[Gmod-gbrowse] Problem displaying multi-segmented features from CHADO in GBROWSE

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[Gmod-gbrowse] Problem displaying multi-segmented features from CHADO in GBROWSE

lpritc@scri.ac.uk
Hi,

I'm not getting consistent results from GBROWSE using the same data with the
different backends, and I'm wondering if this is because of my settings, or
maybe something to do with the CHADO adaptor.

I have a number of multi-segmented features, defined as in this example:

##gff-version 3
supercont1.1    PI_T30-4_FINAL_CALLGENES_3    supercontig    1    6928287
.    .    .    ID=supercont1.1;Name=supercont1.1;Note=seq:7000000037415152
supercont1.1 of Phytophthora
infestans;Alias=seq:7000000037415152,supercont1.1,supercontig1.1
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    gene    39526    41494
.    +    .    ID=7000003035144175;Note=protein%20kinase%2C%20putative;Name
=PITG_00004
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    mRNA    39526    41494
.    +    .    ID=7000003035144176;Parent=7000003035144175;Name=PITG_00004T
0;Alias=PITT_00004
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    39526    40416
.    +    .    ID=7000003035144176.exon1;Parent=7000003035144176
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    39526    40416
.    +    .    ID=7000003035144176.cds1;Parent=7000003035144176
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    40486    40771
.    +    .    ID=7000003035144176.exon2;Parent=7000003035144176
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    40486    40771
.    +    .    ID=7000003035144176.cds2;Parent=7000003035144176
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    40827    41494
.    +    .    ID=7000003035144176.exon3;Parent=7000003035144176
supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    40827    41494
.    +    .    ID=7000003035144176.cds3;Parent=7000003035144176
supercont1.1    PFam    protein_match    40699    41485    9.00e-41    .
.    
ID=PITG_00004.pfam1;Name=Protein%20kinase%20domain;Dbxref=Pfam:PF00069.17;de
scription=PITG_00004
PF00069.17;Note=PITG_00004%20Domain%20PF00069.17%2C%20Protein%20kinase%20dom
ain%2C%20length%3D787%2C%20bit%20score%3D146.36%2C%20E%3D9.000e-41
supercont1.1    PFam    protein_match    40699    41485    1.10e-24    .
.    
ID=PITG_00004.pfam2;Name=Protein%20tyrosine%20kinase;Dbxref=Pfam:PF07714.9;d
escription=PITG_00004
PF07714.9;Note=PITG_00004%20Domain%20PF07714.9%2C%20Protein%20tyrosine%20kin
ase%2C%20length%3D787%2C%20bit%20score%3D92.95%2C%20E%3D1.100e-24

When I display this example (and the other features) using the in-memory,
BDDB or MySQL adaptors, they are represented in GBROWSE such that the gene
and mRNA features are in three linked segments (see attached pi_gff3.png).
Using the CHADO adaptor, the gene and mRNA features are each shown as a
single feature (see attached pi_chado.png).  Is there a way to change this
in the .conf file, or in how I'm uploading to CHADO, or is there a
difference in how the CHADO adaptor represents these features to GBROWSE
internally?  I'm assuming that the CHADO upload was correct, because ARTEMIS
functions normally on the same data.

The CHADO upload command was:

gmod_bulk_load_gff3.pl --gfffile test.gff3 --organism "P.infestans T30-4
release 5" --dbname oomycete_reference --dbuser ****** --dbpass ******
--noexon

And the CHADO adaptor is declared with this in the .conf file

[GENERAL]
description   = infestans test
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=oomycete_reference
                -user ******
                -pass ******
                -organism "P.infestans T30-4 release 5"
                -version 1

Using -srcfeatureslice 1 or recursivMapping 1 doesn't seem to help.  Is
there anything else I can try?

Cheers,

L.


--
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405



______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee.
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


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Re: [Gmod-gbrowse] Problem displaying multi-segmented features from CHADO in GBROWSE

Scott Cain
Hi Leighton,

Darn it, that was one of the main things the 0.25 release of the Chado
adaptor was supposed to fix.  I assume that you have the 0.26 adaptor,
right?  I'll see if I can reproduce this and fix it today.

