,0,1 +Isolate_26,1,- +Isolate_27,0,0 +Isolate_28,1,1 +Isolate_29,1,1 +Isolate_3,0,1 +Isolate_30,1,1 +Isolate_31,1,0 +Isolate_32,0,0 +Isolate_33,0,0 +Isolate_34,1,1 +Isolate_35,1,1 +Isolate_36,1,0 +Isolate_37,0,1 +Isolate_38,1,1 +Isolate_39,1,1 +Isolate_4,1,0 +Isolate_40,1,1 +Isolate_41,0,1 +Isolate_42,0,0 +Isolate_43,0,0 +Isolate_44,0,1 +Isolate_45,0,0 +Isolate_46,0,1 +Isolate_47,0,1 +Isolate_48,0,0 +Isolate_49,1,1 +Isolate_5,0,1 +Isolate_50,1,0 +Isolate_51,0,0 +Isolate_52,0,0 +Isolate_53,0,0 +Isolate_54,1,0 +Isolate_55,0,1 +Isolate_56,1,0 +Isolate_57,1,1 +Isolate_58,0,1 +Isolate_59,0,0 +Isolate_6,0,1 +Isolate_60,0,1 +Isolate_61,0,1 +Isolate_62,0,1 +Isolate_63,0,0 +Isolate_64,0,1 +Isolate_65,0,0 +Isolate_66,1,1 +Isolate_67,0,1 +Isolate_68,1,0 +Isolate_69,1,1 +Isolate_7,0,0 +Isolate_70,0,1 +Isolate_71,0,1 +Isolate_72,0,0 +Isolate_73,0,0 +Isolate_74,0,0 +Isolate_75,1,1 +Isolate_76,0,1 +Isolate_77,1,1 +Isolate_78,0,0 +Isolate_79,1,. +Isolate_8,0,1 +Isolate_80,0,0 +Isolate_81,0,0 +Isolate_82,0,1 +Isolate_83,0,1 +Isolate_84,0,0 +Isolate_85,1,0 +Isolate_86,1,1 +Isolate_87,1,1 +Isolate_88,0,1 +Isolate_89,0,1 +Isolate_9,0,1 +Isolate_90,1,0 +Isolate_91,0,0 +Isolate_92,0,1 +Isolate_93,0,1 +Isolate_94,0,0 +Isolate_95,1,1 +Isolate_96,0,1 +Isolate_97,0,0 +Isolate_98,0,0 +Isolate_99,1,0 +Isolate_100,0,0 |
| b |
| diff -r 000000000000 -r 42a1a5750539 test-data/scoary_output.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scoary_output.nwk Sun Mar 21 12:21:41 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((((('Isolate_1', 'Isolate_55'), ((('Isolate_36', 'Isolate_46'), 'Isolate_97'), 'Isolate_51')), (((((((('Isolate_10', ('Isolate_9', 'Isolate_91')), 'Isolate_31'), ('Isolate_38', ('Isolate_45', 'Isolate_5'))), 'Isolate_59'), (((('Isolate_15', 'Isolate_21'), 'Isolate_70'), 'Isolate_22'), 'Isolate_32')), (((((('Isolate_13', 'Isolate_80'), ('Isolate_50', 'Isolate_63')), 'Isolate_66'), ((('Isolate_23', 'Isolate_69'), 'Isolate_25'), 'Isolate_57')), 'Isolate_72'), ((('Isolate_19', 'Isolate_41'), 'Isolate_82'), 'Isolate_48'))), (('Isolate_52', 'Isolate_81'), ('Isolate_61', 'Isolate_79'))), (((('Isolate_12', 'Isolate_86'), 'Isolate_62'), (('Isolate_29', 'Isolate_84'), ('Isolate_64', 'Isolate_78'))), (((('Isolate_26', ('Isolate_4', 'Isolate_75')), 'Isolate_95'), (('Isolate_7', 'Isolate_74'), 'Isolate_85')), ('Isolate_68', 'Isolate_83'))))), (((('Isolate_11', 'Isolate_18'), 'Isolate_60'), ((('Isolate_14', 'Isolate_73'), (('Isolate_24', 'Isolate_6'), 'Isolate_33')), 'Isolate_54')), ('Isolate_35', 'Isolate_96'))), ((((('Isolate_16', 'Isolate_65'), 'Isolate_90'), 'Isolate_89'), (((('Isolate_17', 'Isolate_8'), 'Isolate_58'), 'Isolate_77'), (('Isolate_44', 'Isolate_100'), 'Isolate_56'))), (((((('Isolate_2', 'Isolate_88'), (('Isolate_28', 'Isolate_49'), 'Isolate_39')), ((((('Isolate_20', 'Isolate_47'), (('Isolate_3', 'Isolate_42'), 'Isolate_53')), 'Isolate_71'), ('Isolate_40', 'Isolate_67')), 'Isolate_92')), 'Isolate_87'), 'Isolate_94'), 'Isolate_99'))), (((('Isolate_27', 'Isolate_43'), ('Isolate_37', 'Isolate_76')), ('Isolate_34', 'Isolate_98')), ('Isolate_30', 'Isolate_93'))); \ No newline at end of file |
