Re: Gmod-schema Digest, Vol 95, Issue 1

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Re: Gmod-schema Digest, Vol 95, Issue 1

Shane McCoy
hey, looks like all the questions are from me! :) 
the only remaining help i need is on this one:

Hello!
During the CHADO install of ontologies GO failed. I am loading 1-4 and 1,2
finished fine and quickly, GO sat at Loading... for 3hrs.
What is the proper restart point for this?
Thank you,
Shane M.
-------------- next part --------------
An HTML attachment was scrubbed...

------------------------------

I'm assuming I just restart at the load ontologies script, but I just want to make sure. 
Thank you all for your time!
Shane M.

On Mon, Dec 1, 2014 at 10:47 AM, <[hidden email]> wrote:
Send Gmod-schema mailing list submissions to
        [hidden email]

To subscribe or unsubscribe via the World Wide Web, visit
        https://lists.sourceforge.net/lists/listinfo/gmod-schema
or, via email, send a message with subject or body 'help' to
        [hidden email]

You can reach the person managing the list at
        [hidden email]

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Gmod-schema digest..."


HEY!  This is important!  If you reply to a thread in a digest, please
1. Change the subject of your response from "Gmod-schema Digest Vol ..." to the original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you are responding to.

Why?
1. This will keep the subject meaningful.  People will have some idea from the subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative.

Today's Topics:

   1. Re: Chado Environment Variable issue (Karl O. Pinc)
   2. Re: Chado Environment Variable issue (Shane McCoy)
   3. Gene Ontology loading fail (Shane McCoy)
   4. Re: Loading GFF / Fasta Questions | CHADO (Krishnakumar, Vivek)


----------------------------------------------------------------------

Message: 1
Date: Wed, 26 Nov 2014 14:24:20 -0600
From: "Karl O. Pinc" <[hidden email]>
Subject: Re: [Gmod-schema] Chado Environment Variable issue
To: Shane McCoy <[hidden email]>
Cc: [hidden email]
Message-ID: <1417033460.24220.0@slate>
Content-Type: text/plain; charset=us-ascii

On 11/26/2014 02:17:41 PM, Shane McCoy wrote:
> Hello!
> Having issue w/ my environment variable during 'perl Makefile.PL' for
> Chado
> install.

> I have this in my .bashrc
>
> GMOD_ROOT=/home/bjreadin/trunk/chado
>
> CHADO_DB_NAME=sbass_ncsu
>
> CHADO_DB_USERNAME=bjreadin
>
>
>
> plus psql -l >>> sbass_ncsu | bjreadin | UTF8     | en_US.UTF-8 |
> en_US.UTF-8 |
>
>
> any thoughts would be great!

You probably want:

export GMOD_ROOT=/home/bjreadin/trunk/chado

(etc.)

Without the "export" child processes, like perl, won't
see the variable.


You probably also want to put them in
.bash_profile instead of .bashrc.  This sets them
up when you login, not whenever bash is invoked.

There's no point in re-executing if you run
some shell program.

(However, if you invoke bash via, e.g,, cron
you will then need to make sure the env vars
are properly setup.  Likely, you'd invoke
perl or whatever directly, in which case
you need to set up the env vars from within,
say, cron, anyway.)


FWIW, I had a very hard time installing chado
from the shell.  I can send you my (cryptic)
notes offlist if you like.

Regards,

Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein



------------------------------

Message: 2
Date: Wed, 26 Nov 2014 15:30:42 -0500
From: Shane McCoy <[hidden email]>
Subject: Re: [Gmod-schema] Chado Environment Variable issue
To: "Karl O. Pinc" <[hidden email]>
Cc: [hidden email]
Message-ID:
        <CAEzGp2LuHnB1aCggDq3H2sek_Jv-EOquQusiC06UMS=[hidden email]>
Content-Type: text/plain; charset="utf-8"

You were correct in the export missing.
Thanks Karl!

On Wed, Nov 26, 2014 at 3:24 PM, Karl O. Pinc <[hidden email]> wrote:

> On 11/26/2014 02:17:41 PM, Shane McCoy wrote:
> > Hello!
> > Having issue w/ my environment variable during 'perl Makefile.PL' for
> > Chado
> > install.
>
> > I have this in my .bashrc
> >
> > GMOD_ROOT=/home/bjreadin/trunk/chado
> >
> > CHADO_DB_NAME=sbass_ncsu
> >
> > CHADO_DB_USERNAME=bjreadin
> >
> >
> >
> > plus psql -l >>> sbass_ncsu | bjreadin | UTF8     | en_US.UTF-8 |
> > en_US.UTF-8 |
> >
> >
> > any thoughts would be great!
>
> You probably want:
>
> export GMOD_ROOT=/home/bjreadin/trunk/chado
>
> (etc.)
>
> Without the "export" child processes, like perl, won't
> see the variable.
>
>
> You probably also want to put them in
> .bash_profile instead of .bashrc.  This sets them
> up when you login, not whenever bash is invoked.
>
> There's no point in re-executing if you run
> some shell program.
>
> (However, if you invoke bash via, e.g,, cron
> you will then need to make sure the env vars
> are properly setup.  Likely, you'd invoke
> perl or whatever directly, in which case
> you need to set up the env vars from within,
> say, cron, anyway.)
>
>
> FWIW, I had a very hard time installing chado
> from the shell.  I can send you my (cryptic)
> notes offlist if you like.
>
> Regards,
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
-------------- next part --------------
An HTML attachment was scrubbed...

