[Tutor] casting string to integer in a list of lists

[Triantafyllos Gkikopoulos]

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-saf1 at 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


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