| b |
| diff -r 000000000000 -r 42a1a5750539 test-data/scoary_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scoary_output.tsv Sun Mar 21 12:21:41 2021 +0000 |
| b |
| b'@@ -0,0 +1,573 @@\n+==> Bogus_trait.results.csv <==\n+"Gene"\t"Non-unique Gene name"\t"Annotation"\t"Number_pos_present_in"\t"Number_neg_present_in"\t"Number_pos_not_present_in"\t"Number_neg_not_present_in"\t"Sensitivity"\t"Specificity"\t"Odds_ratio"\t"Naive_p"\t"Bonferroni_p"\t"Benjamini_H_p"\t"Max_Pairwise_comparisons"\t"Max_supporting_pairs"\t"Max_opposing_pairs"\t"Best_pairwise_comp_p"\t"Worst_pairwise_comp_p"\n+"gene_6942"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"32"\t"35"\t"12"\t"33.9622641509434"\t"27.27272727272727"\t"0.19285714285714287"\t"0.00021060616542660472"\t"1.0"\t"1.0"\t"22"\t"5"\t"20"\t"0.00012111663818359382"\t"0.016900539398193356"\n+"gene_6673"\t""\t"A gene with no relevance to tetracycline resistance"\t"17"\t"30"\t"36"\t"14"\t"32.075471698113205"\t"31.818181818181817"\t"0.22037037037037038"\t"0.0005143108960102311"\t"1.0"\t"1.0"\t"15"\t"6"\t"15"\t"6.103515625e-05"\t"0.6072387695312501"\n+"gene_6911"\t""\t"A gene with no relevance to tetracycline resistance"\t"37"\t"15"\t"16"\t"29"\t"69.81132075471697"\t"65.9090909090909"\t"4.470833333333333"\t"0.00053916149317378"\t"1.0"\t"1.0"\t"24"\t"18"\t"8"\t"0.02265584468841553"\t"0.15158963203430173"\n+"gene_8967"\t""\t"A gene with no relevance to tetracycline resistance"\t"23"\t"34"\t"30"\t"10"\t"43.39622641509434"\t"22.727272727272727"\t"0.22549019607843138"\t"0.0009104065280977792"\t"1.0"\t"1.0"\t"19"\t"9"\t"15"\t"0.019210815429687503"\t"1.0"\n+"gene_7559"\t""\t"A gene with no relevance to tetracycline resistance"\t"30"\t"10"\t"23"\t"34"\t"56.60377358490566"\t"77.27272727272727"\t"4.434782608695652"\t"0.0009104065280977792"\t"1.0"\t"1.0"\t"16"\t"14"\t"6"\t"0.004180908203124999"\t"0.45449829101562506"\n+"gene_6370"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"30"\t"35"\t"14"\t"33.9622641509434"\t"31.818181818181817"\t"0.24"\t"0.0010707763378538038"\t"1.0"\t"1.0"\t"16"\t"8"\t"14"\t"0.004180908203124999"\t"1.0"\n+"gene_4350"\t""\t"A gene with no relevance to tetracycline resistance"\t"8"\t"20"\t"45"\t"24"\t"15.09433962264151"\t"54.54545454545454"\t"0.21333333333333335"\t"0.0014760680299882403"\t"1.0"\t"1.0"\t"15"\t"5"\t"13"\t"0.007385253906249998"\t"0.30175781250000017"\n+"gene_7530"\t""\t"A gene with no relevance to tetracycline resistance"\t"29"\t"10"\t"24"\t"34"\t"54.71698113207547"\t"77.27272727272727"\t"4.108333333333333"\t"0.0017731376170655763"\t"1.0"\t"1.0"\t"15"\t"12"\t"7"\t"0.035156250000000014"\t"0.9999999999999997"\n+"gene_6897"\t""\t"A