Previous changeset 2:593e0f787172 (2022-10-24) |
Commit message:
planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6 |
added:
config/job_conf.xml config/tool_conf.xml img/image3.png img/image46.png macros.xml test-data/converter_proCFPS_parameters.tsv test-data/sampler_sampling.test-1.tsv test-data/sampler_sampling.test-2.tsv |
removed:
optdoe.xml |
b |
diff -r 593e0f787172 -r 34e11d0590fa config/job_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/job_conf.xml Mon May 01 01:29:51 2023 +0000 |
b |
@@ -0,0 +1,1 @@ + <tool id="optdoe" destination="local" /> |
b |
diff -r 593e0f787172 -r 34e11d0590fa config/tool_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/config/tool_conf.xml Mon May 01 01:29:51 2023 +0000 |
b |
@@ -0,0 +1,3 @@ + <section id="sbc-gd" name="SynBioCAD Genetic Design"> + <tool file="synbiocad-galaxy-wrappers/optdoe/optdoe.xml" /> + </section> |
b |
diff -r 593e0f787172 -r 34e11d0590fa img/image3.png |
b |
Binary file img/image3.png has changed |
b |
diff -r 593e0f787172 -r 34e11d0590fa img/image46.png |
b |
Binary file img/image46.png has changed |
b |
diff -r 593e0f787172 -r 34e11d0590fa macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon May 01 01:29:51 2023 +0000 |
b |
@@ -0,0 +1,15 @@ +<macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@LICENSE@">MIT</token> + <xml name="stdio"> + <stdio> + <regex match="WARNING" level="warning" /> + <regex match="ERROR" level="fatal" /> + </stdio> + </xml> + <xml name="creator"> + <creator> + <organization name="BioRetroSynth" url="https://github.com/brsynth"/> + </creator> + </xml> +</macros> |
b |
diff -r 593e0f787172 -r 34e11d0590fa optdoe.xml --- a/optdoe.xml Mon Oct 24 10:22:28 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
[ |
b'@@ -1,262 +0,0 @@\n-<tool id="optdoe" name="Design of Experiment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">\n- <description>An optimal design of experiments (DoE) base package for synthetic biology</description>\n- <macros>\n- <token name="@VERSION_SUFFIX@">0</token>\n- <token name="@TOOL_VERSION@">2.0.2</token>\n- </macros>\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">doebase</requirement>\n- </requirements>\n- <command detect_errors="exit_code"><![CDATA[\n- python -m doebase\n- --func doeGetSBOL\n- #if $adv.genes_sbol_file\n- --sbol_file \'$adv.genes_sbol_file\'\n- #end if\n- #if $adv.ref_parts_file\n- --ref_parts_file \'$adv.ref_parts_file\'\n- #end if\n- --libsize \'$adv.libsize\'\n- $adv.get_sequences\n- $adv.backtranslate\n- --codon_table \'$adv.codon_table\'\n- \'$genes_file\'\n- \'$constructs\'\n- ]]></command>\n- <inputs>\n- <param name="genes_file" type="data" format="csv" label="Genes" help="CSV file with header: Name,Type,Part,Step. Provided by the tool Selenzyme"/>\n- <section name="adv" title="Advanced Options" expanded="false">\n- <param name="genes_sbol_file" type="data" format="xml" optional="true" label="Optimised Genes" help="SBOL file with genes associated with different RBS. Provided by the tool PartsGenie"/>\n- <param argument="--ref_parts_file" type="data" format="csv" value="None" optional="true" label="Ref Parts (default: E. coli compliant)" help="Provide fixed parts"/>\n- <param argument="--libsize" type="integer" value="32" min="32" label="Maximal library size" help="Maximal number of contructs in the output"/>\n- <param argument="--get_sequences" type="boolean" truevalue="--get_sequences true" falsevalue="--get_sequences false" checked="true" label="Get sequences" help="Grab the sequence for each part of the SBOL output"/>\n- <param argument="--backtranslate" type="boolean" truevalue="--backtranslate true" falsevalue="--backtranslate false" checked="true" label="Back translate" help="Translate the protein sequence given by its Uniprot ID to a DNA sequence"/>\n- <param argument="--codon_table" type="select" label="Codon Table">\n- <option value="Eecoli.cut">Escherichia coli K12</option>\n- <option value="Ehuman.cut">Homo sapiens</option>\n- <option value="Eacica.cut">Acinetobacter calcoaceticus</option>\n- <option value="Eagrtu.cut">Agrobacterium tumefaciens