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 _______________________________________________ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: http://mail.python.org/mailman/listinfo/tutor