gene with no relevance to tetracycline resistance"\t"23"\t"33"\t"30"\t"11"\t"43.39622641509434"\t"25.0"\t"0.25555555555555554"\t"0.0020440818682201803"\t"1.0"\t"1.0"\t"6"\t"3"\t"5"\t"0.21875000000000003"\t"1.0"\n+"gene_4212"\t""\t"A gene with no relevance to tetracycline resistance"\t"24"\t"7"\t"29"\t"37"\t"45.28301886792453"\t"84.0909090909091"\t"4.374384236453202"\t"0.0022735568331854012"\t"1.0"\t"1.0"\t"8"\t"7"\t"4"\t"0.0703125"\t"1.0"\n+"gene_5400"\t""\t"A gene with no relevance to tetracycline resistance"\t"36"\t"41"\t"17"\t"3"\t"67.9245283018868"\t"6.8181818181818175"\t"0.15494978479196556"\t"0.0023282582361435827"\t"1.0"\t"1.0"\t"6"\t"2"\t"5"\t"0.21875000000000003"\t"0.6875000000000002"\n+"gene_6136"\t""\t"A gene with no relevance to tetracycline resistance"\t"22"\t"32"\t"31"\t"12"\t"41.509433962264154"\t"27.27272727272727"\t"0.2661290322580645"\t"0.0023288420248875606"\t"1.0"\t"1.0"\t"20"\t"8"\t"19"\t"4.005432128906249e-05"\t"0.5034446716308595"\n+"gene_8588"\t""\t"A gene with no relevance to tetracycline resistance"\t"31"\t"12"\t"22"\t"32"\t"58.490566037735846"\t"72.72727272727273"\t"3.757575757575758"\t"0.0023288420248875606"\t"1.0"\t"1.0"\t"16"\t"14"\t"8"\t"0.004180908203124999"\t"1.0"\n+"gene_8837"\t""\t"A gene with no relevance to tetracycline resistance"\t"27"\t"9"\t"26"\t"35"\t"50.943396226415096"\t"79.54545454545455"\t"4.038461538461538"\t"0.0029166014052459267"\t"1.0"\t"1.0"\t"20"\t"15"\t"7"\t"0.04138946533203125"\t"0.2631759643554687"\n+"gene_6687"\t""\t"A gene with no relevance to tetracycline resistance"\t"22"\t"6"\t"31"\t"38"\t"41.509433962264154"\t"86.36363636363636"\t"4.494623655913978"\t"0.0032469422485313666"\t"1.0"\t"1.0"\t"10"\t"7"\t"5"\t"0.3437499999999999"\t"1.0"\n+"gene_3217"\t""\t"A gene with no relevance to tetracycline resistan'..b'"\t"42.64705882352941"\t"2.6556776556776556"\t"0.04798895931025533"\t"1.0"\t"0.7548757656770544"\t"11"\t"9"\t"6"\t"0.06542968749999997"\t"0.9999999999999997"\n+"gene_3844"\t""\t"A gene with no relevance to tetracycline resistance"\t"7"\t"29"\t"25"\t"39"\t"21.875"\t"57.35294117647059"\t"0.37655172413793103"\t"0.04798895931025533"\t"1.0"\t"0.7548757656770544"\t"18"\t"6"\t"14"\t"0.0308837890625"\t"0.23788452148437486"\n+"gene_4287"\t""\t"A gene with no relevance to tetracycline resistance"\t"7"\t"29"\t"25"\t"39"\t"21.875"\t"57.35294117647059"\t"0.37655172413793103"\t"0.04798895931025533"\t"1.0"\t"0.7548757656770544"\t"17"\t"7"\t"12"\t"0.14346313476562497"\t"0.629058837890625"\n+"gene_5793"\t""\t"A gene with no relevance to tetracycline resistance"\t"24"\t"36"\t"8"\t"32"\t"75.0"\t"47.05882352941176"\t"2.6666666666666665"\t"0.048738926902935104"\t"1.0"\t"0.7548757656770544"\t"11"\t"10"\t"5"\t"0.011718750000000002"\t"0.9999999999999997"\n+"gene_6253"\t""\t"A gene with no relevance to tetracycline