Hello Qianli,
This appears to be the same data as submitted as a recent bug?
Converting the query coordinates to BED format is still the
recommendation. This should be a good solution for most, if not all, of
your prior Extract tool failures and is a good method overall.
First "Convert Formats -> GFF-to-BED", followed by clicking on the
pencil icon to assign the last three columns on the "Edit Attributes"
form, in particular you will want to get strand assigned, so that c4 =
name, c5 = score, and c6 = strand. The datatype will be bed. Then
extract using your custom genome and the sequence will be titled by the
region coordinates.
Best,
Jen
Galaxy team
On 5/29/12 11:58 AM, Qianli Shen wrote:
Hi
I want to fetch sequence from soybean genome, according to a gff file.
My gff3 file and genome file are attached to the email, because it is
not easy to recongnize the format if I paste it in the email. And it
keeps reporting the error:
An error occurred running this job: Traceback (most recent call last):
File
"/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", line
288, in
if __name__ == "__main__": __main__()
File
"/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py"
Could you please tell me where is the problem?
Best
Qianli
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