Re: [GMOD-devel] FW: bp_genbank2gff3- Unflattening error

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Hi Pushkala,

I don't really know, but I wonder if the problem is that the gene
entry is using as a label "CCL14-CCL15" but the transcript is
gene="CCL14".  The unflattener may be confused about whether that
transcript belongs to that gene.  If you change the gene= line in the
gene entry to "CCL14" does it move where the error occurs (presumably
to the next transcript)?

Scott

On Thu, Oct 7, 2010 at 3:55 PM, Jayaraman, Pushkala <pja...@mc...> wrote:
> I am providing the section of the genbank file here as I am not able to
> attach the entire genbank file here(duh!):
>
>
>
>      gene            complement(9047672..9065992)
>
>                      /gene="CCL14-CCL15"
>
>                      /note="chemokine ligand 14, chemokine ligand 15
>
>                      transcription unit"
>
>                      /db_xref="GeneID:348249"
>
>      mRNA            complement(join(9047672..9047904,9048354..9048468,
>
>                      9050587..9050720,9061737..9061876,9062296..9062407,
>
>                      9062882..9062941,9065436..9065992))
>
>                      /gene="CCL14"
>
>                      /product="chemokine (C-C motif) ligand 14 (CCL14),
>
>                      transcript variant 1"
>
>                      /exception="unclassified transcription discrepancy"
>
>                      /transcript_id="NM_004166.3"
>
>                      /db_xref="GI:34335177"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="MIM:601392"
>
>      mRNA            complement(join(9047672..9047904,9048354..9048468,
>
>                      9050587..9050720,9061737..9061876,9062296..9062407,
>
>                      9062882..9062941,9065436..9065992))
>
>                      /gene="CCL15"
>
>                      /product="chemokine (C-C motif) ligand 15 (CCL15),
>
>                      transcript variant 1"
>
>                      /exception="unclassified transcription discrepancy"
>
>                      /transcript_id="NM_032964.2"
>
>                      /db_xref="GI:34335178"
>
>                      /db_xref="GeneID:6359"
>
>                      /db_xref="MIM:601393"
>
>      mRNA            complement(join(9047672..9047904,9048354..9048468,
>
>                      9049764..9049811,9050587..9050720,9061737..9061876,
>
>                      9062296..9062407,9062882..9062941,9065436..9065992))
>
>                      /gene="CCL14"
>
>                      /product="chemokine (C-C motif) ligand 14 (CCL14),
>
>                      transcript variant 2"
>
>                      /exception="unclassified transcription discrepancy"
>
>                      /transcript_id="NM_032962.2"
>
>                      /db_xref="GI:34335175"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="HGNC:10612"
>
>                      /db_xref="MIM:601392"
>
>      mRNA            complement(join(9047672..9047904,9048354..9048468,
>
>                      9049764..9049811,9050587..9050720,9061737..9061876,
>
>                      9062296..9062407,9062882..9062941,9065436..9065992))
>
>                      /gene="CCL15"
>
>                      /product="chemokine (C-C motif) ligand 15 (CCL15),
>
>                      transcript variant 2"
>
>                      /exception="unclassified transcription discrepancy"
>
>                      /transcript_id="NM_004167.3"
>
>                      /db_xref="GI:34335181"
>
>                      /db_xref="GeneID:6359"
>
>                      /db_xref="HGNC:10613"
>
>                      /db_xref="MIM:601393"
>
>      gene            complement(9047672..9050719)
>
>                      /gene="CCL14"
>
>                      /note="chemokine (C-C motif) ligand 14; synonyms: CC-1,
>
>                      CC-3, CKb1, MCIF, NCC2, SY14, HCC-1, HCC-3, NCC-2,
> SCYL2,
>
>                      SCYA14"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="HGNC:10612"
>
>                      /db_xref="MIM:601392"
>
>      mRNA            complement(join(9047672..9047904,9048354..9048468,
>
>                      9050587..9050719))
>
>                      /gene="CCL14"
>
>                      /product="chemokine (C-C motif) ligand 14 (CCL14),
>
>                      transcript variant 3"
>
>                      /transcript_id="NM_032963.2"
>
>                      /db_xref="GI:34335176"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="HGNC:10612"
