| Previous changeset 10:6a1fbacdfaf5 (2019-05-03) Next changeset 12:ced66a3d2814 (2019-06-11) |
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Commit message:
planemo upload commit 58fe26f452c61f1682290f662666043937943b81-dirty |
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modified:
README.md maketool.sh |
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added:
rpviz.xml toolVisualizer.py |
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removed:
Selenzyme_query.ipynb out.csv out1.csv reaction2.csv selenzyme_tool.py |
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| diff -r 6a1fbacdfaf5 -r bce330b97d42 README.md --- a/README.md Fri May 03 05:18:02 2019 -0400 +++ b/README.md Tue Jun 11 04:04:24 2019 -0400 |
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| @@ -2,7 +2,7 @@ ## galaxy_selenzyme -Creating a tool within Galaxy to run Selenzyme. +Creating a tool within Galaxy to run [Selenzyme](http://selenzyme.synbiochem.co.uk). See: @@ -21,3 +21,19 @@ - [x] Install in the Galaxy container from the toolshed. - [ ] Create a tool using Galaxy XML that post JSON request and receives a JSON response (no local tool running in the Galaxy server). - [ ] Submit the purely XML tool to the [Galaxy Tool Shed](https://toolshed.g2.bx.psu.edu/). + +To learn more about Selenzyme: + +Carbonell, Pablo, et al. Selenzyme: enzyme selection tool for pathway design. *Bioinformatics* 34: 2153-2154, (2018). https://doi.org/10.1093/bioinformatics/bty065 + +## galaxy_OptBioDes + +Creating a tool within Galaxy to run OptBioDes (optimal design of experiments). + +Plan: +- [x] Create a basic command line tool using Python that submits a ``CSV`` with the design specifications sheet. +- [x] Create a Galaxy Tool XML file. +- [x] Use planemo in order to create a repository in the toolshed. +- [x] Register in the toolshed. +- [x] Install in the Galaxy container from the toolshed. +- [ ] Write documentiation about the design specifications sheet. \ No newline at end of file |
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| diff -r 6a1fbacdfaf5 -r bce330b97d42 Selenzyme_query.ipynb --- a/Selenzyme_query.ipynb Fri May 03 05:18:02 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,280 +0,0 @@\n-{\n- "cells": [\n- {\n- "cell_type": "code",\n- "execution_count": 1,\n- "metadata": {},\n- "outputs": [],\n- "source": [\n- "import json\\n",\n- "import os\\n",\n- "import sys\\n",\n- "import time\\n",\n- "import signal\\n",\n- "import datetime\\n",\n- "import logging\\n",\n- "import copy\\n",\n- "import requests"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 15,\n- "metadata": {},\n- "outputs": [],\n- "source": [\n- "smarts = \\"O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O\\"\\n",\n- "targets = 2\\n",\n- "noMSA = False"\n- ]\n- },\n- {\n- "cell_type": "markdown",\n- "metadata": {},\n- "source": [\n- "Request with smarts string"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 16,\n- "metadata": {},\n- "outputs": [],\n- "source": [\n- "all_request_data = {\'smarts\': smarts, \\"targets\\": targets, \\"noMSA\\": noMSA}\\n"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 18,\n- "metadata": {},\n- "outputs": [],\n- "source": [\n- "url = \'http://selenzyme.synbiochem.co.uk/REST\'\\n",\n- "url = \'http://localhost:5000/REST\'\\n",\n- "r = requests.post( os.path.join(url, \'Query\') , json=all_request_data )\\n",\n- "res = json.loads( r.content.decode(\'utf-8\') )\\n",\n- "assert res[\'data\'] is not None\\n",\n- "val = json.loads( res[\'data\'] )\\n",\n- "assert \'Seq. ID\' in val and len(val[\'Seq. ID\'])>0"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 19,\n- "metadata": {},\n- "outputs": [\n- {\n- "data": {\n- "text/plain": [\n- "{\'app\': \'Selenzy\',\\n",\n- " \'author\': \'Synbiochem\',\\n",\n- " \'data\': \'{\\"Score\\":{\\"1\\":163.7,\\"2\\":155.9},\\"Seq. ID\\":{\\"1\\":\\"Q68XV9\\",\\"2\\":\\"P85951\\"},\\"Description\\":{\\"1\\":\\"Aspartate aminotransferase\\",\\"2\\":\\"Aspartate aminotransferase 2 (Fragments)\\"},\\"Organism Source\\":{\\"1\\":\\"Rickettsia typhi (strain ATCC VR-144 \\\\\\\\/ Wilmington) \\",\\"2\\":\\"Pseudotsuga menziesii PE=1 SV=1\\"},\\"Tax. distance\\":{\\"1\\":15,\\"2\\":23},\\"Rxn. ID\\":{\\"1\\":\\"MNXR32641\\",\\"2\\":\\"MNXR32641\\"},\\"EC Number\\":{\\"1\\":\\"2.6.1.1\\",\\"2\\":\\"2.6.1.1\\"},\\"Uniprot protein evidence\\":{\\"1\\":3,\\"2\\":1},\\"Consv. Score\\":{\\"1\\":79.0,\\"2\\":79.0},\\"Rxn Sim.\\":{\\"1\\":1.0,\\"2\\":1.0},\\"Direction Used\\":{\\"1\\":1,\\"2\\":1},\\"Direction Preferred\\":{\\"1\\":0,\\"2\\":0},\\"% helices\\":{\\"1\\":42.6,\\"2\\":27.8},\\"% sheets\\":{\\"1\\":24.8,\\"2\\":72.2},\\"% turns\\":{\\"1\\":19.6,\\"2\\":5.6},\\"% coils\\":{\\"1\\":17.2,\\"2\\":83.3},\\"Mol. Weight\\":{\\"1\\":44337.23,\\"2\\":3587.11},\\"Isoelec. Point\\":{\\"1\\":8.3119,\\"2\\":10.4338},\\"Polar %\\":{\\"1\\":45.113,\\"2\\":41.176},\\"Query\\":{\\"1\\":\\"O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O\\",\\"2\\":\\"O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O\\"},\\"Hit\\":{\\"1\\":\\"O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O>>O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O\\",\\"2\\":\\"O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O>>O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O\\"}}\',\\n",\n- " \'version\': \'1.0\'}"\n- ]\n- },\n- "execution_count": 19,\n- "metadata": {},\n- "output_type": "execute_result"\n- }\n- ],\n- "source": [\n- "res"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 5,\n- "metadata": {},\n- "outputs": [\n- {\n- "name": "stdout",\n- "output_type": "stream",\n- "text": [\n- "{\'Score\': {\'1\': 136.7, \'2\': 125.9}, \'Seq. ID\': {\'1\': \'P39643\', \'2\': \'E9L7A5\'}, \'Description\': {\'1\': \'Probable aspartate aminotransferase\', \'2\': \'Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase\'}, \'Organism Source\': {\'1\': \'Bacillus subtilis (strain 168) \', \'2\': \'Petunia hybrida PE=1 SV=1\'}, \'Tax. distance\': {\'1\': 