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

[Aerts, Jan]

I just found out that it _is_ working with 7.3.4, but not with 7.2.2. Seems like I will have to update that postgres server...

Thanks to all,

jan.


-----Original Message-----
From:	Scott Cain [mailto:cain at cshl.org]
Sent:	Fri 12-Mar-04 17:19
To:	Bioperl list; Aerts, Jan
Cc:	
Subject:	Re: [Bioperl-l] bp_pg_bulk_load_gff.pl: invalid command \N
Hi Jan,

What version of Postgres are you using?  At some point, the bulk loading
format for Postgres changed, and bp_pg_bulk_load_gff.pl only supports
the newer format.  I believe that this change occurred between
7.2->7.3.  If you are using an older Postgres, you should be able to
still use bp_load_gff.pl, though it will be slower.

Scott


--------------Original Message---------------
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

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory