[BioRuby] Wu-blast report parsing issue
Yannick Wurm
Yannick.Wurm at unil.ch
Tue Apr 24 19:03:56 UTC 2007
Hello,
I've generated a blast report using wu-blastall with -m7 to get xml
output.
It should be easy to get this into ruby, but I'm having a hard time.
Here's the error I get:
#~/ruby/dotGraphOfStrongHits.rb simple.xml simple.xml.dot 1.0e-5
/sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb:158:in
`clone': can't clone NilClass (TypeError)
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb:
158:in `xmlparser_parse_hit'
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb:
72:in `xmlparser_parse'
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/xmlparser.rb:
41:in `xmlparser_parse'
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/report.rb:
66:in `auto_parse'
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast/report.rb:
89:in `initialize'
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast.rb:115:in
`reports'
from /sw/lib/ruby/site_ruby/1.8/bio/appl/blast.rb:109:in
`reports'
from /Users/yannickwurm/ruby/wublastReportParser.rb:49:in
`loadBlastReport'
from /Users/yannickwurm/ruby/dotGraphOfStrongHits.rb:30:in
`parseFile'
from /Users/yannickwurm/ruby/dotGraphOfStrongHits.rb:61
The corresponding lines of wublastReportParser.rb are:
48: @file = File.open(@blast_report, IO::RDONLY)
49: @reportsArray = Bio::Blast.reports(@file)
Does wublast not respect the standard blast xml output?
I've tried feeding my script normal (-m0) wublast output too. It
doesn't crash - but @reportsArray.length == 0).
My xml-ed blast report is here:
http://wwwpeople.unil.ch/yannick.wurm/simple.xml
What am I doing wrong? Do you have ideas how to solve this issue?
My version info:
wu-blastall 2.2.6
ruby 1.8.4 (2005-12-24) [powerpc-darwin]
bio.rb,v 1.84 2007/04/05
Thanks in advance for any pointers!
yannick
--------------------------------------------
yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
http://www.unil.ch/dee/page28685_fr.html
More information about the BioRuby
mailing list