| Previous changeset 22:638dcd2d93bc (2019-06-14) Next changeset 24:8f42eba7e2eb (2019-07-05) |
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Commit message:
planemo upload commit 6f56159bc3cd5339f88517f6822240410bc9e4dd-dirty |
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modified:
reaction.csv toolSelenzyme.py |
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added:
out.csv |
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| diff -r 638dcd2d93bc -r 635b76a9bd7a out.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out.csv Fri Jul 05 06:26:22 2019 -0400 |
| [ |
| b'@@ -0,0 +1,101 @@\n+smarts,Seq. ID,Score,Organism Source,Description\r\n+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,P00509,98.9,Escherichia coli (strain K12) ,Aspartate aminotransferase\r\n+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,P58661,90.7,Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) ,Aspartate aminotransferase\r\n+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,Q53IZ1,89.9,Pseudomonas sp. ,Bifunctional aspartate aminotransferase and L-aspartate beta-decarboxylase\r\n+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,P44425,88.7,Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) ,Aspartate aminotransferase\r\n+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,Q3IED5,88.7,Pseudoalteromonas haloplanktis (strain TAC 125) ,AspC protein\r\n+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,Q06191,86.7,Rhizobium meliloti ,Aspartate aminotransferase B\r\n+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,P52069,86.7,Methylobacterium extorquens PE=3 SV=1,Putative aspartate aminotransferase (Fragment)\r\n+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,Q9X0Y2,84.9,Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) ,Aspartate aminotransferase\r\n+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,Q59228,84.7,Geobacillus stearothermophilus ,Aspartate aminotransferase\r\n+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,Q60013,84.7,Streptomyces virginiae ,Aspartate aminotransferase\r\n+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,Q1RGV0,84.7,Rickettsia bellii (strain RML369-C) ,Aspartate aminotransferase\r\n+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,Q54SF7,84.7,Dictyostelium discoideum ,Aspartate aminotransferase; cytoplasmic\r\n+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,Q55F21,84.7,Dictyostelium discoideum ,Aspartate aminotransferase; mitochondrial\r\n+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,O67781,84.7,Aquifex aeolicus (strain VF5) ,Aspartate aminotransferase\r\n+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,O33822,84.7,Thermus aquaticus ,Aspartate aminotransferase\r\n+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,Q55128,83.7,Synechocystis sp. (strain PCC 6803 / Kazusa) ,Aspartate aminotransferase\r\n+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,Q58097,82.9,Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) ,Probable aspartate aminotransferase 2\r\n+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,O58489,82.7,Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) ,Aspartate aminotransferase\r\n+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,Q60317,82.7,Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) ,Probable aspartate aminotransferase 1\r\n+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,Q58369,82.7,Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) ,Uncharacterized aminotransferase MJ0959\r\n+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,P36692,82.7,Streptomyc'..b'>>NC(CS)C(=O)O,Q9UV64,59.727,Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q4WPE6,59.627,Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A2QIK9,59.627,Aspergillus niger (strain CBS 513.88 / FGSC A1513) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A1CHL0,59.627,Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A1CX75,59.627,Neosartorya fischeri (strain ATCC 1020 / DSM 3700 / FGSC A1164 / NRRL 181) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q0CLW8,59.627,Aspergillus terreus (strain NIH 2624 / FGSC A1156) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A6SRX6,59.627,Botryotinia fuckeliana (strain B05.10) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B0Y691,59.627,Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A8X493,59.627,Caenorhabditis briggsae ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q21657,59.627,Caenorhabditis elegans ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q2HE65,58.627,Chaetomium globosum (strain ATCC 6205 / CBS 148.51 / DSM 1962 / NBRC 6347 / NRRL 