collapsing GFF coordinates with common start OR stop

Question

[Anand Rao]

I have inherited some GFF files where identified features often have common start or stop coordinates. I need to collapse such occurrences to the longest instance. As examples, I have provided an example problem and the solution below. Are there readily available tools that can do this? OR someone's Perl / Python / Bioconductor scripting? Thanks!

PROBLEM

case 1 - plus strand, common start coord

chr1 fBS CDS 1000 2000 + . PfamID1

chr1 fBS CDS 1000 3000 + . PfamID1

chr1 fBS CDS 1000 4000 + . PfamID1

chr1 fBS CDS 1000 5000 + . PfamID1

normal

chr2 fBS CDS 9000 10000 + . PfamID1

case 2 - minus strand, common end coord

chr4 fBS CDS 5000 1000 - . PfamID1

chr4 fBS CDS 4000 1000 - . PfamID1

chr4 fBS CDS 3000 1000 - . PfamID1

normal

chr9 fBS CDS 6431 15000 + . PfamID1

case 3 - plus strand, common end coord

chr10 fBS CDS 1000 5000 + . PfamID2

chr10 fBS CDS 2000 5000 + . PfamID2

chr10 fBS CDS 3000 5000 + . PfamID2

chr10 fBS CDS 4000 5000 + . PfamID2

case 4 - minus strand, common start coord

chr12 fBS CDS 5000 4000 - . PfamID2

chr12 fBS CDS 5000 3000 - . PfamID2

chr12 fBS CDS 5000 2000 - . PfamID2

SOLUTION - should contain only 6 lines after collapsing each of cases 1, 2, 3 and 4 into one line each

chr1 fBS CDS 1000 5000 + . PfamID1

chr2 fBS CDS 9000 10000 + . PfamID1

chr4 fBS CDS 5000 1000 - . PfamID1

chr9 fBS CDS 6431 15000 + . PfamID1

chr10 fBS CDS 1000 5000 + . PfamID2

chr12 fBS CDS 5000 2000 - . PfamID2

[h.mon]

chr4 fBS CDS 5000 1000 - . PfamID1

chr4 fBS CDS 4000 1000 - . PfamID1

chr4 fBS CDS 3000 1000 - . PfamID1

If I am not mistaken, for GFF "start" coordinate has always to be equal or smaller then "end" coordinate, so the above is not valid GFF.

Answer 1

[h.mon]

First ensure your GFF is compliant with the specifications (see my comment above), then you can use bedtools merge.