mkrasinski
commented
9 years ago @wjurkowski : niestety nie znalazlem dobrego sposobu na interaktywne pobieranie architektury na podstwie pierwszych liczb z CATH, dlatego utworzylem w skrypcie tablice wartosci (na podstawie informacji z podanego przez Pana linka), ktorej uzywam jako zrodla danych. Ponizej wkleilem przykladowy output skryptu w jego obecnej postaci oraz ta utworzana tablice.
C:\Python27\python.exe C:/Users/sg0206054/Documents/GitHub/CodonProb/get_cath_domain.py homo_sapiens NP_055040
gene ENSG00000105568 transcript ENST00000322088 translation ENSP00000324804 Query is being processed ... Results are ready ! Retrieving results ... Superfamily : 1.25.10.10 Architecture : Alpha Horseshoe
Tablica :
architectures = (('1.10','Orthogonal Bundle'),
('1.20','Up-down Bundle'),
('1.25','Alpha Horseshoe'),
('1.40','Alpha solenoid'),
('1.50','Alpha/alpha barrel'),
('2.10','Ribbon '),
('2.100','Aligned Prism'),
('2.102','3-layer Sandwich'),
('2.105','3 Propellor'),
('2.110','4 Propellor'),
('2.115','5 Propellor'),
('2.120','6 Propellor'),
('2.130','7 Propellor'),
('2.140','8 Propellor'),
('2.150','2 Solenoid'),
('2.160','3 Solenoid'),
('2.170','Beta Complex'),
('2.20','Single Sheet'),
('2.30','Roll '),
('2.40','Beta Barrel'),
('2.50','Clam '),
('2.60','Sandwich '),
('2.70','Distorted Sandwich'),
('2.80','Trefoil '),
('2.90','Orthogonal Prism'),
('3.10','Roll '),
('3.100','Ribosomal Protein'),
('3.15','Super Roll'),
('3.20','Alpha-Beta Barrel'),
('3.30','2-Layer Sandwich'),
('3.40','3-Layer(aba) Sandwich'),
('3.50','3-Layer(bba) Sandwich'),
('3.55','3-Layer(bab) Sandwich'),
('3.60','4-Layer Sandwich'),
('3.65','Alpha-beta prism'),
('3.70','Box '),
('3.75','5-stranded Propeller'),
('3.80','Alpha-Beta Horseshoe'),
('3.90','Alpha-Beta Complex'),
('4.10','Irregular '))
wjurkowski
Pobierz architekture z dwoch pierwszych liczb kodu superfamily http://cath.biochem.ucl.ac.uk/browse/sunburst?from_cath_id=3.30