This seems easy, it just doesnt seem to work.
I want to:
loop through each file in a directory.
each file contains a number of lines like this ">XXXXX"
I want to extract each line that contains this,move it to a new file labelled almost identical to the old.
so basically: fam0.aln has 10000 lines containing just">XXXX", and other lines, I want Nfam0.aln to just contain the 10000 ">XXXXX" lines and no other stuff up to fam199.aln which will be moved to Nfam199.aln
I came up with this:
#!/bin/usr/env python import os import sys import glob count = 0 file_list = glob.glob(fam*.aln) for file in file_list: fileOPEN = open(file, 'r') for line in fileOPEN: handle = "Nfam" + str(count) + ".aln" test = open(handle, 'a') if line==">": test.write(line +'\n') count+=1
the problem is it doesnt move on to Nfam1.aln.....it seems to jsut put everything from fam0.aln - fam199.aln into one file, Nfam0.aln