Scott


On Mon, May 17, 2010 at 4:41 AM, Leighton Pritchard <[hidden email]> wrote:

> Hi,
>
> I'm not getting consistent results from GBROWSE using the same data with the
> different backends, and I'm wondering if this is because of my settings, or
> maybe something to do with the CHADO adaptor.
>
> I have a number of multi-segmented features, defined as in this example:
>
> ##gff-version 3
> supercont1.1    PI_T30-4_FINAL_CALLGENES_3    supercontig    1    6928287
> .    .    .    ID=supercont1.1;Name=supercont1.1;Note=seq:7000000037415152
> supercont1.1 of Phytophthora
> infestans;Alias=seq:7000000037415152,supercont1.1,supercontig1.1
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    gene    39526    41494
> .    +    .    ID=7000003035144175;Note=protein%20kinase%2C%20putative;Name
> =PITG_00004
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    mRNA    39526    41494
> .    +    .    ID=7000003035144176;Parent=7000003035144175;Name=PITG_00004T
> 0;Alias=PITT_00004
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    39526    40416
> .    +    .    ID=7000003035144176.exon1;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    39526    40416
> .    +    .    ID=7000003035144176.cds1;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    40486    40771
> .    +    .    ID=7000003035144176.exon2;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    40486    40771
> .    +    .    ID=7000003035144176.cds2;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    40827    41494
> .    +    .    ID=7000003035144176.exon3;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    40827    41494
> .    +    .    ID=7000003035144176.cds3;Parent=7000003035144176
> supercont1.1    PFam    protein_match    40699    41485    9.00e-41    .
> .
> ID=PITG_00004.pfam1;Name=Protein%20kinase%20domain;Dbxref=Pfam:PF00069.17;de
> scription=PITG_00004
> PF00069.17;Note=PITG_00004%20Domain%20PF00069.17%2C%20Protein%20kinase%20dom
> ain%2C%20length%3D787%2C%20bit%20score%3D146.36%2C%20E%3D9.000e-41
> supercont1.1    PFam    protein_match    40699    41485    1.10e-24    .
> .
> ID=PITG_00004.pfam2;Name=Protein%20tyrosine%20kinase;Dbxref=Pfam:PF07714.9;d
> escription=PITG_00004
> PF07714.9;Note=PITG_00004%20Domain%20PF07714.9%2C%20Protein%20tyrosine%20kin
> ase%2C%20length%3D787%2C%20bit%20score%3D92.95%2C%20E%3D1.100e-24
>
> When I display this example (and the other features) using the in-memory,
> BDDB or MySQL adaptors, they are represented in GBROWSE such that the gene
> and mRNA features are in three linked segments (see attached pi_gff3.png).
> Using the CHADO adaptor, the gene and mRNA features are each shown as a
> single feature (see attached pi_chado.png).  Is there a way to change this
> in the .conf file, or in how I'm uploading to CHADO, or is there a
> difference in how the CHADO adaptor represents these features to GBROWSE
> internally?  I'm assuming that the CHADO upload was correct, because ARTEMIS
> functions normally on the same data.
>
> The CHADO upload command was:
>
> gmod_bulk_load_gff3.pl --gfffile test.gff3 --organism "P.infestans T30-4
> release 5" --dbname oomycete_reference --dbuser ****** --dbpass ******
> --noexon
>
> And the CHADO adaptor is declared with this in the .conf file
>
> [GENERAL]
> description   = infestans test
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -dsn dbi:Pg:dbname=oomycete_reference
>                -user ******
>                -pass ******
>                -organism "P.infestans T30-4 release 5"
>                -version 1
>
> Using -srcfeatureslice 1 or recursivMapping 1 doesn't seem to help.  Is
> there anything else I can try?
>
> Cheers,
>
> L.
>
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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

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Re: [Gmod-gbrowse] Problem displaying multi-segmented features from CHADO in GBROWSE

