[Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N

[Aaron J Mackey]

The bulk loaders work by writing the data to files that are read by
Pg/MySQL directly into the tables in a single operation; the \N's are the
NULL entries for your GFF fields with "." in them.  I would look through 
the documentation of your version of Pg to find out what the NULL 
encoding should be for your version; perhaps there was a change?

-Aaron

On Fri, 12 Mar 2004, Aerts, Jan wrote:

> Thanks Sean,
> 
> I did try bp_load_gff.pl, and that one works. But the gff file I want to upload is almost 140,000 lines big, so it would take more than a day to get that into Postgres. I did use bp_pg_bulk_load_gff.pl before (must have been another version), and it worked then.
> 
> So I'm afraid I'm still stuck here.
> Jan
> 
> 
> -----Original Message-----
> From:	Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent:	Fri 12-Mar-04 16:39
> To:	Aerts, Jan
> Cc:	
> Subject:	Re: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N
> I have had problems using the bp_bulk_load scripts for mysql on macos.  I
> ended up solving the problem by using the bp_load script instead.  If there
> is one for postgresql, you might try it, as I think the functionality is the
> same.
> 
> Sean
> 
> On 3/12/04 10:00 AM, "Aerts, Jan" <Jan.Aerts at wur.nl> wrote:
> 
> > I forgot to say: the command used was this: bp_pg_bulk_load_gff.pl -d my_db
> > file.gff
> > 
> > Jan
> > 
> > 
> > -----Original Message-----
> > From:    bioperl-l-bounces at portal.open-bio.org on behalf of Aerts, Jan
> > Sent:    Fri 12-Mar-04 15:36
> > To:    bioperl-l at bioperl.org
> > Cc:    
> > Subject:    [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N
> > Hi all,
> > 
> > Has anyone encountered the following errors when trying to load a gff file
> > into a PostgresQL database? The bioperl version is 1.4. The gff file looks
> > like this:
> > 
> > [start gff file]
> > GGA10_random    Blast   Gene    1906433 1908278 1e-102  +       .       Gene
> > VIM ; Accession NM_003380.1
> > GGA10_random    Blast   Gene    1539573 1542536 0.0     +       .       Gene
> > GTF2E1 ; Accession NM_005513.1
> > [stop gff file]
> > 
> > [start error]
> > ...
> > psql:/usr/tmp/fdata.30284:85393: invalid command \N
> > psql:/usr/tmp/fdata.30284:85393: invalid command \N
> > psql:/usr/tmp/fdata.30284:85394: invalid command \N
> > psql:/usr/tmp/fdata.30284:85394: invalid command \N
> > psql:/upsql:/usr/tmp/ftype.30284:1: ERROR:  parser: parse error at or near "("
> > psql:/usr/tmp/ftype.30284:3: invalid command \.
> > psql:/usr/tmp/ftype.30284:4: ERROR:  parser: parse error at or near "1"
> > psql:/usr/tmp/fgroup.30284:1: ERROR:  parser: parse error at or near "("
> > psql:/usr/tmp/fgroup.30284:13694: invalid command \.
> > psql:/usr/tmp/fgroup.30284:13695: ERROR:  parser: parse error at or near "1"
> > psql:/usr/tmp/fattribute.30284:1: ERROR:  parser: parse error at or near "("
> > psql:/usr/tmp/fattribute.30284:3: invalid command \.
> > psql:/usr/tmp/fattribute.30284:4: ERROR:  parser: parse error at or near "1"
> > psql:/usr/tmp/fattribute_to_feature.30284:1: ERROR:  parser: parse error at or
> > near "("
> > psql:/usr/tmp/fattribute_to_feature.30284:139850: invalid command \.
> > psql:/usr/tmp/fattribute_to_feature.30284:139851: ERROR:  parser: parse error
> > at or near "1"
> > [stop error]
> > 
> > Any help appreciated.
> > Thanks,
> > Jan Aerts
> > 
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> > 
> > 
> > 
> > 
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> 
> 
> 
> 
> 
> 
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