Re: gmod_gff3_preprocessor.pl splitfile option help

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Re: gmod_gff3_preprocessor.pl splitfile option help

Scott Cain
Hi Sanjay,

I cc'ed this to the schema mailing list, since that's where Chado and Chado-related utilities get discussed.

I wonder from the error message if there is something wrong with the GFF file which results in the undefined value message.  Can you "head -n 500 file > temp.gff" and send it to the list?

Additionally, my suggestion for you is that you not sort unless you are sure you need to; the preprocessor uses a very dumb sorting algorithm, so sorting on long files can take a very long time.

Finally, the preprocessor deposits the fasta squence in a separate file, but those can be loaded with the GFF bulk loader after the GFF has been loaded.

Scott


On Thu, Nov 1, 2012 at 7:58 PM, Sanjay Chellapilla <[hidden email]> wrote:
Hi Scott,

I'm trying to split a 1.4GB gff3 file containing embedded fasta sequences using the following
command-line, but getting an error. I'd like the gff3 to be sorted, chunked by the sequence id
in column 1 of the gff3 and also contain the corresponding fasta sequence in the footer of each
sorted gff3 chunk, so that they can be loaded one by one into Chado using gmod_bulk_load_gff3.pl

gmod_gff3_preprocessor.pl --splitfile 1 --outfile chunk.gff3 --gfffile ./file.gff3
Can't call method "print" on an undefined value at /usr/local/bin/gmod_gff3_preprocessor.pl line 201, <GFFIN> line 2.

Is there a way to to use this script to sort and chunk the gff3 by column 1 seqid.

Thanks,
Sanjay.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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