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Biojava fails to parse Genbank and EMBL format #843
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Thank you, @innovate-invent. I've also created an issue for biojava-legacy at biojava/biojava-legacy#50 |
hi , i am new to embl format parsing |
Hi @josemduarte , |
Thanks @MaxGreil . The issue is quite well explained above. BioJava should be able to parse wrapped records as one record:
Best would be to have that in a unit test and develop a fix based on the unit test. There are more details on parse recommendations in the email pasted above:
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Biojava fails to parse
anticodon
andtransl_except
feature qualifiers when they line wrap.Biojava expects the values to be quoted, this is invalid.
This causes applications like Mauve and Colombo/SigiHMM to emit
and discard large portions of the dataset.
This line is from 15584_genome.embl from Biopython:
The matching line from 15584_genome.embl from Bioperl:
The difference between biopython and bioperl is that bioperl quotes anticodons if they wrap.
Copying NIH statement here for reference. Some messages were removed/edited for brevity.
bioperl/bioperl-live#321
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