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

[Aerts, Jan]

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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