18, \'2\': 29}, \'Rxn. ID\': {\'1\': \'MNXR32641\', \'2\': \'MNXR32641\'}, \'EC Number\': {\'1\': \'2.6.1.1\', \'2\': \'2.6.1.1\'}, \'Uniprot protein evidence\': {\'1\': 3, \'2\': 1}, \'Consv. Score'..b'\\u001b[0m\\u001b[0mval\\u001b[0m\\u001b[0;34m[\\u001b[0m\\u001b[0;34m\'Seq. ID\'\\u001b[0m\\u001b[0;34m]\\u001b[0m\\u001b[0;34m)\\u001b[0m\\u001b[0;34m>\\u001b[0m\\u001b[0;36m0\\u001b[0m\\u001b[0;34m\\u001b[0m\\u001b[0m\\n",\n- "\\u001b[0;31mAssertionError\\u001b[0m: "\n- ]\n- }\n- ],\n- "source": [\n- "url = \'http://selenzyme.synbiochem.co.uk/REST\'\\n",\n- "r = requests.post( os.path.join(url, \'Query\') , json=all_request_data )\\n",\n- "res = json.loads( r.content.decode(\'utf-8\') )\\n",\n- "assert res[\'data\'] is not None\\n",\n- "val = json.loads( res[\'data\'] )\\n",\n- "assert \'Seq. ID\' in val and len(val[\'Seq. ID\'])>0"\n- ]\n- },\n- {\n- "cell_type": "markdown",\n- "metadata": {},\n- "source": [\n- "same reaction with its EC number"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 73,\n- "metadata": {},\n- "outputs": [],\n- "source": [\n- "all_request_data = {\\"db\\": \\"ec\\", \\"rxnid\\": \\"3.2.1.2\\", \\"targets\\": targets, \\"noMSA\\": noMSA}"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 74,\n- "metadata": {\n- "scrolled": true\n- },\n- "outputs": [],\n- "source": [\n- "url = \'http://selenzyme.synbiochem.co.uk/REST\'\\n",\n- "r = requests.post( os.path.join(url, \'Query\') , json=all_request_data )\\n",\n- "res = json.loads( r.content.decode(\'utf-8\') )\\n",\n- "assert res[\'data\'] is not None\\n",\n- "val = json.loads( res[\'data\'] )\\n",\n- "assert \'Seq. ID\' in val and len(val[\'Seq. ID\'])>0"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": 75,\n- "metadata": {},\n- "outputs": [\n- {\n- "data": {\n- "text/plain": [\n- "{\'app\': \'Selenzy\',\\n",\n- " \'author\': \'Synbiochem\',\\n",\n- " \'data\': \'{\\"Score\\":{\\"1\\":134.6,\\"2\\":121.9},\\"Seq. ID\\":{\\"1\\":\\"Q9HHC8\\",\\"2\\":\\"O23553\\"},\\"Description\\":{\\"1\\":\\"Cyclomaltodextrinase\\",\\"2\\":\\"Beta-amylase 3; chloroplastic\\"},\\"Organism Source\\":{\\"1\\":\\"Thermococcus sp. B1001 \\",\\"2\\":\\"Arabidopsis thaliana \\"},\\"Tax. distance\\":{\\"1\\":16,\\"2\\":29},\\"Rxn. ID\\":{\\"1\\":\\"MNXR87651\\",\\"2\\":\\"MNXR87683\\"},\\"EC Number\\":{\\"1\\":\\"3.2.1\\",\\"2\\":\\"3.2.1.2\\"},\\"Uniprot protein evidence\\":{\\"1\\":4,\\"2\\":1},\\"Consv. Score\\":{\\"1\\":51.0,\\"2\\":51.0},\\"Rxn Sim.\\":{\\"1\\":1.0,\\"2\\":1.0},\\"Direction Used\\":{\\"1\\":-1,\\"2\\":-1},\\"Direction Preferred\\":{\\"1\\":-1,\\"2\\":-1},\\"% helices\\":{\\"1\\":45.7,\\"2\\":33.8},\\"% sheets\\":{\\"1\\":20.7,\\"2\\":17.9},\\"% turns\\":{\\"1\\":18.5,\\"2\\":24.6},\\"% coils\\":{\\"1\\":17.7,\\"2\\":26.7},\\"Mol. Weight\\":{\\"1\\":78842.79,\\"2\\":61353.16},\\"Isoelec. Point\\":{\\"1\\":9.1162,\\"2\\":7.0599},\\"Polar %\\":{\\"1\\":45.455,\\"2\\":47.993},\\"Query\\":{\\"1\\":\\"O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O\\",\\"2\\":\\"O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O\\"},\\"Hit\\":{\\"1\\":\\"O.