str C58</option>\n- <option value="Eanasp.cut">Anabaena sp</option>\n- <option value="Earath.cut">Arabidopsis thaliana</option>\n- <option value="Eazovi.cut">Azotobacter vinelandii</option>\n- <option value="Ebacme.cut">Bacillus megaterium</option>\n- <option value="Ebacst.cut">Geobacillus stearothermophilus</option>\n- <option value="Ebacsu.cut">Bacillus subtilis</option>\n- <option value="Ebacsu_high.cut">Bacillus subtilis (high)</option>\n- <option value="Ebommo.cut">Bombyx mori (silkmoth)</option>\n- <option value="Ebovin.cut">Bos taurus</option>\n- <option value="Ebpphx.cut">Bacteriophage phi-X174</option>\n- <option value="Ebraja.cut">Bradyrhizobium japonicum USDA 110</option>\n- <option value="Ebrana.cut">Brassica napus (rape)</option>\n- <option value="Ebrare.cut">Brachydanio rerio (zebrafish)</option>\n- <option value="Ecaeel.cut">Caenorhabditis elegans (nematode)</option>\n- <option value="Ecanal.cut">Candida albicans</option>\n- <option value="Ecanfa.cut">Canis familiaris (dog)</option>\n- <option value="Ecaucr.cut">Caulobacter crescentus CB15</option>\n- '..b'ttps://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image3.png\n-\t:width: 80 %\n-\t:align: center\n-\n-\n-.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image46.png\n-\t:width: 80 %\n-\t:align: center\n-\n-|\n-\n-Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub.\n-Note: if advanced parameter "input_parts" is left empty, the following parts are used:\n-\n-\n- +---------+------------+--------------------------------------------------+\n- | Name | Type | SynBioHub |\n- +=========+============+==================================================+\n- | PlacUV5 | Promoter | https://synbiohub.org/public/igem/BBa_K1847014/1 |\n- +---------+------------+--------------------------------------------------+\n- | Ptrc | Promoter | https://synbiohub.org/public/igem/BBa_J56012/1 |\n- +---------+------------+--------------------------------------------------+\n- | BBR1 | Origin | https://synbiohub.org/public/igem/BBa_I50041/1 |\n- +---------+------------+--------------------------------------------------+\n- | p15A | Origin | https://synbiohub.org/public/igem/BBa_I50032/1 |\n- +---------+------------+--------------------------------------------------+\n- | ColE1 | Origin | https://synbiohub.org/public/igem/BBa_J64101/1 |\n- +---------+------------+--------------------------------------------------+\n- | res1 | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1 |\n- +---------+------------+--------------------------------------------------+\n- | Ter | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1 |\n- +---------+------------+--------------------------------------------------+\n-\t \n-The source of this file can be found here as a model: https://raw.githubusercontent.com/pablocarb/doebase/master/doebase/data/ref_parts.csv\n-\n-Input\n------\n-\n-Required:\n-\n-* **Genes**\\ : Output of Selenzyme. The CSV file contains four columnds: Name,Type,Part,Step. The column "Name" contains the Uniprot ID found by Selenzyme. The column "Type" represents the type of the "Part", a *gene*. The column "Part" has the same information as the column "Name". The column "Step" contains the order of the position in the pathway of the gene.\n-\n-Advanced options:\n-\n-* **Optimised Genes**\\ : SBOL file containing optimized versions of the genes associated with different RBS. Output of the PartsGenie tool.\n-* **Ref Parts**\\ : CSV with the genetic parts. Default (if left empty) is the above table. To generate a new compatible CSV file, please use the "OptDoE Parts Reference Generator" tool\n-* **Maximal library size**\\ : (integer, default: 32) Maximal number of constructs in the SBOL output. \n-* **Get sequences**\\ : (boolean, default: True) Grab the sequence for each part of the SBOL output.\n-* **Back translate**\\ : (boolean, default: True) Translate the protein sequence given by its Uniprot ID to a DNA sequence.\n-* **Codon Table**\\ : (text, default: Eecoli.cut) Codon Usage Table. See `codon_table <https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBOSS+backtranseq+Help+and+Documentation#EMBOSSbacktranseqHelpandDocumentation-WebServices>`_ for more codons.