1970) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A4RK48,58.627,Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q7SE17,58.627,Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q9C5X8,54.827,Arabidopsis thaliana ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q8LGM7,52.727,Solanum lycopersicum ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q655R6,52.727,Oryza sativa subsp. japonica ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,A2VD33,47.727,Danio rerio ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q16GH0,47.627,Aedes aegypti ,Molybdenum cofactor sulfurase 1\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q16P87,47.627,Aedes aegypti ,Molybdenum cofactor sulfurase 2\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q16P90,47.627,Aedes aegypti ,Molybdenum cofactor sulfurase 3\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q9N0E7,46.727,Bos taurus ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B0WSX1,46.627,Culex quinquefasciatus ,Molybdenum cofactor sulfurase 2\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B0WSW8,46.627,Culex quinquefasciatus ,Molybdenum cofactor sulfurase 1\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q7QFL7,46.627,Anopheles gambiae ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q8IU29,45.727,Bombyx mori ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q96EN8,44.827,Homo sapiens ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q9Y697,44.827,Homo sapiens ,Cysteine desulfurase; mitochondrial\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q14CH1,44.727,Mus musculus ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B4M3C9,42.627,Drosophila virilis ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q9VRA2,41.827,Drosophila melanogaster ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B4PYH5,41.627,Drosophila yakuba ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B3NY19,41.627,Drosophila erecta ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B4H0S8,41.627,Drosophila persimilis ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B4L340,40.627,Drosophila mojavensis ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,Q29GM0,40.627,Drosophila pseudoobscura pseudoobscura ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B3MZN7,40.627,Drosophila ananassae ,Molybdenum cofactor sulfurase\r\n+NC(CS)C(=O)O>>NC(CS)C(=O)O,B4JXP7,39.627,Drosophila grimshawi ,Molybdenum cofactor sulfurase\r\n' |
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| diff -r 638dcd2d93bc -r 635b76a9bd7a reaction.csv --- a/reaction.csv Fri Jun 14 12:14:23 2019 -0400 +++ b/reaction.csv Fri Jul 05 06:26:22 2019 -0400 |
| [ |
| @@ -1,3 +1,3 @@ name,smarts test,"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" -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 +test2,"NC(CS)C(=O)O>>NC(CS)C(=O)O" \ No newline at end of file |
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| diff -r 638dcd2d93bc -r 635b76a9bd7a toolSelenzyme.py --- a/toolSelenzyme.py Fri Jun 14 12:14:23 2019 -0400 +++ b/toolSelenzyme.py Fri Jul 05 06:26:22 2019 -0400 |
| [ |
| @@ -24,25 +24,31 @@ return parser # Output columns, to be improved -columns = ['Seq. ID', 'Score', 'Organism Source', 'Description'] +columns = ['smarts', 'Seq. ID', 'Score', 'Organism Source', 'Description'] if __name__ == "__main__": parser = arguments() arg = parser.parse_args() assert os.path.exists(arg.infile) - with open(arg.infile) as handler: + header = True + with open(arg.infile) as handler, open(arg.outfile, 'w' ) as writer: + cw = csv.writer( writer ) cv = csv.DictReader(handler) - row = next(cv) - url = arg.server - assert 'smarts' in row - r = requests.post( os.path.join(url, 'Query') , json={'smarts': row['smarts']} ) - res = json.loads( r.content.decode('utf-8') ) - assert res['data'] is not None - val = json.loads( res['data'] ) - assert 'Seq. ID' in val and len(val['Seq. ID'])>0 - with open(arg.outfile, 'w' ) as writer: - cw = csv.writer( writer ) - cw.writerow( columns ) - for ix in sorted(val['Seq. ID'], key=lambda z: int(z)): - cw.writerow( [val[j][ix] for j in columns] ) + for row in cv: + url = arg.server + assert 'smarts' in row + smarts = row['smarts'] + r = requests.post( os.path.join(url, 'Query') , json={'smarts': smarts} ) + res = json.loads( r.content.decode('utf-8') ) + try: + assert res['data'] is not None + val = json.loads( res['data'] ) + assert 'Seq. ID' in val and len(val['Seq. ID'])>0 + if header: + cw.writerow( columns ) + header = False + for ix in sorted(val['Seq. ID'], key=lambda z: int(z)): + cw.writerow( [smarts]+[val[j][ix] for j in columns[1:]] ) + except: + continue |