[*]OC1C(CO)OC(OC2C(CO)OC(OC3C(CO)OC(O)C(O)C3O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O.OCC1OC(O)C(O)C(O)C1O\\",\\"2\\":\\"O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O\\"}}\',\\n",\n- " \'version\': \'1.0\'}"\n- ]\n- },\n- "execution_count": 75,\n- "metadata": {},\n- "output_type": "execute_result"\n- }\n- ],\n- "source": [\n- "res"\n- ]\n- },\n- {\n- "cell_type": "code",\n- "execution_count": null,\n- "metadata": {},\n- "outputs": [],\n- "source": []\n- },\n- {\n- "cell_type": "code",\n- "execution_count": null,\n- "metadata": {},\n- "outputs": [],\n- "source": []\n- }\n- ],\n- "metadata": {\n- "anaconda-cloud": {},\n- "kernelspec": {\n- "display_name": "Python 3",\n- "language": "python",\n- "name": "python3"\n- },\n- "language_info": {\n- "codemirror_mode": {\n- "name": "ipython",\n- "version": 3\n- },\n- "file_extension": ".py",\n- "mimetype": "text/x-python",\n- "name": "python",\n- "nbconvert_exporter": "python",\n- "pygments_lexer": "ipython3",\n- "version": "3.6.6"\n- }\n- },\n- "nbformat": 4,\n- "nbformat_minor": 2\n-}\n' |
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| diff -r 6a1fbacdfaf5 -r bce330b97d42 maketool.sh --- a/maketool.sh Fri May 03 05:18:02 2019 -0400 +++ b/maketool.sh Tue Jun 11 04:04:24 2019 -0400 |
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| @@ -27,6 +27,20 @@ --example_input 'example.xlsx' \ --example_output 'out.csv out2.csv' \ --help_from_command 'python3 toolOptBioDes.py -h' + +# Generate tool backbone (additional params need to be entered manually +planemo tool_init --force \ + --id 'rpviz' \ + --name 'rpVisualizer' \ + --description 'Pathway visualizer' \ + --requirement libsbml \ + --requirement networkx \ + --requirement beatifulsoup4 \ + --example_command 'python $__tool_directory__/toolVisualizer.py $input1 $output1' \ + --example_input 'path.sbml' \ + --example_output 'out.html' \ + --help_from_command 'python3 toolVisualizer.py -h' + # Init shed repository planemo shed_init . --force \ |
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| diff -r 6a1fbacdfaf5 -r bce330b97d42 out.csv --- a/out.csv Fri May 03 05:18:02 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,51 +0,0 @@ -Seq. ID,Score,Organism Source,Description -Q56114,91.7,Salmonella typhi ,Aspartate aminotransferase -Q53IZ1,89.9,Pseudomonas sp. ,Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase -P44425,88.7,Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) ,Aspartate aminotransferase -Q3IED5,88.7,Pseudoalteromonas haloplanktis (strain TAC 125) ,AspC protein -Q93QX0,87.9,Comamonas testosteroni ,Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase -P52069,86.7,Methylobacterium extorquens PE=3 SV=1,Putative aspartate aminotransferase (Fragment) -O86459,85.7,Rhizobium leguminosarum bv. phaseoli ,Aspartate aminotransferase -Q54SF7,84.7,Dictyostelium discoideum ,Aspartate aminotransferase; cytoplasmic -Q55F21,84.7,Dictyostelium discoideum ,Aspartate aminotransferase; mitochondrial -Q9ZE56,84.7,Rickettsia prowazekii (strain Madrid E) ,Aspartate aminotransferase -O67781,84.7,Aquifex aeolicus (strain VF5) ,Aspartate aminotransferase -O33822,84.7,Thermus aquaticus ,Aspartate aminotransferase -Q60013,84.7,Streptomyces virginiae ,Aspartate aminotransferase -Q68XV9,84.7,Rickettsia typhi (strain ATCC VR-144 / Wilmington) ,Aspartate aminotransferase -Q1RGV0,84.7,Rickettsia bellii (strain RML369-C) ,Aspartate aminotransferase -Q56232,83.9,Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) ,Aspartate aminotransferase -P9WQ90,82.7,Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) ,Probable aspartate aminotransferase -Q9V0L2,82.7,Pyrococcus abyssi (strain GE5 / Orsay) ,Aspartate aminotransferase -Q60317,82.7,Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) ,Probable aspartate aminotransferase 1 -O93744,82.7,Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) ,Aspartate aminotransferase -P39643,81.7,Bacillus subtilis (strain 168) ,Probable aspartate aminotransferase -Q972A2,81.7,Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) ,Aspartate aminotransferase -Q4J8X2,81.7,Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) ,Aspartate aminotransferase -P53001,81.7,Bacillus subtilis (strain 168) ,Aspartate aminotransferase -O42652,78.7,Schizosaccharomyces pombe (strain 972 / ATCC 24843) ,Aspartate aminotransferase; cytoplasmic -O94320,78.7,Schizosaccharomyces pombe (strain 972 / ATCC 24843) ,Aspartate aminotransferase; mitochondrial -P23542,77.9,Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ,Aspartate aminotransferase; cytoplasmic -P85951,76.9,Pseudotsuga menziesii PE=1 SV=1,Aspartate aminotransferase 2 (Fragments) -P85906,76.9,Pseudotsuga menziesii PE=1 SV=1,Aspartate aminotransferase 1 (Fragments) -Q5F4K8,75.9,Pinus pinaster ,Aspartate aminotransferase -E9L7A5,70.9,Petunia hybrida PE=1 SV=1,Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase -P46645,70.9,Arabidopsis thaliana ,Aspartate aminotransferase; cytoplasmic isozyme 1 -Q9SIE1,70.9,Arabidopsis thaliana ,Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase -P26563,69.8,Lupinus angustifolius PE=2 SV=1,Aspartate aminotransferase P2; mitochondrial (Fragment) -P85310,68.9,Catharanthus roseus PE=1 SV=1,Aspartate aminotransferase; mitochondrial (Fragments) -Q42391,68.8,Panicum miliaceum ,Aspartate aminotransferase -P37833,68.8,Oryza sativa subsp. japonica ,Aspartate aminotransferase; cytoplasmic -Q43305,68.8,Panicum miliaceum ,Aspartate aminotransferase -P12343,64.9,Oryctolagus cuniculus ,Aspartate aminotransferase; cytoplasmic (Fragment) -P08907,64.9,Equus caballus ,Aspartate aminotransferase; mitochondrial -P00506,64.9,Sus scrofa ,Aspartate aminotransferase; mitochondrial -P12344,62.9,Bos taurus ,Aspartate aminotransferase; mitochondrial -P33097,62.9,Bos taurus ,Aspartate aminotransferase; cytoplasmic -P13221,61.9,Rattus norvegicus ,Aspartate aminotransferase; cytoplasmic -P05202,60.9,Mus musculus ,Aspartate aminotransferase; mitochondrial -P05201,60.9,Mus musculus ,Aspartate aminotransferase; cytoplasmic -P17174,60.9,Homo sapiens ,Aspartate aminotransferase; cytoplasmic -Q5R691,60.8,Pongo abelii ,Aspartate aminotransferase; cytoplasmic -A5A6K8,60.8,Pan troglodytes ,Aspartate aminotransferase; cytoplasmic -P00504,58.9,Gallus gallus ,Aspartate aminotransferase; cytoplasmic |