Scott Cain
In reply to this post by lpritc@scri.ac.uk
Hi Leighton,

Things you might need:

1. In the database section, you probably need to add "-inferCDS 1" to
the db_args.

2. In the track definition, you may need to add "ignore_sub_part = polypeptide".

Scott


On Mon, May 17, 2010 at 4:41 AM, Leighton Pritchard <[hidden email]> wrote:

> Hi,
>
> I'm not getting consistent results from GBROWSE using the same data with the
> different backends, and I'm wondering if this is because of my settings, or
> maybe something to do with the CHADO adaptor.
>
> I have a number of multi-segmented features, defined as in this example:
>
> ##gff-version 3
> supercont1.1    PI_T30-4_FINAL_CALLGENES_3    supercontig    1    6928287
> .    .    .    ID=supercont1.1;Name=supercont1.1;Note=seq:7000000037415152
> supercont1.1 of Phytophthora
> infestans;Alias=seq:7000000037415152,supercont1.1,supercontig1.1
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    gene    39526    41494
> .    +    .    ID=7000003035144175;Note=protein%20kinase%2C%20putative;Name
> =PITG_00004
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    mRNA    39526    41494
> .    +    .    ID=7000003035144176;Parent=7000003035144175;Name=PITG_00004T
> 0;Alias=PITT_00004
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    39526    40416
> .    +    .    ID=7000003035144176.exon1;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    39526    40416
> .    +    .    ID=7000003035144176.cds1;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    40486    40771
> .    +    .    ID=7000003035144176.exon2;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    40486    40771
> .    +    .    ID=7000003035144176.cds2;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    exon    40827    41494
> .    +    .    ID=7000003035144176.exon3;Parent=7000003035144176
> supercont1.1    PI_T3-4_FINAL_CALLGENES_3.coords    CDS    40827    41494
> .    +    .    ID=7000003035144176.cds3;Parent=7000003035144176
> supercont1.1    PFam    protein_match    40699    41485    9.00e-41    .
> .
> ID=PITG_00004.pfam1;Name=Protein%20kinase%20domain;Dbxref=Pfam:PF00069.17;de
> scription=PITG_00004
> PF00069.17;Note=PITG_00004%20Domain%20PF00069.17%2C%20Protein%20kinase%20dom
> ain%2C%20length%3D787%2C%20bit%20score%3D146.36%2C%20E%3D9.000e-41
> supercont1.1    PFam    protein_match    40699    41485    1.10e-24    .
> .
> ID=PITG_00004.pfam2;Name=Protein%20tyrosine%20kinase;Dbxref=Pfam:PF07714.9;d
> escription=PITG_00004
> PF07714.9;Note=PITG_00004%20Domain%20PF07714.9%2C%20Protein%20tyrosine%20kin
> ase%2C%20length%3D787%2C%20bit%20score%3D92.95%2C%20E%3D1.100e-24
>
> When I display this example (and the other features) using the in-memory,
> BDDB or MySQL adaptors, they are represented in GBROWSE such that the gene
> and mRNA features are in three linked segments (see attached pi_gff3.png).
> Using the CHADO adaptor, the gene and mRNA features are each shown as a
> single feature (see attached pi_chado.png).  Is there a way to change this
> in the .conf file, or in how I'm uploading to CHADO, or is there a
> difference in how the CHADO adaptor represents these features to GBROWSE
> internally?  I'm assuming that the CHADO upload was correct, because ARTEMIS
> functions normally on the same data.
>
> The CHADO upload command was:
>
> gmod_bulk_load_gff3.pl --gfffile test.gff3 --organism "P.infestans T30-4
> release 5" --dbname oomycete_reference --dbuser ****** --dbpass ******
> --noexon
>
> And the CHADO adaptor is declared with this in the .conf file
>
> [GENERAL]
> description   = infestans test
> db_adaptor    = Bio::DB::Das::Chado
> db_args       = -dsn dbi:Pg:dbname=oomycete_reference
>                -user ******
>                -pass ******
>                -organism "P.infestans T30-4 release 5"
>                -version 1
>
> Using -srcfeatureslice 1 or recursivMapping 1 doesn't seem to help.  Is
> there anything else I can try?
>
> Cheers,
>
> L.
>
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



