Hello Trias and all, Glad to see that somebody recognized the BED genomic annotation format.
Your naive approach is probably the first thing that one could try. It is sure to work. The problem is that your code becomes unnecessarily long/cumbersome: every time I would have to use a particular element I would have to cast it first. So, an alternative idea is to modify the entire list of lists and get done with once and for all. This could be done manually with a couple of FOR loops. It would be easy and somebody already provided a solution early on (thank you!). Being a relative newcomer to python, my question was if there was an ELEGANT way to do this casting, perhaps as a list comprehension operation. I wondered if the beauty of python could reach that far. I thank you all for your comments, culpritNr1 trias wrote: > > Hi Your, > > I work with genomic datasets as well and have recently only started > working with python (so my advice is a bit naive) > > I would say although there may be different ways you can cast an integer > or float type into your list of lists you may actually no need to do so > with your starting file/list... ie: > > if for example you want to do stuff with the location chrX with start > 160944034 and end 160944035 > > you could: > for x in LoL: > startstring=LoL[1] #this would be '160944034' > startint=int(startstring) #this would be 160944034 > > now if you also use a counter you can iterate and do all sort of > calculations for different genomic locations. > > I use the csv module and then append into a numpy array that takes type > float, so you could work with that as well, > > cheers > > > Dr Triantafyllos Gkikopoulos >>>> culpritNr1 <ig2ar-s...@yahoo.co.uk> 01/08/09 8:42 PM >>> > > Hi All, > > Say I have this nice list of lists: > > LoL = [['chrX', '160944034', '160944035', 'gnfX.145.788', '63.60'], > ['chrX', '161109992', '161109993', 'rs13484104', '63.60'], > ['chrX', '161414112', '161414113', 'rs13484105', '63.60'], > ['chrX', '161544071', '161544072', 'rs13484106', '63.60'], > ['chrX', '162030736', '162030737', 'gnfX.146.867', '67.05'], > ['chrX', '164171913', '164171914', 'gnfX.148.995', '70.45']] > > Now I want to cast the second and third "columns" from string to integer, > like this > > LoL = [['chrX', 160944034, 160944035, 'gnfX.145.788', '63.60'], > ['chrX', 161109992, 161109993, 'rs13484104', '63.60'], > ['chrX', 161414112, 161414113, 'rs13484105', '63.60'], > ['chrX', 161544071, 161544072, 'rs13484106', '63.60'], > ['chrX', 162030736, 162030737, 'gnfX.146.867', '67.05'], > ['chrX', 164171913, 164171914, 'gnfX.148.995', '70.45']] > > Is there any elegant way to do this? I can't assume that all lines will > have > the same number of elements. > > Thank you, > > Your Culprit > > > -- > View this message in context: > http://www.nabble.com/casting-string-to-integer-in-a-list-of-lists-tp21359600p21359600.html > Sent from the Python - tutor mailing list archive at Nabble.com. > > _______________________________________________ > Tutor maillist - Tutor@python.org > http://mail.python.org/mailman/listinfo/tutor > > The University of Dundee is a registered Scottish charity, No: SC015096 > _______________________________________________ > Tutor maillist - Tutor@python.org > http://mail.python.org/mailman/listinfo/tutor > > -- View this message in context: http://www.nabble.com/casting-string-to-integer-in-a-list-of-lists-tp21359600p21373193.html Sent from the Python - tutor mailing list archive at Nabble.com. _______________________________________________ Tutor maillist - Tutor@python.org http://mail.python.org/mailman/listinfo/tutor