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| diff -r 6a1fbacdfaf5 -r bce330b97d42 out1.csv --- a/out1.csv Fri May 03 05:18:02 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,129 +0,0 @@ -promoter3,promoter5,promoter7,promoter9,gene10,promoter11,pos -1,3,2,2,1,0,0 -0,1,2,0,0,2,15 -1,0,3,3,0,1,16 -0,2,1,2,1,3,13 -1,2,2,0,1,2,7 -1,0,1,1,0,0,15 -0,1,0,1,1,2,19 -0,0,3,2,0,3,6 -1,3,3,1,0,2,7 -1,2,2,1,0,0,10 -0,3,3,0,1,3,11 -0,3,2,3,0,0,18 -1,1,0,3,1,1,6 -0,1,3,2,1,1,1 -0,3,3,0,0,0,5 -1,3,0,3,1,2,0 -1,2,3,2,0,2,11 -0,3,0,2,0,2,2 -1,1,1,2,0,3,18 -1,3,0,1,1,2,10 -1,3,0,0,0,3,4 -0,2,1,3,0,3,7 -0,2,3,1,1,1,14 -1,2,2,0,1,3,2 -0,2,1,3,0,2,6 -1,2,0,1,0,1,11 -1,2,1,3,1,2,3 -1,3,2,2,0,1,14 -0,2,2,2,0,2,17 -0,1,3,3,1,2,5 -0,3,1,1,0,1,17 -1,3,2,1,0,0,5 -1,1,1,2,1,3,8 -1,1,2,2,0,2,13 -0,1,3,1,1,2,14 -1,2,3,0,0,2,2 -0,1,2,2,0,0,17 -1,1,0,0,1,0,7 -0,0,2,1,0,2,16 -1,1,3,1,1,0,3 -0,0,0,1,1,0,19 -1,0,2,2,1,1,7 -0,2,3,0,0,3,0 -1,2,2,1,0,2,0 -0,0,1,0,0,2,3 -0,3,1,3,1,1,7 -1,3,1,0,0,2,13 -0,0,3,0,1,0,10 -1,2,3,1,0,1,9 -0,2,0,3,0,3,3 -1,3,3,3,1,3,8 -1,0,2,3,0,2,8 -0,1,3,2,0,3,0 -1,3,1,1,1,3,6 -0,2,1,2,1,0,12 -1,1,1,1,0,3,5 -0,1,2,3,0,0,9 -0,3,3,3,1,0,13 -0,3,2,2,1,3,9 -0,1,0,1,0,3,7 -1,1,1,1,1,1,0 -1,0,0,0,0,3,13 -0,2,1,0,0,1,8 -1,3,3,1,0,3,18 -0,3,0,2,0,1,3 -0,0,2,1,0,3,4 -0,2,2,0,1,1,19 -1,0,2,2,1,1,18 -0,0,0,1,1,1,13 -1,1,0,0,0,1,12 -0,0,3,3,1,2,15 -0,1,3,1,1,2,8 -0,0,2,3,1,0,11 -1,2,3,2,1,0,15 -0,2,0,2,1,0,12 -1,1,1,2,0,0,19 -1,3,3,0,0,1,9 -0,3,2,0,1,3,15 -0,0,0,0,1,2,18 -0,1,2,1,0,1,6 -1,0,1,0,1,0,9 -1,3,3,0,0,0,3 -0,0,0,2,0,0,8 -1,1,1,0,1,2,17 -0,2,2,3,0,3,1 -0,1,1,3,1,3,2 -0,2,0,1,1,2,9 -0,3,1,3,0,0,4 -0,1,3,3,0,1,13 -1,0,3,2,0,3,19 -0,1,0,0,1,3,16 -1,0,1,3,0,2,12 -1,2,0,1,1,3,1 -1,1,3,2,1,2,4 -1,3,2,3,1,1,2 -0,3,2,1,1,3,12 -1,1,0,3,0,0,1 -0,2,1,0,1,1,5 -1,2,1,1,1,0,16 -1,3,1,3,0,2,19 -0,0,1,0,1,1,0 -0,0,1,1,0,0,2 -0,0,1,0,0,3,14 -1,3,1,2,1,1,11 -1,2,0,2,1,0,4 -1,1,2,0,1,1,10 -1,2,3,0,1,0,6 -0,2,2,3,1,1,4 -1,2,0,3,0,3,10 -0,0,1,2,1,2,10 -0,2,3,3,1,0,18 -0,3,0,2,0,2,14 -0,3,0,2,1,2,16 -1,1,2,0,0,0,16 -0,3,1,1,1,0,1 -0,3,0,0,0,1,8 -0,0,3,2,0,1,1 -0,1,0,0,0,0,11 -0,1,1,3,0,1,10 -1,0,2,0,1,2,1 -1,0,3,3,1,3,17 -1,1,2,3,1,3,14 -1,0,0,2,1,3,5 -1,0,0,3,1,1,17 -1,2,0,2,0,1,15 -1,0,0,3,0,0,14 -0,0,2,1,1,3,3 -1,0,3,1,0,1,12 |
| b |