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

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Re: [Gmod-gbrowse] Problem displaying multi-segmented features from CHADO in GBROWSE

lpritc@scri.ac.uk
Hi Scott,

On 18/05/2010 Tuesday, May 18, 16:11, "Scott Cain" <[hidden email]>
wrote:

> Things you might need:
>
> 1. In the database section, you probably need to add "-inferCDS 1" to
> the db_args.
>
> 2. In the track definition, you may need to add "ignore_sub_part =
> polypeptide".

I'm repopulating the database just now, but I'll give those a go as soon as
I can and get back to you via the list.

Cheers,

L.


--
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee.
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
______________________________________________________

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Re: Problem displaying multi-segmented features from CHADO in GBROWSE

lpritc@scri.ac.uk
Hi,

On 18/05/2010 Tuesday, May 18, 16:13, "Leighton Pritchard"
<[hidden email]> wrote:

> On 18/05/2010 Tuesday, May 18, 16:11, "Scott Cain" <[hidden email]>
> wrote:
>
>> Things you might need:
>>
>> 1. In the database section, you probably need to add "-inferCDS 1" to
>> the db_args.

Aha!  That works - I'm pretty sure I must have seen that option in
documentation or on the list somewhere, but it completely slipped my mind.
Thank you.
 
>> 2. In the track definition, you may need to add "ignore_sub_part =
>> polypeptide".

That doesn't seem to have any influence, but I should remember that the
option exists, now.

Thanks again,

L.


--
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
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The Scottish Crop Research Institute is a charitable company limited by guarantee.
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Re: Problem displaying multi-segmented features from CHADO in GBROWSE

Scott Cain
Hi Leighton,

I'm glad it wasn't a new bug.  The inferCDS feature has no doubt been
mentioned on the mailing list, but you mentioning documentation made
me realize the the arguments for the Chado constructor are not
documented at all, so I added the following to the pod for Chado.pm.
Thanks for spurring me to do it :-)

Scott

       new

        Title   : new
        Usage   : $db    = Bio::DB::Das::Chado(
                                   -dsn  => 'dbi:Pg:dbname=gadfly;host=lajolla'
                                   -user => 'jimbo',
                                   -pass => 'supersecret',
                                              );

        Function: Open up a Bio::DB::DasI interface to a Chado database
        Returns : a new Bio::DB::Das::Chado object
        Args    :

       -dsn [dsn string]
           A full dbi dsn string for the database, optionally including host
           and port information, like
           "dbi:Pg:dbname=chado;host=localhost;port=5432".

       -user [username]
           The database user name.

       -pass [password]
           The users password for the database.

       -organism [common_name|abbreviation|"Genus species"]
           Used to specify the organism that the features should be drawn from
           in Chado instances that have more than one organism.  The argument
           can be the common name, the abbreviation or "Genus species".  Since
           common name and abbreviation are not guaranteed to be unique, if
           one of those is supplied and it corresponds to more than one
           organism_id, the Chado adaptor will die.  Since the combination is
           guaranteed to be unique by table constraints, supplying "Genus
           species" should always work.

       -srcfeatureslice [1|0] default: 0
           Setting this to 1 will enable searching for features using a
           function and a corresponding index that can significantly speed
           searches, as long as the featureloc_slice function is present in
           the Chado instance (all "modern" instances of Chado do have this
           function).  Since it available in nearly all Chado instances, in a
           future release of this adaptor, the default value of
           -srcfeatureslice will be set to 1 (on).

       -inferCDS [1|0] default: 0
           Given mRNA features that have exons and polypeptide features as
           children, when inferCDS is set, the Chado adaptor will calculate
           the intersection of the exons and polypeptide features and create
           CDS features that result.  This is generally needed when using gene
           and mRNA features with glyphs in GBrowse that show subparts, like
           the gene and processed_transcript glyphs.  Since this is almost
           always required, in a future release of this adaptor, the default
           will be switched to 1 (on).

