[maker-devel] Problems parsing iprscan results with iprscan2gff3

[Carson Holt]

Some of your iprscan results contain truncated names

Example:
maker-NODE_5172_length_118591_cov_102.277115-snap-gene-0.100-mR

This seems to be the case for almost all HMMPanther and HMMSmart results.

Try just removing those two groups of results from your file for now.

Then use the iprscan_wrap script that comes with maker to just re-run just
those two application within iprscan it will fix the truncation issue (it
creates temporary short names and then converts back to the longer names
when it parses the results).

Thanks,
Carson

From:  Fourie Joubert <fourie.joubert at up.ac.za>
Date:  Friday, 21 September, 2012 9:58 AM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Problems parsing iprscan results with iprscan2gff3

    
 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.zahttp://www.bi.up.ac.za
Tel. +27-12-420-5825
Fax. +27-12-420-5800

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