[Bioperl-l] Tag in feature not written correctly

[Hilmar Lapp]

What's the accession of that record?

This is probably one of the weirdest things I've seen the genbank parser doing ...

Are you absolutely sure your code couldn't possibly have messed with the tags?

	-hilmar

> -----Original Message-----
> From: Michael Muratet [mailto:mam@torchconcepts.com]
> Sent: Thursday, August 22, 2002 10:38 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Tag in feature not written correctly
> 
> 
> Greetings All
> 
> I am working on an application with bioperl 1.0.1 that reads 
> in records in Genbank or EMBL format, extracts CDS data, 
> processes it, and writes out a subset of the data with new 
> features to a new file in EMBL format. Subsequent processing 
> of this new file is crashing, because the /product tag in the 
> CDS feature is not getting written correctly. Here's an example:
> 
> Starting with....
> 
>      CDS             join(97289..99104,99214..99330,99429..99604,
>                      100135..100280,100599..100617)
>                      /gene="OSJNBa0082M15.18"
>                      /codon_start=1
>                      /product="putative
>                      UDP-N-acetylmuramoylananyl-D-glutamate-2,6
>                      -diaminopimelate ligase"
>                      /protein_id="AAK43503.1"
>                      /db_xref="GI:13876527"
>                      
> /translation="MATAPLAFHLPFPFPSASRPPPRLLPPSRRPPAARLAATRRFRP
>                      
> PTADDEPPEAAEDSSHGLNRYDQLTRHVERARRRQQAEQPEITPDHPLFSSPPSSGEA
>                      
> GSYDPDDEFFDEIDRAIAEKREEFTRRGLIKPSAPAPSQPEEEDGLADELSPEEVIDL
>                      
> DEIRRLQGLSVVSLADEEDEEANGGGGGVDYGDDGVPLDDDGEVFDVADEVGLEGARV
>                      
> RYPAFRMTLAELLDESKLVPVAVTGDQDVALAGVQRDASLVAAGDLYVCVGEEGLAGL
>                      
> TEADKRGAVAVVADQTVDIEGTLACRALVIVDDITAALRMLPACLYRRPSKDMAVIGV
>                      
> AGTDGVTTTAHLVRAMYEAMGVRTGMVGVLGAYAFGNNKLDAQPDASGDPIAVQRLMA
>                      
> TMLYNGAEAALLEATTDGMPSSGVDSEIDYDIAVLTNVRHAGDEAGMTYEEYMNSMAS
>                      
> LFSRMVDPERHRKVVNIDDPSAPFFAAQGGQDVPVVTYSFENKKADVHTLKYQLSLFE
>                      
> TEVLVQTPHGILEISSGLLGRDNIYNILASVAVGVAVGAPLEDIVKGIEEVDAIPGRC
>                      
> ELIDEEQAFGVIVDHARTPESLSRLLDGVKELGPRRIVTVIGCCGERERGKRPVMTKV
>                      
> AAEKSDVVMLTSDNPANEDPLDILDDMLAGVGWTMEEYLKHGTNDYYPPLPNGHRIFL
>                      
> HDIRRVAVRAAVAMGEQGDVVVITGKGNDTYQIEVDKKEFFDDREECREALQYVDQLH
>                      RAGIDTSEFPWRLPESH"
> 
> The output looks like...
> 
> /gene="OSJNBa0082M15.18"
> roduct="putativeUDP-N-acetylmuramoylananyl-D-glutamate-2,6
> -diaminopimelate ligase"
> /proteinId="AAK43503.1"
> /ec_number="NA"
> /translation="MATAPLAFHLPFPFPSASRPPPRLLPPSRRPPAARLAATRRFRPP
> TADDEPPEAAEDSSHGLNRYDQLTRHVERARRRQQAEQPEITPDHPLFSSPPSSGEAGS
> YDPDDEFFDEIDRAIAEKREEFTRRGLIKPSAPAPSQPEEEDGLADELSPEEVIDLDEI
> RRLQGLSVVSLADEEDEEANGGGGGVDYGDDGVPLDDDGEVFDVADEVGLEGARVRYPA
> FRMTLAELLDESKLVPVAVTGDQDVALAGVQRDASLVAAGDLYVCVGEEGLAGLTEADK
> RGAVAVVADQTVDIEGTLACRALVIVDDITAALRMLPACLYRRPSKDMAVIGVAGTDGV
> TTTAHLVRAMYEAMGVRTGMVGVLGAYAFGNNKLDAQPDASGDPIAVQRLMATMLYNGA
> EAALLEATTDGMPSSGVDSEIDYDIAVLTNVRHAGDEAGMTYEEYMNSMASLFSRMVDP
> ERHRKVVNIDDPSAPFFAAQGGQDVPVVTYSFENKKADVHTLKYQLSLFETEVLVQTPH
> GILEISSGLLGRDNIYNILASVAVGVAVGAPLEDIVKGIEEVDAIPGRCELIDEEQAFG
> VIVDHARTPESLSRLLDGVKELGPRRIVTVIGCCGERERGKRPVMTKVAAEKSDVVMLT
> SDNPANEDPLDILDDMLAGVGWTMEEYLKHGTNDYYPPLPNGHRIFLHDIRRVAVRAAV
> AMGEQGDVVVITGKGNDTYQIEVDKKEFFDDREECREALQYVDQLHRAGIDTSEFPWRL
> PESH"
> 
> The read program will throw:
> 
> ------------- EXCEPTION  -------------
> MSG: Can't see new qualifier in: 
> roduct="putativeUDP-N-acetylmuramoylananyl-D-glutamate-2,6
> from:
> 
> Note that the product tag is missing "/p".
> 
> I've looked in the bioperl source, but I can't locate the 
> modules that read or write tags. If somebody could point me 
> towards those, I'll chase it. Better yet, if anyone 
> recognizes a silly error I've made, pass it along.
> 
> Thanks.
> 
> Mike
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