\n-\n-Output\n-------\n-\n-* **Constructs**\\ : Output SBOL file. It contains some combinations of constructs according to the algorithm described above.\n-\n-Project Link\n-------------\n-\n-* `Original Project <https://github.com/pablocarb/doebase>`_\n-\n-License\n--------\n-\n-`MIT <https://raw.githubusercontent.com/pablocarb/appoptdes/master/LICENSE>`_\n-\n-Acknowledgments\n----------------\n-\n-* Joan H\xc3\xa9risson\n-* Thomas Duigou\n- ]]></help>\n- <creator>\n- <person givenName="Pablo" familyName="Carbonell" email="pablo.carbonell@upv.es" identifier="https://orcid.org/0000-0002-0993-5625" />\n- </creator>\n-</tool>\n\\ No newline at end of file\n' |
b |
diff -r 593e0f787172 -r 34e11d0590fa test-data/converter_proCFPS_parameters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/converter_proCFPS_parameters.tsv Mon May 01 01:29:51 2023 +0000 |
b |
@@ -0,0 +1,17 @@ +Parameter maxValue stockConcentration deadVolume Ratios +Mg-glutamate 4 168 0 0.0 0.1 0.3 0.5 1.0 +k-glutamate 80 3360 0 +CoA 0.26 210 0 +3-PGA 30 1400 0 +NTP 1.5 630 0 +NAD 0.33 138.6 0 +Folinic acid 0.068 28.56 0 +Spermidine 1 420 0 +tRNA 0.2 84 0 +Amino acids 1.5 6 0 +CAMP 0.75 200 0 +Extract 30 300 2000 1 +HEPES 50 2100 0 1 +PEG 2 200 4000 1 +Promoter 10 300 0 1 +RBS 10 200 0 1 \ No newline at end of file |
b |
diff -r 593e0f787172 -r 34e11d0590fa test-data/sampler_sampling.test-1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampler_sampling.test-1.tsv Mon May 01 01:29:51 2023 +0000 |
b |
b'@@ -0,0 +1,100 @@\n+Mg-glutamate\tk-glutamate\tCoA\t3-PGA\tNTP\tNAD\tFolinic acid\tSpermidine\ttRNA\tAmino acids\tCAMP\tExtract\tHEPES\tPEG\tPromoter\tRBS\n+2.0\t20.0\t0.26\t0.0\t1.5\t0.2475\t0.0\t0.25\t0.05\t0.375\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t80.0\t0.26\t7.5\t1.5\t0.0\t0.068\t0.5\t0.05\t1.5\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t20.0\t0.0\t15.0\t1.125\t0.0\t0.017\t0.25\t0.0\t1.125\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t20.0\t0.26\t22.5\t0.0\t0.165\t0.051000000000000004\t0.0\t0.05\t0.375\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t0.0\t0.0\t15.0\t1.5\t0.33\t0.017\t0.25\t0.2\t1.5\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.195\t0.0\t0.0\t0.165\t0.051000000000000004\t0.5\t0.05\t0.375\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t80.0\t0.0\t0.0\t0.375\t0.2475\t0.0\t0.0\t0.05\t1.125\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t20.0\t0.195\t30.0\t1.125\t0.0825\t0.034\t1.0\t0.2\t1.5\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t20.0\t0.13\t7.5\t1.5\t0.33\t0.0\t0.25\t0.15000000000000002\t0.375\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t40.0\t0.065\t0.0\t0.0\t0.165\t0.051000000000000004\t0.5\t0.1\t0.0\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t80.0\t0.195\t7.5\t1.125\t0.0825\t0.068\t0.25\t0.05\t1.5\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t40.0\t0.195\t7.5\t0.75\t0.0825\t0.051000000000000004\t1.0\t0.15000000000000002\t0.0\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t60.0\t0.13\t22.5\t1.125\t0.33\t0.068\t0.75\t0.15000000000000002\t1.125\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t80.0\t0.13\t7.5\t0.75\t0.0825\t0.034\t0.0\t0.1\t0.0\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t60.0\t0.0\t7.5\t1.5\t0.0\t0.034\t0.25\t0.05\t1.125\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.065\t7.5\t1.5\t0.2475\t0.0\t1.0\t0.0\t0.375\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t0.0\t0.26\t22.5\t0.375\t0.0\t0.051000000000000004\t0.5\t0.0\t1.5\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t60.0\t0.0\t22.5\t1.5\t0.33\t0.017\t0.5\t0.05\t0.75\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t60.0\t0.065\t30.0\t1.125\t0.2475\t0.0\t0.5\t0.15000000000000002\t0.0\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t0.0\t0.26\t15.0\t0.375\t0.33\t0.068\t1.0\t0.05\t0.375\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t60.0\t0.26\t22.5\t0.375\t0.0\t0.068\t1.0\t0.1\t1.125\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t40.0\t0.065\t7.5\t0.375\t0.0\t0.0\t0.75\t0.15000000000000002\t0.375\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.13\t0.0\t0.0\t0.0825\t0.034\t1.0\t0.2\t1.125\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t20.0\t0.195\t7.5\t1.125\t0.2475\t0.068\t0.5\t0.0\t1.125\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t40.0\t0.195\t30.0\t1.125\t0.0825\t0.034\t0.75\t0.15000000000000002\t0.375\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t40.0\t0.195\t30.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t0.0\t0.065\t0.0\t0.75\t0.0\t0.034\t0.75\t0.0\t0.75\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t20.0\t0.0\t30.0\t1.125\t0.165\t0.034\t0.0\t0.05\t1.125\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t0.0\t0.195\t0.0\t0.75\t0.2475\t0.0\t0.5\t0.1\t1.5\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t0.0\t0.0\t22.5\t0.375\t0.165\t0.068\t0.5\t0.05\t0.75\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t60.0\t0.195\t7.5\t1.125\t0.33\t0.068\t0.0\t0.2\t1.5\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t0.0\t0.065\t30.0\t1.125\t0.33\t0.017\t0.0\t0.0\t0.375\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t60.0\t0.065\t15.0\t0.0\t0.165\t0.068\t0.75\t0.2\t0.75\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.0\t22.5\t0.375\t0.0\t0.068\t0.5\t0.1\t0.75\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t40.0\t0.13\t7.5\t0.75\t0.0\t0.017\t1.0\t0.0\t0.375\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.065\t15.0\t1.5\t0.0\t0.017\t0.75\t0.2\t1.125\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t0.0\t0.0\t0.0\t1.125\t0.165\t0.034\t0.75\t0.0\t0.75\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.13\t7.5\t0.375\t0.2475\t0.034\t0.75\t0.1\t0.0\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.065\t0.0\t0.375\t0.33\t0.034\t0.25\t0.0\t0.0\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t0.0\t0.13\t30.0\t0.75\t0.0\t0.0\t0.25\t0.2\t0.0\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t40.0\t0.13\t15.0\t0.375\t0.33\t0.0\t0.25\t0.1\t0.0\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.195\t0.0\t0.75\t0.0\t0.0\t0.0\t0.15000000000000002\t0.0\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t20.0\t0.26\t30.0\t0.375\t0.165\t0.068\t0.25\t0.2\t0.375\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t80.0\t0.26\t22.5\t0.75\t0.0825\t0.068\t1.0\t0.2\t1.5\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t60.0\t0.26\t7.5\t1.5\t0.33\t0.068\t1.0\t0.15000000000000002\t0.75\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.0\t22.5\t0.75\t0.0\t0.034\t0.25\t0.0\t1.5\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.195\t22'..b'2\t40.0\t0.26\t22.5\t1.5\t0.0\t0.0\t0.25\t0.05\t0.75\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t0.0\t0.26\t15.0\t0.0\t0.165\t0.051000000000000004\t0.5\t0.2\t0.0\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t60.0\t0.26\t0.0\t0.0\t0.0825\t0.034\t0.75\t0.15000000000000002\t0.0\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t40.0\t0.065\t30.0\t0.0\t0.2475\t0.068\t0.75\t0.15000000000000002\t0.75\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t60.0\t0.13\t0.0\t0.75\t0.2475\t0.034\t0.75\t0.15000000000000002\t0.375\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t0.0\t0.195\t15.0\t1.125\t0.165\t0.017\t0.25\t0.2\t1.125\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t40.0\t0.13\t7.5\t1.5\t0.33\t0.051000000000000004\t0.0\t0.15000000000000002\t1.125\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t40.0\t0.0\t30.0\t1.125\t0.0825\t0.017\t1.0\t0.2\t0.375\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t80.0\t0.13\t30.0\t1.125\t0.33\t0.068\t0.0\t0.2\t0.75\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.065\t30.0\t1.5\t0.0825\t0.017\t0.75\t0.2\t1.5\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.195\t0.0\t0.0\t0.165\t0.034\t0.75\t0.15000000000000002\t0.75\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t40.0\t0.065\t22.5\t1.125\t0.0825\t0.051000000000000004\t1.0\t0.0\t1.125\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t80.0\t0.195\t7.5\t