[maker-devel] Problems parsing iprscan results with iprscan2gff3

[Fourie Joubert]

Hi Folks

I am running into some problems parsing iprscan results.

I run iprscan as follows:

>  iprscan -cli -i bot.all.maker.proteins.fasta -o 
bot.all.maker.proteins.raw -format raw -goterms -iprlookup

and obtain the iprscan output (the iprscan output file is at  
http://www.bi.up.ac.za/~fourie/bot.all.maker.proteins.raw  if anyone is 
interested in the detailed output, and the initial maker gff3 file is at 
http://www.bi.up.ac.za/~fourie/bot.all.gff).

I then try to run the conversion to gff3, but I get very long list of 
errors:

>  iprscan2gff3 bot.all.maker.proteins.raw bot.all.gff > domains.gff

ERROR: In maker-NODE_4797_length_138874_cov_96.632576-augustus-gene-0.113
Use of uninitialized value $seqid in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 255.
Use of uninitialized value $start in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 255.
Use of uninitialized value $end in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 255.
Use of uninitialized value $strand in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 255.
Use of uninitialized value $off in subtraction (-) at 
/usr/local/maker/bin/iprscan2gff3 line 267.
Use of uninitialized value $pB in subtraction (-) at 
/usr/local/maker/bin/iprscan2gff3 line 267.
Use of uninitialized value $off in subtraction (-) at 
/usr/local/maker/bin/iprscan2gff3 line 267.
Use of uninitialized value $pE in subtraction (-) at 
/usr/local/maker/bin/iprscan2gff3 line 267.
Use of uninitialized value $seqid in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 269.
Use of uninitialized value $start in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 269.
Use of uninitialized value $end in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 269.
Use of uninitialized value $strand in concatenation (.) or string at 
/usr/local/maker/bin/iprscan2gff3 line 269.
.......
.......
.......

for most of the entries.

Any advice or help would be sincerely appreciated!

Best regards!

Fourie



-- 
--------------
Prof Fourie Joubert
Bioinformatics and Computational Biology Unit
Department of Biochemistry
University of Pretoria
fourie.joubert at up.ac.za
http://www.bi.up.ac.za
Tel. +27-12-420-5825
Fax. +27-12-420-5800

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