[Tutor] Help

[Dave Angel]

she haohao wrote:
> Hi,
>
> I have some questions that I am unable to figure out. 
>
> Let say I have a file name peaks.txt.
>
> Chr1    7       9          4.5         5.5
> chr10   6       9          3.5         4.5
> chr1     10     6          2.5         4.4
>
> Question is how can i sort the file so that it looks like this:
>
>
>
> Chr1    7       9          4.5         5.5
> chr1     10     6          2.5         4.4
> chr10   6       9          3.5         4.5
>
> Next is how do I extract out the p-values(those highlighted in red)
>
> After I extracted out all the p-values. for example all the p-values from chr1 is 6,7,9,10 and for chr10 are 6 and 9.
>
> So for example if the p-value is 7 from chr1, i would open out a file called chr1.fa which look like this:
>
>   
>> chr1
>>     
> ATTGTACT
> ATTTGTAT
> ATTCGTCA
>
> and I will extract out the subsequence TACTA. Basically p-value(in this case its 7) position counting from second line of the chr1.fa file and print out the subsequence from starting from position 7-d and 7+d, where d=2. Thus if the p-values is taken from chr10 then we read from the a file with file name chr10.fa which can look like like:
>
> chr10
> TTAGTACT
> GTACTAGT
> ACGTATTT
>
> So the question is how do I do this for all the p-values.(i.e all the p-values from chr1 and all the p-values from chr10) if let say we dont know peaks.txt files have how many lines.
>
> And how do i output it to a file such that it will have the following format:
>
> Chr1
>
> peak value 6: TTGTA
>
> peak value 7: TACTA
>
> etc etc for all the p-values of chr1
>
> chr10
>
> peak value 7: TTACT
>
> etc etc etc...
>
>
> thanks for the help,
> Angeline
>
>
>   
Red has no meaning in a text message, which is what this list is
comprised of.

What does your code look like now? Where are you stuck?

str.split() can be used to divide a line up by whitespace into "words".
So if you split a line (string), you get a list. You can use use [] to
extract specific items from that list.

The first item in that list is your key, so you can then put it into a
dictionary. Don't forget that a dictionary doesn't allow dups, so when
you see the dictionary already has a match, append to it, rather than
replacing it.

DaveA