1.5\t0.0825\t0.034\t1.0\t0.0\t1.5\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t60.0\t0.13\t30.0\t0.0\t0.165\t0.017\t0.25\t0.0\t0.0\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t0.0\t0.26\t30.0\t1.125\t0.33\t0.051000000000000004\t0.0\t0.1\t1.125\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t20.0\t0.0\t30.0\t1.5\t0.2475\t0.034\t0.25\t0.1\t1.5\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.26\t7.5\t0.75\t0.2475\t0.034\t0.0\t0.05\t1.5\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t0.0\t0.0\t0.0\t0.75\t0.2475\t0.017\t1.0\t0.1\t1.5\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t60.0\t0.0\t7.5\t0.375\t0.0\t0.051000000000000004\t0.75\t0.1\t1.125\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t0.0\t0.195\t22.5\t0.0\t0.165\t0.068\t1.0\t0.0\t0.375\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t20.0\t0.13\t0.0\t0.75\t0.2475\t0.051000000000000004\t0.25\t0.15000000000000002\t0.75\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t40.0\t0.26\t0.0\t1.5\t0.33\t0.017\t0.5\t0.1\t1.5\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t20.0\t0.0\t30.0\t0.375\t0.0\t0.017\t0.0\t0.0\t1.5\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t40.0\t0.0\t15.0\t1.5\t0.33\t0.0\t0.75\t0.1\t0.375\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t60.0\t0.13\t0.0\t1.125\t0.0825\t0.051000000000000004\t0.0\t0.2\t0.75\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t0.0\t0.065\t22.5\t0.75\t0.2475\t0.017\t1.0\t0.05\t0.75\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t0.0\t0.065\t15.0\t0.0\t0.165\t0.068\t0.0\t0.05\t1.5\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t60.0\t0.13\t15.0\t0.75\t0.0825\t0.017\t0.5\t0.0\t0.0\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t60.0\t0.0\t30.0\t0.0\t0.0\t0.051000000000000004\t0.5\t0.15000000000000002\t1.125\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t40.0\t0.065\t15.0\t0.375\t0.2475\t0.051000000000000004\t0.75\t0.15000000000000002\t0.75\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t40.0\t0.26\t22.5\t0.375\t0.0\t0.0\t0.75\t0.05\t1.125\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t60.0\t0.13\t22.5\t0.0\t0.2475\t0.034\t0.25\t0.05\t0.0\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t80.0\t0.26\t30.0\t0.75\t0.0\t0.0\t0.0\t0.2\t0.75\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t20.0\t0.065\t15.0\t0.0\t0.33\t0.017\t0.0\t0.2\t1.125\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t80.0\t0.195\t15.0\t0.0\t0.2475\t0.017\t0.5\t0.15000000000000002\t0.375\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t80.0\t0.195\t0.0\t0.375\t0.0825\t0.017\t0.0\t0.2\t0.0\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t0.0\t0.0\t0.0\t1.5\t0.165\t0.068\t1.0\t0.2\t1.5\t0.0\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t60.0\t0.26\t22.5\t0.75\t0.33\t0.0\t0.25\t0.0\t0.75\t0.75\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t80.0\t0.0\t0.0\t0.375\t0.165\t0.017\t0.5\t0.1\t0.0\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t80.0\t0.13\t22.5\t1.5\t0.165\t0.068\t0.25\t0.1\t0.0\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t60.0\t0.065\t30.0\t1.125\t0.2475\t0.068\t1.0\t0.15000000000000002\t0.75\t0.1875\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t40.0\t0.26\t15.0\t1.125\t0.0825\t0.034\t0.0\t0.1\t0.0\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t20.0\t0.065\t22.5\t1.5\t0.165\t0.051000000000000004\t0.5\t0.0\t1.5\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t40.0\t0.26\t15.0\t0.0\t0.0825\t0.051000000000000004\t1.0\t0.15000000000000002\t0.375\t0.375\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t40.0\t0.195\t30.0\t1.5\t0.0825\t0.017\t1.0\t0.1\t1.125\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t20.0\t0.065\t15.0\t0.75\t0.0825\t0.0\t0.0\t0.1\t0.375\t0.5625\t30.0\t50.0\t2.0\t10.0\t10.0\n' |
b |
diff -r 593e0f787172 -r 34e11d0590fa test-data/sampler_sampling.test-2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sampler_sampling.test-2.tsv Mon May 01 01:29:51 2023 +0000 |
b |
