Question

what I want to do is to write a script wich get some files as input and then run some command on them! I first want to know how many files dose the user has and then ask for him/her to upload it and later I want to run some command on it.
So I had used this command: for cnt inseq 19 2 31 in a similar situation long time ago but now when I use this command I get a syntex error!
this is my comand:

readnumber= raw_input("How many pares do you have?" )
for cnt in `seq 1 1 int(readnumber)`; do
    pare$cnt-a = raw_input("filename of pare$cnt-a: ")
    pare$cnt-b = raw_input("filename of pare$cnt-b: ")
    cmd = "samtools merge   pare$cnt.bam pare$cnt-a pare$cnt-b"

And this is the error that I get:

>         for cnt in 'seq 1 1 int(readnumber)'; do
>                                             ^
>     SyntaxError: invalid syntax

so what I expext is when you put the readnumber=3 then it ask you to upload (or input) this:

pare1-a:
pare1-b:
pare2-a:
pare2-b:
pare3-a:
pare3-b:

and then run my command on it!

Answer 1

You probably want something like this:

pairs = int(raw_input("How many pairs do you have?"))
for pair_n in xrange(1, pairs + 1):
  file1 = raw_input("pair%d-a: " % pair_n)
  file2 = raw_input("pair%d-b: " % pair_n)
  cmd = "samtools merge pair%d.bam '%s' '%s'" % (pair_n, file1, file2)
  # os.system(cmd) to run the command.