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/85869

It 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 GFFParser

File "/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 sio

ImportError: 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

http://bioinformatics.uab.edu

University of Alabama at Birmingham

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