------------------------------

Message: 3
Date: Fri, 28 Nov 2014 11:10:25 -0500
From: Shane McCoy <[hidden email]>
Subject: [Gmod-schema] Gene Ontology loading fail
To: [hidden email]
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset="utf-8"

Hello!
During the CHADO install of ontologies GO failed. I am loading 1-4 and 1,2
finished fine and quickly, GO sat at Loading... for 3hrs.
What is the proper restart point for this?
Thank you,
Shane M.
-------------- next part --------------
An HTML attachment was scrubbed...

------------------------------

Message: 4
Date: Mon, 1 Dec 2014 10:46:54 -0500
From: "Krishnakumar, Vivek" <[hidden email]>
Subject: Re: [Gmod-schema] Loading GFF / Fasta Questions | CHADO
To: "[hidden email]"
        <[hidden email]>
Cc: Shane McCoy <[hidden email]>
Message-ID: <[hidden email]>
Content-Type: text/plain; charset="iso-8859-1"

Hi Shane,

Given that you have Maker output, have you by any chance tried using the `maker2chado` script?
The developers of Maker have built an easy-to-use wrapper, optimized specifically for the GFF3 (containing embedded FASTA) generated by their pipeline. Just an FYI.

More documentation about this and other very useful scripts (e.g. maker2jbrowse, chado2gff3, etc.) is available within the MAKER release tarball.

Thank you.
Vivek

On Nov 6, 2014, at 10:52 AM, Andrew Farmer <[hidden email]<mailto:[hidden email]>> wrote:

Hi Shane-
if I'm understanding your question correctly, I think you're asking about how to get the sequence data
in the Transcript/Protein fasta files to be added to the feature.residues field in chado for the mRNA and polypeptide
features that the gff bulk loader creates?

There may be better approaches, but I believe this can be done using gmod_bulk_load_gff3.pl with the --fastafile option.
Others on the list can probably give you better guidance about this, but in my experience this can be a little tricky because
of the way that the loader assigns auto-generated names to the polypeptide features it creates. In the loading process our
group is using, we've so far just worked around this by first sql-updating the auto-assigned polypeptide names after running
the loader on the gff, then running the loader again with the fastafile option supplied. One potential difficulty with this is that I
believe the code that does the lookup to get features matching the ids in the fasta headers does not have information
about the type of feature, so if you have mRNA with the same uniquename as the corresponding polypeptide, it
will likely get confused.

I think there have been a few discussions on this list before about possible changes to the way this loader handles
polypeptide naming, so maybe this would be a good use case for driving that topic forward?

hope that helps, or at least provokes others with more knowledge of the loader to suggest better alternatives...

Andrew Farmer






On 11/5/14 2:26 PM, Shane McCoy wrote:
Hello! I am preparing in the coming weeks to load data for a fish genome into PostgreSQL/Chado to be used w/ Jbrowse/WebApollo.

The files I am receiving from the Maker output are coming in 5 parts, as they were too large to to do in one take. Each of the 5 GFF files comes w/ Protein and Transcript (Augustus, SNAP & Maker for each) .fasta files (so 6 total per GFF file). As well as one .fa file of all the .fasta files in one.
this is what i'm looking at essentially,
GFF_part1_of_5.gff
      AUG_Protein_1_5.fasta
      AUG_Tranx_1_5.fasta
      SNAP_Protein_1_5.fasta
      SNAP_Tranx_1_5.fasta etc(maker protein/tranx)
 AUG_SNAP_MAKER_PROTEIN_TRANX_1_5.fa (all in one fasta)


Following the 2013 Tutorial<http://gmod.org/wiki/Chado_Tutorial_2013> I understand loading all 5 GFF files in the bulk loader but i'm not fully grasping how to handle the .fasta files.
please bear w/ me as i am not used to working w/ these files :)

It is noted in the 2013 Tutorial under 'Preparing GFF data for loading'
for 'fasta --> GFF' but gives no details.
How are the .fasta files loaded into the database? I saw a short description<http://gmod.org/wiki/Load_RefSeq_Into_Chado> on converting into gff3 files from genbank. Is this the proper course, to convert the .fasta to gff?

If so, would i be ok just converting the (all in one) .fa file or should i convert all 6 .fasta files individually?

Also, is there any issue w/ the fact that there are 5 parts to each .fasta file to go w/ the 5 parts of GFF?

I'd appreciate any feedback, i am looking forward to learning how to use CHADO more extensively in the future,
Thanks for your time!
Shane






------------------------------------------------------------------------------




_______________________________________________
Gmod-schema mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-schema



--
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

------------------------------------------------------------------------------
_______________________________________________
Gmod-schema mailing list
[hidden email]<mailto:[hidden email]>
https://lists.sourceforge.net/lists/listinfo/gmod-schema

-------------- next part --------------
An HTML attachment was scrubbed...

------------------------------

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk

------------------------------

_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


End of Gmod-schema Digest, Vol 95, Issue 1
******************************************


------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema