converting infernal -tblout output to gff

[standonn]

Dear all,

I have run cmsearch from infernal 1.1 to annotate non-coding RNAs in my genome of interest.
With the option --tblout I get a tabular output. I would like to convert this tabular output to gff. Do you know about any script able to do it?

Here are the first lines of mt output:

#target name          accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target
#-------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
nRsb347.2.0.scaf00004 -         5S_rRNA              RF00001    cm        1      119  1190769  1190887      +    no    1 0.57   0.2  100.1   7.2e-21 !   -
nRsb347.2.0.scaf00004 -         5S_rRNA              RF00001    cm        1      119  1454089  1453971      -    no    1 0.57   0.2  100.1   7.2e-21 !   -
nRsb347.2.0.scaf00009 -         5S_rRNA              RF00001    cm        1      119   343954   343836      -    no    1 0.57   0.2  100.1   7.2e-21 !   -
nRsb347.2.0.scaf00011 -         5S_rRNA              RF00001    cm        1      119   110229   110111      -    no    1 0.57   0.2  100.1   7.2e-21 !   -

I found a script (infernal_tab2gff.pl from easel) that I thought would work but my tabular output is not what it expects.

Any help would be greatly appreciated.

Best,
Sophie

[Michael.Ante]

You can use awk or perl to convert your data. Just use the gff- description (http://www.sanger.ac.uk/resources/so.../gff/spec.html) to re-arrange the columns of your table.
Something like:

awk 'NR>2{printf "%s\tinfernal\t%s\t%d\t%dADD_MORE\n" ,$1,$3,$8,$9}'  infernal_output > infernal.gff

You need to include some attributes in order to have a correct gff-file. You can, e.g include the E-value likewise to the spec's example.

[standonn]

Thank you so much! I thought it would involve much more coding.