I just ran repseek on a +/- 100kb BAC sequence and got this output.
Distant.dir 27938 36273 1434 1433 6901 28288-36623-148-2.00 94.491 1240.45 2.00 2 1.00
Distant.dir 47964 55552 2765 2771 4823 48291-55879-127-2.00 97.367 2483.76 2.00 2 1.00
There is a script available from DAWGPAWS to convert repseek output to GFF3 format, so I did and got the following.
$ ./cnv_repseek2gff.pl < repseek.out
Expecting input from STDIN
seq repseek direct_repeat 27938 29372 1240.45 + . repseek1:dir
seq repseek direct_repeat 36273 37706 1240.45 + . repseek1:dir
seq repseek direct_repeat 47964 50729 2483.76 + . repseek2:dir
seq repseek direct_repeat 55552 58323 2483.76 + . repseek2:dir
Ok, this format is much more familiar. However, the last column (attributes) is not valid GFF3. This script creates two lines of GFF3 for each line in the repseek output. How are these pairs of features related and what is the proper way to represent that relationship in GFF3?
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written
by
Daniel Standage
2 answers
I would try coding this using a parent-child relationship, e.g.
seq repseek direct_repeat 27938 37706 . + . ID=repseek1
seq repseek repeat_unit 27938 29372 1240.45 + . ID=repseek1.1;Parent=repseek1
seq repseek repeat_unit 36273 37706 1240.45 + . ID=repseek1.2;Parent=repseek1
seq repseek direct_repeat 47964 58323 . + . ID=repseek2
seq repseek repeat_unit 47964 50729 2483.76 + . ID=repseek2.1;Parent=repseek2
seq repseek repeat_unit 55552 58323 2483.76 + . ID=repseek2.2;Parent=repseek2
It looks like the GFF3 validator is currently down (not loading the so.obo file), so I can't tell if this is "valid" GFF3. I'll send them a mail and update this post when it is back online.
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written
by
Casey Bergman
Looks like that scripts was last edited in 2007. it's probably GFF2 just substitute : for = and it may be valid.
regarding the format, this part of the code in cnv_repseek2gff.pl shows what's going on:
my $copy1_start = $rep_parts[1];
my $copy2_start = $rep_parts[2];
my $copy1_end = $copy1_start + $rep_parts[3];
my $copy2_end = $copy2_start + $rep_parts[4];
So the columns are start1, start2, len1, len2. that's how you get two gff rows per repseek row.
EDIT: in response to comment
The relationship is determined by the shared value in the attribute column
@brentp I understand attribute syntax for GFF3. My question is more focused on how to maintain the relationship between the two features.
@brentp Yes, I know the relationship is determined by the shared value in the attribute column, but (back to my original question)...how do I represent that in GFF3 format? These features need to have their own unique ID attributes, so some other attribute is required to maintain the relationship between them. Is there an attribute key (in terms of ontology) that is appropriate here?
@brentp I guess I could just give them all unique ID attributes and then give matching pairs the same Name attribute to maintain the relationship. I'm just wondering if there is a better way of doing this.
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