Hi Curtis,
Sorry for the trouble in using the converter package. I will fix the issues which you mentioned below.
For a quick fix, I can point you to my working repository: https://github.com/vipints/GFFtools-GX
This program will help you to convert the gff to 12 column bed file: https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.py
the associated galaxy wrapper: https://github.com/vipints/GFFtools-GX/blob/master/gff_to_bed.xml
I know this is not the best way to fix the issue but I will update the public repository soon.
Vipin | Rätsch Lab
On Mon, Apr 6, 2015 at 4:35 PM, Curtis Hendrickson (Campus) <curtish@uab.edu
wrote:
Folks
I installed this very useful looking tool repository (fml_gff3togtf https://toolshed.g2.bx.psu.edu/view/vipints/fml_gff3togtf) to convert GFF3->BED12 based on this BioStars.
https://www.biostars.org/p/85869It installed fine, but when I run it on
ftp://ftp.ncbi.nih.gov/genomes/Viruses/Human_herpesvirus_5_uid14559/NC_006273.gff
I get
Traceback (most recent call last):
File "/share/apps/galaxy/test-shed-tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/gff_to_bed.py", line 18, in <module>
import GFFParserFile "/share/apps/galaxy/test-shed-tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/6e589f267c14/fml_gff3togtf/GFFParser.py", line 20, in <module>
import scipy.io as sioImportError: No module named scipy.io
Anyone know the trick to get the python libraries set up correctly?
(also note that this failed nightly tests on 2015-04-06 – but that looks like a lack of test data/configuration)
I see some other packages (like htseq_count https://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) have numpy as a dependency…. Using the devteam’s numpy 1.7 package:
https://toolshed.g2.bx.psu.edu/view/devteam/package_numpy_1_7
Regards,
Curtis
Research Associate, Informatics Unit
Center for Clinical and Translational Science
University of Alabama at Birmingham
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