| diff -r 6a1fbacdfaf5 -r bce330b97d42 reaction2.csv --- a/reaction2.csv Fri May 03 05:18:02 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,2 +0,0 @@ -name,smarts -test2,"([#7&v3:1](=[#6&v4:2](-[#8&v2:3]-[#1&v1:4])-[#6&v4:5]1:[#6&v4:6](:[#6&v4:7](:[#6&v4:8](:[#7&+&v4:9](:[#6&v4:10]:1-[#1&v1:11])-[#6&v4:12]1(-[#8&v2:13]-[#6&v4:14](-[#6&v4:15](-[#8&v2:16]-[#15&v5:17])(-[#1&v1:18])-[#1&v1:19])(-[#6&v4:20](-[#8&v2:21]-[#1&v1:22])(-[#6&v4:23]-1(-[#8&v2:24]-[#1&v1:25])-[#1&v1:26])-[#1&v1:27])-[#1&v1:28])-[#1&v1:29])-[#1&v1:30])-[#1&v1:31])-[#1&v1:32])-[#1&v1:33])>>([#7&v3:1](=[#6&v4:2](-[#8&v2:3]-[#1&v1:4])-[#6&v4:5]1-[#6&v4:6](-[#6&v4:7](=[#6&v4:8](-[#7&+0&v3:9](-[#6&v4:10]=1-[#1&v1:11])-[#6&v4:12]1(-[#8&v2:13]-[#6&v4:14](-[#6&v4:15](-[#8&v2:16]-[#15&v5:17])(-[#1&v1:18])-[#1&v1:19])(-[#6&v4:20](-[#8&v2:21]-[#1&v1:22])(-[#6&v4:23]-1(-[#8&v2:24]-[#1&v1:25])-[#1&v1:26])-[#1&v1:27])-[#1&v1:28])-[#1&v1:29])-[#1&v1:30])-[#1&v1:31])(-[#1&v1:32])-[#1&v1])-[#1&v1:33])" \ No newline at end of file |
| b |
| diff -r 6a1fbacdfaf5 -r bce330b97d42 rpviz.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpviz.xml Tue Jun 11 04:04:24 2019 -0400 |
| [ |
| @@ -0,0 +1,28 @@ +<tool id="rpviz" name="rpVisualizer" version="0.1.0" python_template_version="3.5"> + <description>Pathway visualizer</description> + <requirements> + <requirement type="package">libsbml</requirement> + <requirement type="package">networkx</requirement> + <requirement type="package">beatifulsoup4</requirement> + <requirement type="package">rdkit</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + if [ ! -d rpviz ] + then + git clone https://github.com/pablocarb/rpviz.git $__tool_directory__/rpviz > /dev/null + else + cd $__tool_directory__/rpviz; git pull; cd .. + fi + cd $__tool_directory__ + python $__tool_directory__/toolVisualizer.py $input1 $output1 + ]]></command> + <inputs> + <param type="data" name="input1" format="sbml" /> + </inputs> + <outputs> + <data name="output1" format="html" from_work_dir="out.html" /> + </outputs> + <help><![CDATA[ + python3 toolVisualizer.py inputfile outputfile + ]]></help> +</tool> |
| b |
| diff -r 6a1fbacdfaf5 -r bce330b97d42 selenzyme_tool.py --- a/selenzyme_tool.py Fri May 03 05:18:02 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,3 +0,0 @@ -import requests -url = 'http://selenzyme.synbiochem.co.uk/REST' -r = requests.post(url, data= {'smarts': O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O |
| b |
| diff -r 6a1fbacdfaf5 -r bce330b97d42 toolVisualizer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/toolVisualizer.py Tue Jun 11 04:04:24 2019 -0400 |
| b |
| @@ -0,0 +1,31 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Mar 19 + +@author: Pablo Carbonell +@description: Pathway visualizer. + +""" +import argparse +import os +from rpviz.main import run + +def arguments(): + parser = argparse.ArgumentParser(description='toolVisualizer: Pathway visualizer. Pablo Carbonell, SYNBIOCHEM, 2019') + parser.add_argument('infile', + help='Input SBML pathway file.') + parser.add_argument('outfile', + help='Output HTML file.') + return parser + +def runVisualizer( infile, outfile ): + run(infile,outfile) + + + +if __name__ == "__main__": + parser = arguments() + arg = parser.parse_args() + assert os.path.exists(arg.infile) + runVisualizer( arg.infile, arg.outfile ) |