Difference between revisions of "Release to BRC"

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(How to create and upload GFF3 files to the BRC)
 
(How to Create and Release GFF3 files to the BRCs)
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=== How to Create and Release GFF3 files to the BRCs ===
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== How to Create and Release GFF3 files to the BRCs ==
  
 
We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data.
 
We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data.
  
* Creating the files
+
===Creating the files===
 +
 
 +
Choose a machine that is upto date, and create an empty directory. For this example, we'll use the directory NMPDR
  
Choose a machine that is upto date, and create an empty directory.
 
 
Run the command  
 
Run the command  
  
nmpdr2gff NMPDR
+
nmpdr2gff NMPDR
  
 
This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set.
 
This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set.
 +
 +
The creation takes about 30-40 seconds per genome, so you can expect it to run for some time.
  
 
Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism):
 
Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism):
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***Vibrio.cholerae.O395.gff3
 
***Vibrio.cholerae.O395.gff3
 
***...
 
***...
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 +
===Uploading the files===
 +
 +
One the creation of the GFF3 files is complete, you need to use the [http://iowg.brcdevel.org/gff3validator/ brc-central validator] to validate and upload the data to the site. The one tricky thing about this was that it requires the GO::Parser PERL module. This should be part of the standard install everywhere now, but you may run into problems if it is missing. Please contact Bob for help.
 +
 +
Use this command to validate and upload our data:
 +
 +
gff3_validator.pl -b NMPDR -d /path/to/directory/NMPDR -p CDS
 +
 +
One this has completed you should ftp to [ftp://ftp.brc-central.org] and check that the files are correct. If there are problems with the validator or upload you should email Todd Creasy at TIGR for help.

Revision as of 14:18, 14 November 2006

How to Create and Release GFF3 files to the BRCs

We regularly release our data to BRC-central via GFF3 files. This page describes the steps to release the data.

Creating the files

Choose a machine that is upto date, and create an empty directory. For this example, we'll use the directory NMPDR

Run the command

nmpdr2gff NMPDR

This looks through all genomes for the NMPDR flag, and if it is found then a GFF3 file is created. If you suspect that files are not created for some genomes that should have them, then the NMPDR flag has not been set.

The creation takes about 30-40 seconds per genome, so you can expect it to run for some time.

Once complete you will have a directory structure that looks something like this (only the first two genomes are shown for each organism):

  • NMPDR
    • Campylobacter
      • Campylobacter.coli.RM2228.gff3
      • Campylobacter.jejuni.subsp.jejuni.84-25.gff3
      • ...
    • Listeria
      • Listeria.innocua.Clip11262.gff3
      • Listeria.monocytogenes.EGD-e.gff3
      • ...
    • Staphylococcus
      • Staphylococcus.aureus.RF122.gff3
      • Staphylococcus.aureus.subsp.aureus.MRSA252.gff3
      • ...
    • Streptococcus
      • Streptococcus.pneumoniae.R6.gff3
      • Streptococcus.pyogenes.MGAS10270.gff3
      • ...
    • Vibrio
      • Vibrio.cholerae.MO10.gff3
      • Vibrio.cholerae.O395.gff3
      • ...

Uploading the files

One the creation of the GFF3 files is complete, you need to use the brc-central validator to validate and upload the data to the site. The one tricky thing about this was that it requires the GO::Parser PERL module. This should be part of the standard install everywhere now, but you may run into problems if it is missing. Please contact Bob for help.

Use this command to validate and upload our data:

gff3_validator.pl -b NMPDR -d /path/to/directory/NMPDR -p CDS

One this has completed you should ftp to [1] and check that the files are correct. If there are problems with the validator or upload you should email Todd Creasy at TIGR for help.