resistance"\t"24"\t"36"\t"8"\t"32"\t"75.0"\t"47.05882352941176"\t"2.6666666666666665"\t"0.048738926902935104"\t"1.0"\t"0.7548757656770544"\t"21"\t"17"\t"5"\t"0.0071973800659179705"\t"0.026603698730468753"\n+"gene_4147"\t""\t"A gene with no relevance to tetracycline resistance"\t"8"\t"32"\t"24"\t"36"\t"25.0"\t"52.94117647058824"\t"0.375"\t"0.048738926902935104"\t"1.0"\t"0.7548757656770544"\t"20"\t"5"\t"17"\t"0.002576828002929687"\t"0.04138946533203125"\n+"gene_6446"\t""\t"A gene with no relevance to tetracycline resistance"\t"14"\t"45"\t"18"\t"23"\t"43.75"\t"33.82352941176471"\t"0.39753086419753086"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"16"\t"11"\t"9"\t"0.21011352539062492"\t"0.8036193847656252"\n+"gene_7230"\t""\t"A gene with no relevance to tetracycline resistance"\t"14"\t"45"\t"18"\t"23"\t"43.75"\t"33.82352941176471"\t"0.39753086419753086"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"20"\t"5"\t"15"\t"0.04138946533203125"\t"0.04138946533203125"\n+"gene_8369"\t""\t"A gene with no relevance to tetracycline resistance"\t"14"\t"45"\t"18"\t"23"\t"43.75"\t"33.82352941176471"\t"0.39753086419753086"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"20"\t"9"\t"12"\t"0.5034446716308595"\t"0.8238029479980463"\n+"gene_8470"\t""\t"A gene with no relevance to tetracycline resistance"\t"14"\t"45"\t"18"\t"23"\t"43.75"\t"33.82352941176471"\t"0.39753086419753086"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"21"\t"10"\t"15"\t"0.07835388183593749"\t"1.0"\n+"gene_3545"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"23"\t"14"\t"45"\t"56.25"\t"66.17647058823529"\t"2.515527950310559"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"17"\t"9"\t"9"\t"0.9999999999999998"\t"0.9999999999999998"\n+"gene_3787"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"23"\t"14"\t"45"\t"56.25"\t"66.17647058823529"\t"2.515527950310559"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"13"\t"9"\t"9"\t"0.26684570312499983"\t"0.26684570312499983"\n+"gene_3812"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"23"\t"14"\t"45"\t"56.25"\t"66.17647058823529"\t"2.515527950310559"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"14"\t"11"\t"9"\t"0.05737304687500002"\t"0.4239501953124999"\n+"gene_5725"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"23"\t"14"\t"45"\t"56.25"\t"66.17647058823529"\t"2.515527950310559"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"16"\t"13"\t"8"\t"0.021270751953125"\t"1.0"\n+"gene_6271"\t""\t"A gene with no relevance to tetracycline resistance"\t"18"\t"23"\t"14"\t"45"\t"56.25"\t"66.17647058823529"\t"2.515527950310559"\t"0.049235180840507584"\t"1.0"\t"0.7548757656770544"\t"22"\t"13"\t"12"\t"0.5234670639038081"\t"0.831811904907225"\n+"gene_8965"\t""\t"A gene with no relevance to tetracycline resistance"\t"2"\t"16"\t"30"\t"52"\t"6.25"\t"76.47058823529412"\t"0.21666666666666667"\t"0.049444547909927236"\t"1.0"\t"0.7548757656770544"\t"6"\t"2"\t"5"\t"0.21875000000000003"\t"0.6875000000000002"\n+"gene_3227"\t""\t"A gene with no relevance to tetracycline resistance"\t"7"\t"5"\t"25"\t"63"\t"21.875"\t"92.64705882352942"\t"3.528"\t"0.049975899747462166"\t"1.0"\t"0.7548757656770544"\t"9"\t"7"\t"5"\t"0.17968750000000003"\t"1.0"\n' |
| b |
| diff -r 000000000000 -r 42a1a5750539 test-data/scoary_output_2.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scoary_output_2.nwk Sun Mar 21 12:21:41 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +(((((('Isolate_1', 'Isolate_55'), ((('Isolate_36', 'Isolate_46'), 'Isolate_97'), 'Isolate_51')), (((((((('Isolate_10', ('Isolate_9', 'Isolate_91')), 'Isolate_31'), ('Isolate_38', ('Isolate_45', 'Isolate_5'))), 'Isolate_59'), (((('Isolate_15', 'Isolate_21'), 'Isolate_70'), 'Isolate_22'), 'Isolate_32')), (((((('Isolate_13', 'Isolate_80'), ('Isolate_50', 'Isolate_63')), 'Isolate_66'), ((('Isolate_23', 'Isolate_69'), 'Isolate_25'), 'Isolate_57')), 'Isolate_72'), ((('Isolate_19', 'Isolate_41'), 'Isolate_82'), 'Isolate_48'))), (('Isolate_52', 'Isolate_81'), ('Isolate_61', 'Isolate_79'))), (((('Isolate_12', 'Isolate_86'), 'Isolate_62'), (('Isolate_29', 'Isolate_84'), ('Isolate_64', 'Isolate_78'))), (((('Isolate_26', ('Isolate_4', 'Isolate_75')), 'Isolate_95'), (('Isolate_7', 'Isolate_74'), 'Isolate_85')), ('Isolate_68', 'Isolate_83'))))), (((('Isolate_11', 'Isolate_18'), 'Isolate_60'), ((('Isolate_14', 'Isolate_73'), (('Isolate_24', 'Isolate_6'), 'Isolate_33')), 'Isolate_54')), ('Isolate_35', 'Isolate_96'))), ((((('Isolate_16', 'Isolate_65'), 'Isolate_90'), 'Isolate_89'), (((('Isolate_17', 'Isolate_8'), 'Isolate_58'), 'Isolate_77'), (('Isolate_44', 'Isolate_100'), 'Isolate_56'))), (((((('Isolate_2', 'Isolate_88'), (('Isolate_28', 'Isolate_49'), 'Isolate_39')), ((((('Isolate_20', 'Isolate_47'), (('Isolate_3', 'Isolate_42'), 'Isolate_53')), 'Isolate_71'), ('Isolate_40', 'Isolate_67')), 'Isolate_92')), 'Isolate_87'), 'Isolate_94'), 'Isolate_99'))), (((('Isolate_27', 'Isolate_43'), ('Isolate_37', 'Isolate_76')), ('Isolate_34', 'Isolate_98')), ('Isolate_30', 'Isolate_93'))); \ No newline at end of file |
| b |
| diff -r 000000000000 -r 42a1a5750539 test-data/scoary_output_2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scoary_output_2.tsv Sun Mar 21 12:21:41 2021 +0000 |
| b |
| @@ -0,0 +1,27 @@ +==> Bogus_trait.results.csv <== +"Gene" "Non-unique Gene name" "Annotation" "Number_pos_present_in" "Number_neg_present_in" "Number_pos_not_present_in" "Number_neg_not_present_in" "Sensitivity" "Specificity" "Odds_ratio" "Naive_p" "Bonferroni_p" "Benjamini_H_p" "Max_Pairwise_comparisons" "Max_supporting_pairs" "Max_opposing_pairs" "Best_pairwise_comp_p" "Worst_pairwise_comp_p" +"gene_6942" "" "A gene with no relevance to tetracycline