inconsistent indentation with Python after split

Question

edit in progress will re-submit sometimes later edit in progress will re-submit sometimes later edit in progress will re-submit sometimes later

Answer 1

You can use .strip() to remove any whitespace around an item before entering it. This would allow a bit more clarity and solve any indentation issues.

For example:

b=a.split('chr').strip() # No white space either side now
c=b[1].split(':').strip() # No white space
d=c[1].split('..').strip()
e=b[0]+'\t'+c[0]+'\t'+d[0]+'\t'+d[1]+'\t'+'\n'
rfh.write(e)

What this will have done is remove any existing whitespace, and let only your \t's exist.

Answer 2

Your question is probably has been answered by others but since you are dealing with very large file, you should use generator method to input line by line.

See this question for details. Lazy Method for Reading Big File in Python?

Answer 3

Why not use a regex split ?

import re
with open(<infile>) as inf:
    for annot_info in f:
        split_array = re.split(r'(\W+)(chr\w+):(\d+)..(\d+)', annot_info)
        #do your sql processing here.
        #write out to a file if you wish to.

would give you ['', '+', 'chr6', '140302505', '140302604', '']. You can use the same in your current mysql methods.

PS: The regex pattern I've used would give you empty strings at the beginning and end. Modify the regex or change your sql insert to exclude first and last elements of array while pushing.

Answer 4

That should work:

import re #Regex may be the easiest way to split that line

with open(infile) as in_f, open(outfile,'w') as out_f:
    f = (i for i in in_f if i.rstrip()) #iterate over non empty lines
    for line in f:
        _, k = line.split('\t', 1)
        x = re.findall(r'^1..100\t([+-])chr(\d+):(\d+)\.\.(\d+).+$',k)
        if not x:
            continue
        out_f.write(' '.join(x[0]) + '\n')