A collection of tools for converting genome annotation between GTF, BED, GenBank and GFF.
Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. These programs can be easily integrated into your galaxy instance.
Included utilities are:
BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
GBK-to-GFF: convert data from genbank format to GFF
GFF-to-BED: convert data from GFF to 12 column BED format
GFF-to-GTF: convert data from GFF to GTF
GTF-to-GFF: convert data from GTF to valid GFF
test-data: Test data set. (move to your galaxy-root-folder/test-data/)
You may need to move the test files into your test-data directory so galaxy can find them.
If you want to run the functional tests eg as:
exmaple:
sh run_functional_tests.sh -id fml_gtf2gff
python2.6 or 2.7 and biopython
Galaxy should be able to automatically install biopython via Galaxy toolshed.
I can be reached at vipin [at] cbio.mskcc.org
Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society
2013-2015, Memorial Sloan Kettering Cancer Center
Vipin T Sreedharan <[email protected]>
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