FW: bp_genbank2gff3- Unflattening error

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FW: bp_genbank2gff3- Unflattening error

Jayaraman, Pushkala

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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala
Sent: Thursday, October 07, 2010 2:43 PM
To: [hidden email]
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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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Re: FW: bp_genbank2gff3- Unflattening error

Scott Cain
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 <[hidden email]> 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: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> From: Jayaraman, Pushkala
> Sent: Thursday, October 07, 2010 2:43 PM
> To: [hidden email]
> 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: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
> Beautiful is writing same markup. Internet Explorer 9 supports
> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
> http://p.sf.net/sfu/beautyoftheweb
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
Gmod-devel mailing list
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Re: FW: bp_genbank2gff3- Unflattening error

Jayaraman, Pushkala
Hi Scott,
I downloaded this entry directly from GenBank.. so I wasn't sure if the error occurred in my side or was due to something else in the data. I could modify it and check..
Will keep you updated on this.. it was worrying me because the chromosome region has these huge 'holes'  in them wherein there is no gene data because of these errors in the contig. None of the genes inside the problem contig get processed..

Thanks,
Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, October 07, 2010 3:09 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [GMOD-devel] FW: bp_genbank2gff3- Unflattening error

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 <[hidden email]> 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: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> From: Jayaraman, Pushkala
> Sent: Thursday, October 07, 2010 2:43 PM
> To: [hidden email]
> 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: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>
>
> ------------------------------------------------------------------------------
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> Spend less time writing and  rewriting code and more time creating great
> experiences on the web. Be a part of the beta today.
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> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
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