resistance" "18" "32" "35" "12" "33.9622641509434" "27.27272727272727" "0.19285714285714287" "0.00021060616542660472" "1.0" "1.0" "22" "5" "20" "0.00012111663818359382" "0.016900539398193356" +"gene_3729" "" "A gene with no relevance to tetracycline resistance" "14" "24" "39" "20" "26.41509433962264" "45.45454545454545" "0.29914529914529914" "0.0065460411579812364" "1.0" "1.0" "21" "5" "17" "0.0071973800659179705" "0.026603698730468753" +"gene_5224" "" "A gene with no relevance to tetracycline resistance" "26" "12" "27" "32" "49.056603773584904" "72.72727272727273" "2.567901234567901" "0.03714290661271735" "1.0" "1.0" "17" "15" "4" "0.002349853515625" "0.049041748046874986" + +==> Tetracycline_resistance.results.csv <== +"Gene" "Non-unique Gene name" "Annotation" "Number_pos_present_in" "Number_neg_present_in" "Number_pos_not_present_in" "Number_neg_not_present_in" "Sensitivity" "Specificity" "Odds_ratio" "Naive_p" "Bonferroni_p" "Benjamini_H_p" "Max_Pairwise_comparisons" "Max_supporting_pairs" "Max_opposing_pairs" "Best_pairwise_comp_p" "Worst_pairwise_comp_p" +"TetRCG" "" "A fictitious gene known to cause resistance against tetracycline" "29" "8" "3" "60" "90.625" "88.23529411764706" "72.5" "1.0862106610751666e-14" "6.45209132678649e-11" "6.45209132678649e-11" "25" "25" "1" "5.960464477539063e-08" "1.5497207641601558e-06" +"gene_6012" "" "A gene with no relevance to tetracycline resistance" "27" "33" "5" "35" "84.375" "51.470588235294116" "5.7272727272727275" "0.0008645575374418531" "1.0" "0.40703322054963476" "20" "17" "5" "0.002576828002929687" "0.04138946533203125" +"gene_8999" "" "A gene with no relevance to tetracycline resistance" "27" "33" "5" "35" "84.375" "51.470588235294116" "5.7272727272727275" "0.0008645575374418531" "1.0" "0.40703322054963476" "22" "18" "5" "0.004343509674072266" "0.016900539398193356" +"gene_5447" "" "A gene with no relevance to tetracycline resistance" "5" "33" "27" "35" "15.625" "51.470588235294116" "0.19640852974186307" "0.0018172689092071626" "1.0" "0.46422476150565434" "21" "5" "19" "0.00022125244140625" "0.026603698730468753" +"gene_7634" "" "A gene with no relevance to tetracycline resistance" "12" "48" "20" "20" "37.5" "29.411764705882355" "0.25" "0.0022133680087893675" "1.0" "0.46422476150565434" "19" "4" "18" "7.62939453125e-05" "0.019210815429687503" +"gene_6122" "" "A gene with no relevance to tetracycline resistance" "8" "39" "24" "29" "25.0" "42.64705882352941" "0.24786324786324787" "0.0028134834030645707" "1.0" "0.46422476150565434" "20" "5" "16" "0.011817932128906248" "0.04138946533203125" +"gene_8059" "" "A gene with no relevance to tetracycline resistance" "24" "29" "8" "39" "75.0" "57.35294117647059" "4.0344827586206895" "0.0028134834030645716" "1.0" "0.46422476150565434" "21" "17" "5" "0.0071973800659179705" "0.026603698730468753" +"gene_8605" "" "A gene with no relevance to tetracycline