matthiaskoenig / brendapy

BRENDA parser in python
GNU Lesser General Public License v3.0
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Issues with BRENDA flat file format #5

Open matthiaskoenig opened 5 years ago

matthiaskoenig commented 5 years ago
ERROR:root:1.14.12.20_): BRENDA key not supported in line: `)`
ERROR:root:1.14.21.12_): BRENDA key not supported in line: `)`
ERROR:root:1.2.99.8_PR: could not be parsed: `#1# Sulfolobus acidocaldarius Q4J6M3 AND Q4J6M6 AND Q4J6M5`
ERROR:root:1.2.99.8_<1>: BRENDA key not supported in line: `  <1>`
ERROR:root:2.3.1.144_SY: could not be parsed: `#2# hydroxycinnamoyl/benzoyl-CoA/anthranilate`
ERROR:root:2.3.1.144_N: BRENDA key not supported in line: `N`
ERROR:root:2.7.1.69_): BRENDA key not supported in line: `)`
ERROR:root:2.8.1.6_results in more than simple additive: BRENDA key not supported in line: `results in more than simple additive`
ERROR:root:2.8.1.6_IN: could not be parsed: `#2# L-methionine (#2# product inhibition. The combination of both products in equimolar concentrations`
ERROR:root:2.8.1.6_results in more than simple: BRENDA key not supported in line: `results in more than simple`
ERROR:root:3.1.3.13_): BRENDA key not supported in line: `)`
ERROR:root:3.4.24.79_ST: could not be parsed: `#14# NCI-H1744 cell`
ERROR:root:3.4.24.79_<49>: BRENDA key not supported in line: ` <49>`
ERROR:root:4.2.1.119_SY: could not be parsed: `#4# hydratase 2`
ERROR:root:4.2.1.89_): BRENDA key not supported in line: `)`
ERROR:root:5.1.3.2_RF: could not be parsed: `<16> Gabrial, O.; Kalckar, H.M.; Darrow, R.A.: UDP-galactose-4-epimerase. ubunit enzymes: biochemistry and function`
ERROR:root:5.1.3.2_(Ebner, K. B., ed.) (1975) 2, 85-135. {Pubmed:} (c,review): BRENDA key not supported in line: `(Ebner, K. B., ed.) (1975) 2, 85-135. {Pubmed:} (c,review)`
ERROR:root:6.6.1.2_PR: could not be parsed: `#6# Pseudomonas denitrificans (nomen rejiciendum) P29933 AND P29934 AND Q9HZQ3 AND P29929`
ERROR:root:6.6.1.2_<2>: BRENDA key not supported in line: `  <2>`

edit: update v.03.0

matthiaskoenig commented 4 years ago

These are all incorrect intendations/new lines in the flat file. These must be fixed in the original file, Nothing we can do here for now.