Output consolidation

[garfield39]

I ran SPALN as multiple jobs and to each job, I gave genome and a chunk of protein as an input.
After a successful run, I obtained the GFF3 files for all the individual jobs.
Is there a way of consolidating the gene predictions obtained from all these individual files into a single file while processing and filtering the output?

[ogotoh]

I don’t know how to merge existing Gff files, but spaln + sortgrcd can do an equivalent job as follows.

Run several spaln separately with –O12 option:
% spaln –Q7 –O12 –d xxx –T yyy A.faa (or A.fna)
% spaln –Q7 –O12 –d xxx –T yyy B.faa (or B.fna)
…
% spaln –Q7 –O12 –d xxx –T yyy Z.faa (or Z.fna)

Then,
% sortgrcd –O0 [other options] A.grd B.grd … Z.grd

The output is sorted on the chromosomal location of the predicted genes. Please refer to the document for more details.