       -recursivMapping [1|0] default: 0
           In the case where features are mapped to a "small" srcfeature (like
           a contig) and then that small feature is mapped to a larger feature
           (like a chromosome), setting -recursivMapping will allow the Chado
           adaptor to calculate the coordinates of the feature on the larger
           feature even though it isn't explicitly mapped to it.  The Chado
           adaptor suffers an approximately 20% performance penalty to do this
           mapping.

       -allow_obsolete [1|0] default: 0
           If set to 1, allow_obsolete will tell the Chado adaptor to ignore
           the feature.is_obsolete column when querying to find features.

       -enable_seqscan [1|0] default: 1
           If set to zero, the -enable_seqscan will send a query planner hint
           to the PostgreSQL server to make it more costly to do sequential
           scans on a table.  This is generally not necessary, as the query
           planner in Pg 8+ is smarter than it used to be.

       -do2Level [1|0] default: 0
           do2Level is a flag for specifying that two "levels" at most of
           features should be fetch when getting child features.  This flag is
           generally unnecessary as Bio::Graphics::Glyph supports specifying
           on a per glyph basis what should be fetch.  Use of this flag is
           incompatible with the -recursivMapping flag.

       -reference_class [SO type name]
           Used to specify what the "base type" is.  Typically, this would be
           chromosome or contig, but setting it is only necessary in the case
           where features are mapped to more than one srcfeature and you don't
           want to use the one that is lowest on the graph.  For example, you
           have polypeptides that are mapped to chromosomes and motifs that
           are mapped to polypeptides.  If you want to display the motifs on
           the polypeptide, you need to set "polypeptide" as the argument for
           -reference_class.


On Wed, May 19, 2010 at 4:06 AM, Leighton Pritchard <[hidden email]> wrote:

> Hi,
>
> On 18/05/2010 Tuesday, May 18, 16:13, "Leighton Pritchard"
> <[hidden email]> wrote:
>
>> On 18/05/2010 Tuesday, May 18, 16:11, "Scott Cain" <[hidden email]>
>> wrote:
>>
>>> Things you might need:
>>>
>>> 1. In the database section, you probably need to add "-inferCDS 1" to
>>> the db_args.
>
> Aha!  That works - I'm pretty sure I must have seen that option in
> documentation or on the list somewhere, but it completely slipped my mind.
> Thank you.
>
>>> 2. In the track definition, you may need to add "ignore_sub_part =
>>> polypeptide".
>
> That doesn't seem to have any influence, but I should remember that the
> option exists, now.
>
> Thanks again,
>
> L.
>
>
> --
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
>
>
> ______________________________________________________
> SCRI, Invergowrie, Dundee, DD2 5DA.
> The Scottish Crop Research Institute is a charitable company limited by guarantee.
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
>
>
> DISCLAIMER:
>
> This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.
>
> Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
> ______________________________________________________
>



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

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Re: Problem displaying multi-segmented features from CHADO in GBROWSE

lpritc@scri.ac.uk
Hi Scott,

On 19/05/2010 Wednesday, May 19, 15:54, "Scott Cain" <[hidden email]>
wrote:

> I'm glad it wasn't a new bug.  The inferCDS feature has no doubt been
> mentioned on the mailing list, but you mentioning documentation made
> me realize the the arguments for the Chado constructor are not
> documented at all, so I added the following to the pod for Chado.pm.
> Thanks for spurring me to do it :-)

I'm just glad to know I'm useful for something ;)

Thanks for the documentation, it will be very handy.

Cheers,

L.


--
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:[hidden email]       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


______________________________________________________
SCRI, Invergowrie, Dundee, DD2 5DA.  
The Scottish Crop Research Institute is a charitable company limited by guarantee.
Registered in Scotland No: SC 29367.
Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.


DISCLAIMER:

This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries.  This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed.  It may not be disclosed or used by any other than that addressee.
If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [hidden email] quoting the name of the sender and delete the email from your system.

Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any).
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