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How To Remove Nonstandard Lines In Bed File

Hi

does anybody know how to remove lines that are not in the format

chr    5759    6184    ORF5759    1    -

I have bed file that contain

chr    5759    6184    ORF5759    1    -

sirna some number

How can remove all the lines that does not follow the format so I can upload file to ucsc. Thank you so much appreciate it

bed
• 5,243 views • link
updated by Ram Ram • written by Phuong • Phuong

This is not clear. What do the badly formatted lines look like? How did you come by this badly formatted BED file? What do you mean by "sirna some number"?

• 0 views • link
written by Martin A Hansen Martin A Hansen

@phuong: could you be little descriptive in your question, it will help in answering it. SECONDLY, WHO SO EVER DOWN VOTED this question should have given a chance to phuong to ammend her question or a chance to describe it from a more clear perspective..... I am completely against of down voting questions... unless they are exact copies..

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written by Dataminer Dataminer

it appears that "sirna some number" is the bad line.

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written by brentp brentp

Questions are down-voted when unclear or not useful - as it is explained in the mouse-over tooltip. This one was unclear. I am in fact helping out.

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written by Martin A Hansen Martin A Hansen

If "sirna some number" is the problem you can remove those with grep -v "sirna".

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written by Martin A Hansen Martin A Hansen

1 answer

If all you want is to remove lines that

  1. Dont have at least 3 columns (BED must have at least Chr, start, end)
  2. have integers in the 2nd and 3rd columns.

Then you can use this python script filter_bed.py):

import sys
for toks in (line.rstrip("\r\n").split("\t") for line in open(sys.argv[1])):
    if len(toks) < 3: continue
    if not (toks[1].isdigit() and toks[2].isdigit()): continue
    print "\t".join(toks)

Called like:

$ python filter_bed.py my.bad.bed > my.good.bed

UCSC may have other requirements, I can't recall, but this should give you a start.

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written by brentp brentp

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