Details
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Type: Bug
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Status: Open
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Priority: Critical
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Resolution: Unresolved
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Affects Version/s: 2.9, 2.9.0b1, 2.9.0b2
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Fix Version/s: None
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Component/s: file format issue
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Labels:None
Description
I picked an arbitrary page from PANDIT to try and load an alignment from:
http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=PF00903&field=nam-dsq
Copying and pasting the alignment data directly into Jalview or importing via a text file lead to an 'unsupported format' message, however checking with the Identify.main routine and stepping through with a debugger the PFAM parser extracts valid sequence data.
It looks like the 'hasValidSequence()' method is too strict to allow the data from this page to be imported.
-- Correction
After trying a simple test datafile - it seems all PFAM files imported get rejected by the hasValidSequence() test
http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=browse&fam=PF00903&field=nam-dsq
Copying and pasting the alignment data directly into Jalview or importing via a text file lead to an 'unsupported format' message, however checking with the Identify.main routine and stepping through with a debugger the PFAM parser extracts valid sequence data.
It looks like the 'hasValidSequence()' method is too strict to allow the data from this page to be imported.
-- Correction
After trying a simple test datafile - it seems all PFAM files imported get rejected by the hasValidSequence() test
Attachments
Issue Links
- related with
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JAL-2175 Pfam roundtrip adds spaces to sequence
- Closed