b'@@ -0,0 +1,101 @@\n+Mg-glutamate\tk-glutamate\tCoA\t3-PGA\tNTP\tNAD\tFolinic acid\tSpermidine\ttRNA\tAmino acids\tCAMP\tExtract\tHEPES\tPEG\tPromoter\tRBS\n+2.0\t32.0\t0.052000000000000005\t9.0\t0.44999999999999996\t0.066\t0.013600000000000001\t0.2\t0.06\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t24.0\t0.078\t6.0\t0.30000000000000004\t0.099\t0.013600000000000001\t0.4\t0.04000000000000001\t0.6000000000000001\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t24.0\t0.052000000000000005\t12.0\t0.6000000000000001\t0.099\t0.013600000000000001\t0.4\t0.06\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t16.0\t0.10400000000000001\t6.0\t0.30000000000000004\t0.066\t0.027200000000000002\t0.2\t0.08000000000000002\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t16.0\t0.052000000000000005\t6.0\t0.44999999999999996\t0.099\t0.0204\t0.3\t0.04000000000000001\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t16.0\t0.052000000000000005\t12.0\t0.30000000000000004\t0.099\t0.013600000000000001\t0.4\t0.06\t0.6000000000000001\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t24.0\t0.078\t6.0\t0.30000000000000004\t0.066\t0.013600000000000001\t0.4\t0.06\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t24.0\t0.078\t12.0\t0.30000000000000004\t0.066\t0.0204\t0.3\t0.08000000000000002\t0.44999999999999996\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t32.0\t0.10400000000000001\t9.0\t0.30000000000000004\t0.066\t0.013600000000000001\t0.2\t0.04000000000000001\t0.44999999999999996\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t16.0\t0.052000000000000005\t12.0\t0.6000000000000001\t0.132\t0.0204\t0.2\t0.04000000000000001\t0.30000000000000004\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t24.0\t0.052000000000000005\t9.0\t0.44999999999999996\t0.132\t0.0204\t0.4\t0.08000000000000002\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t16.0\t0.078\t6.0\t0.30000000000000004\t0.132\t0.0204\t0.4\t0.04000000000000001\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t24.0\t0.078\t9.0\t0.44999999999999996\t0.099\t0.0204\t0.4\t0.08000000000000002\t0.44999999999999996\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t24.0\t0.10400000000000001\t6.0\t0.6000000000000001\t0.066\t0.013600000000000001\t0.3\t0.08000000000000002\t0.44999999999999996\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t32.0\t0.078\t12.0\t0.6000000000000001\t0.099\t0.027200000000000002\t0.4\t0.04000000000000001\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t32.0\t0.078\t6.0\t0.6000000000000001\t0.099\t0.027200000000000002\t0.4\t0.08000000000000002\t0.6000000000000001\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t24.0\t0.078\t9.0\t0.6000000000000001\t0.066\t0.013600000000000001\t0.3\t0.06\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t32.0\t0.10400000000000001\t12.0\t0.6000000000000001\t0.066\t0.0204\t0.2\t0.06\t0.6000000000000001\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t32.0\t0.078\t9.0\t0.6000000000000001\t0.099\t0.0204\t0.2\t0.04000000000000001\t0.44999999999999996\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t24.0\t0.052000000000000005\t6.0\t0.44999999999999996\t0.099\t0.0204\t0.3\t0.04000000000000001\t0.6000000000000001\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t16.0\t0.052000000000000005\t9.0\t0.6000000000000001\t0.099\t0.0204\t0.2\t0.08000000000000002\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t24.0\t0.052000000000000005\t12.0\t0.6000000000000001\t0.099\t0.027200000000000002\t0.4\t0.06\t0.6000000000000001\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t32.0\t0.10400000000000001\t6.0\t0.44999999999999996\t0.066\t0.013600000000000001\t0.2\t0.06\t0.30000000000000004\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t32.0\t0.052000000000000005\t12.0\t0.6000000000000001\t0.099\t0.027200000000000002\t0.4\t0.06\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t16.0\t0.10400000000000001\t12.0\t0.30000000000000004\t0.066\t0.0204\t0.4\t0.06\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t24.0\t0.052000000000000005\t6.0\t0.6000000000000001\t0.132\t0.0'..b'000000001\t0.132\t0.027200000000000002\t0.2\t0.06\