>
>                      /db_xref="MIM:601392"
>
>      STS             9047707..9047892
>
>                      /standard_name="STS-H22017"
>
>                      /db_xref="UniSTS:13833"
>
>      STS             9047767..9047885
>
>                      /standard_name="GDB:607751"
>
>                      /db_xref="UniSTS:158278"
>
>      CDS             complement(join(9047817..9047904,9048354..9048468,
>
>                      9050587..9050665))
>
>                      /gene="CCL14"
>
>                      /note="small inducible cytokine subfamily A (Cys-Cys),
>
>                      member 14; chemokine CC-1; chemokine CC-3"
>
>                      /codon_start=1
>
>                      /product="chemokine (C-C motif) ligand 14 isoform 1
>
>                      precursor"
>
>                      /protein_id="NP_116739.1"
>
>                      /db_xref="GI:14589961"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="HGNC:10612"
>
>                      /db_xref="MIM:601392"
>
>      CDS             complement(join(9047817..9047904,9048354..9048468,
>
>                      9050587..9050665))
>
>                      /gene="CCL14"
>
>                      /note="small inducible cytokine subfamily A (Cys-Cys),
>
>                      member 14; chemokine CC-1; chemokine CC-3"
>
>                      /codon_start=1
>
>                      /product="chemokine (C-C motif) ligand 14 isoform 1
>
>                      precursor"
>
>                      /protein_id="NP_004157.1"
>
>                      /db_xref="GI:4759070"
>
>                      /db_xref="CCDS:CCDS32624.1"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="HGNC:10612"
>
>                      /db_xref="MIM:601392"
>
>      CDS             complement(join(9047817..9047904,9048354..9048468,
>
>                      9049764..9049811,9050587..9050665))
>
>                      /gene="CCL14"
>
>                      /note="small inducible cytokine subfamily A (Cys-Cys),
>
>                      member 14; chemokine CC-1; chemokine CC-3"
>
>                      /codon_start=1
>
>                      /product="chemokine (C-C motif) ligand 14 isoform 2
>
>                      precursor"
>
>                      /protein_id="NP_116738.1"
>
>                      /db_xref="GI:14589959"
>
>                      /db_xref="GeneID:6358"
>
>                      /db_xref="HGNC:10612"
>
>                      /db_xref="MIM:601392"
>
>
>
>
>
>
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: pja...@mc...
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> From: Jayaraman, Pushkala
> Sent: Thursday, October 07, 2010 2:43 PM
> To: gmo...@li...
> Subject: bp_genbank2gff3- Unflattening error
>
>
>
> Hello,
>
> Running the bp_genbank2gff3.pm gives me:
>
>
>
> NT_010799 Unflattening error:
>
> Details:
>
> ------------- EXCEPTION -------------
>
> MSG: PROBLEM, SEVERITY==1
>
> Container feature does not spatially contain subfeature. Perhaps this is a
> dicistronic gene? I am expanding the parent feature
>
> SF [Bio::SeqFeature::Generic=HASH(0x149297a0)]: gene; CCL14
>
>
>
> SF [Bio::SeqFeature::Generic=HASH(0x1492d860)]: mRNA; CCL14; chemokine (C-C
> motif) ligand 14 (CCL14), transcript variant 1
>
>
>
> STACK Bio::SeqFeature::Tools::Unflattener::problem
> /usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattener.pm:952
>
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_group
> /usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattener.pm:2170
>
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_groups
> /usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattener.pm:1798
>
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq
> /usr/local/perl5.8.9/lib/site_perl/5.8.9/Bio/SeqFeature/Tools/Unflattener.pm:1503
>
> STACK (eval) /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:915
>
> STACK main::unflatten_seq /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:914
>
> STACK toplevel /usr/local/perl5.8.9/bin/bp_genbank2gff3.pl:411
>
>
>
>
>
>
>
> Ive never seen this error before and have no clue how to resolve this as the
> input is a .gbk file and the script is a BIOPerl script.  Because we seem to
> be losing a  lot of gene information in a particular contig.
>
> Am I doing anything wrong?
>
>
>
> Thanks,
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: pja...@mc...
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research