resistance" "24" "31" "8" "37" "75.0" "54.41176470588235" "3.5806451612903225" "0.009189307337123247" "1.0" "0.5783687387971439" "22" "20" "5" "0.00012111663818359382" "0.016900539398193356" +"gene_4838" "" "A gene with no relevance to tetracycline resistance" "9" "38" "23" "30" "28.125" "44.11764705882353" "0.30892448512585813" "0.010775926587020253" "1.0" "0.5872385681367001" "22" "5" "18" "0.004343509674072266" "0.016900539398193356" +"gene_4048" "" "A gene with no relevance to tetracycline resistance" "15" "50" "17" "18" "46.875" "26.47058823529412" "0.3176470588235294" "0.013224151736154797" "1.0" "0.6416380377968907" "20" "5" "16" "0.011817932128906248" "0.04138946533203125" +"gene_5164" "" "A gene with no relevance to tetracycline resistance" "6" "30" "26" "38" "18.75" "55.88235294117647" "0.2923076923076923" "0.014990405659144048" "1.0" "0.6416380377968907" "20" "5" "16" "0.011817932128906248" "0.04138946533203125" +"gene_3566" "" "A gene with no relevance to tetracycline resistance" "7" "32" "25" "36" "21.875" "52.94117647058824" "0.315" "0.017224467186043528" "1.0" "0.6416380377968907" "20" "5" "16" "0.011817932128906248" "0.04138946533203125" +"gene_7366" "" "A gene with no relevance to tetracycline resistance" "10" "39" "22" "29" "31.25" "42.64705882352941" "0.337995337995338" "0.01871864669744245" "1.0" "0.6416380377968907" "24" "6" "18" "0.02265584468841553" "0.02265584468841553" +"gene_6471" "" "A gene with no relevance to tetracycline resistance" "5" "27" "27" "41" "15.625" "60.29411764705882" "0.2812071330589849" "0.021064705280855585" "1.0" "0.7069172280693907" "14" "2" "14" "0.0001220703125" "0.012939453124999998" +"gene_4300" "" "A gene with no relevance to tetracycline resistance" "25" "37" "7" "31" "78.125" "45.588235294117645" "2.9922779922779923" "0.02775538417436529" "1.0" "0.7137686008678433" "19" "17" "4" "0.0007286071777343752" "0.019210815429687503" +"gene_8285" "" "A gene with no relevance to tetracycline resistance" "7" "31" "25" "37" "21.875" "54.41176470588235" "0.33419354838709675" "0.02775538417436529" "1.0" "0.7137686008678433" "20" "5" "17" "0.002576828002929687" "0.04138946533203125" +"gene_6253" "" "A gene with no relevance to tetracycline resistance" "24" "36" "8" "32" "75.0" "47.05882352941176" "2.6666666666666665" "0.048738926902935104" "1.0" "0.7548757656770544" "21" "17" "5" "0.0071973800659179705" "0.026603698730468753" +"gene_4147" "" "A gene with no relevance to tetracycline resistance" "8" "32" "24" "36" "25.0" "52.94117647058824" "0.375" "0.048738926902935104" "1.0" "0.7548757656770544" "20" "5" "17" "0.002576828002929687" "0.04138946533203125" +"gene_7230" "" "A gene with no relevance to tetracycline resistance" "14" "45" "18" "23" "43.75" "33.82352941176471" "0.39753086419753086" "0.049235180840507584" "1.0" "0.7548757656770544" "20" "5" "15" "0.04138946533203125" "0.04138946533203125" |