Question

I got problem with using split command.
The input string is as follows:

080821_HWI-EAS301_0002_30ALBAAXX:1:8:1649:2027  83  chr10   42038185    255 36M =   42037995    -225    GCCAGGTTTAATAAATTATTTATAGAATACTGCATC    @?DDEAEFDAD@FBG@CDA?DBCDEECD@D?CBA>A    NM:i:0  MD:Z:36

I want to grab ‘2027’ from this string
my command is: line.split(':',4)[1].split()[0]
However, it doesn’t work. The output is ‘1’

Then I switch to line.split(':',4)
And output is still ‘1’, and I see the first-step split is already problematic.

However, when I try line.split(':',1), I got expected result as:

1:8:1649:2027   83  chr10   42038185    255 36M =   42037995-225    GCCAGGTTTAATAAATTATTTATAGAATACTGCATC    @?DDEAEFDAD@FBG@CDA?DBCDEECD@D?CBA>A    NM:i:0  MD:Z:36

I’m confused by this split command! (I asked the similar question before, and split command worked at that time)
thanks

Answer 1

It appears that what you want is

line.split(':',4)[4].split()[0]

The numeric parameter to split indicates the maximum number of splits that will occur. So you have:

>>> line='080821_HWI-EAS301_0002_30ALBAAXX:1:8:1649:2027 ...'
>>> line.split(':',4)
['080821_HWI-EAS301_0002_30ALBAAXX', '1', '8', '1649', '2027 ...']

If you pull element [1] out of this return value, you get ‘1’. I don’t see why you are surprised by this.

Since you are allowing up to 4 splits, and the item you want will be the last one, the subscript you want is [4]:

>>> line.split(':',4)[4]
'2027 ...'

Then you can split that on space and get element [0] from it to produce your result.

You get the same result if you don’t pass a split limit value at all:

>>> line.split(':')[4].split()[0]
'2027'