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t24.0\t0.10400000000000001\t12.0\t0.30000000000000004\t0.132\t0.0204\t0.3\t0.06\t0.6000000000000001\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t32.0\t0.10400000000000001\t12.0\t0.30000000000000004\t0.132\t0.0204\t0.2\t0.04000000000000001\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t24.0\t0.078\t12.0\t0.30000000000000004\t0.099\t0.013600000000000001\t0.3\t0.04000000000000001\t0.30000000000000004\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t16.0\t0.078\t6.0\t0.6000000000000001\t0.099\t0.013600000000000001\t0.4\t0.06\t0.6000000000000001\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t24.0\t0.052000000000000005\t12.0\t0.30000000000000004\t0.099\t0.0204\t0.3\t0.04000000000000001\t0.6000000000000001\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t16.0\t0.078\t9.0\t0.6000000000000001\t0.099\t0.0204\t0.4\t0.04000000000000001\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t32.0\t0.078\t12.0\t0.30000000000000004\t0.132\t0.027200000000000002\t0.3\t0.06\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t24.0\t0.078\t9.0\t0.30000000000000004\t0.066\t0.027200000000000002\t0.4\t0.06\t0.30000000000000004\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t16.0\t0.10400000000000001\t6.0\t0.44999999999999996\t0.132\t0.0204\t0.4\t0.08000000000000002\t0.30000000000000004\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t24.0\t0.10400000000000001\t12.0\t0.30000000000000004\t0.132\t0.027200000000000002\t0.2\t0.06\t0.6000000000000001\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t32.0\t0.052000000000000005\t12.0\t0.30000000000000004\t0.066\t0.0204\t0.3\t0.04000000000000001\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t16.0\t0.078\t6.0\t0.44999999999999996\t0.132\t0.013600000000000001\t0.4\t0.08000000000000002\t0.44999999999999996\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t16.0\t0.10400000000000001\t12.0\t0.44999999999999996\t0.066\t0.027200000000000002\t0.3\t0.08000000000000002\t0.6000000000000001\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t16.0\t0.052000000000000005\t6.0\t0.30000000000000004\t0.132\t0.013600000000000001\t0.2\t0.04000000000000001\t0.44999999999999996\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t16.0\t0.10400000000000001\t9.0\t0.44999999999999996\t0.099\t0.027200000000000002\t0.2\t0.04000000000000001\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t16.0\t0.10400000000000001\t12.0\t0.30000000000000004\t0.132\t0.027200000000000002\t0.2\t0.08000000000000002\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+4.0\t32.0\t0.052000000000000005\t12.0\t0.44999999999999996\t0.066\t0.0204\t0.4\t0.08000000000000002\t0.6000000000000001\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t32.0\t0.052000000000000005\t9.0\t0.44999999999999996\t0.099\t0.027200000000000002\t0.3\t0.08000000000000002\t0.44999999999999996\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t32.0\t0.078\t6.0\t0.44999999999999996\t0.132\t0.0204\t0.3\t0.06\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+1.2\t32.0\t0.052000000000000005\t9.0\t0.30000000000000004\t0.099\t0.027200000000000002\t0.3\t0.08000000000000002\t0.44999999999999996\t0.30000000000000004\t30.0\t50.0\t2.0\t10.0\t10.0\n+2.0\t32.0\t0.078\t9.0\t0.44999999999999996\t0.099\t0.027200000000000002\t0.3\t0.04000000000000001\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.4\t32.0\t0.10400000000000001\t12.0\t0.30000000000000004\t0.066\t0.0204\t0.2\t0.06\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t24.0\t0.10400000000000001\t6.0\t0.6000000000000001\t0.099\t0.013600000000000001\t0.2\t0.04000000000000001\t0.30000000000000004\t0.22499999999999998\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t16.0\t0.10400000000000001\t9.0\t0.44999999999999996\t0.066\t0.027200000000000002\t0.2\t0.08000000000000002\t0.30000000000000004\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n+0.0\t16.0\t0.10400000000000001\t12.0\t0.6000000000000001\t0.099\t0.027200000000000002\t0.3\t0.04000000000000001\t0.6000000000000001\t0.15000000000000002\t30.0\t50.0\t2.0\t10.0\t10.0\n' |