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arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Does bedtools handle the ##FASTA tag in gff files? #78

Closed ctSkennerton closed 11 years ago

ctSkennerton commented 11 years ago

I have been using the bedtools getfasta command with a gff file as the argument to -bed. The gff file contains the ##FASTA section and when I run the bedtools command I get the following message:

It looks as though you have less than 3 columns at line: 4830. Are you sure your files are tab-delimited?

Line 4830 of the gff file is inside the fasta section of the gff file

arq5x commented 11 years ago

It does not. The -bed file is only used to identify intervals that should be extracted from the -fasta file.

ctSkennerton commented 11 years ago

But does it stop parsing at the ##FASTA tag or will it keep going? and will that affect the results from my output file? I did a quick sanity check on the output files, they seem OK, I just wanted to make sure that there was no hidden side effects if bedtools does not stop

arq5x commented 11 years ago

It should just skip and continue with subsequent records.

On Aug 9, 2013, at 10:08 AM, "Connor T. Skennerton" notifications@github.com wrote:

But does it stop parsing at the ##FASTA tag or will it keep going? and will that affect the results from my output file? I did a quick sanity check on the output files, they seem OK, I just wanted to make sure that there was no hidden side effects if bedtools does not stop

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