Ben Kellman

My code: ``` PROJECT = 'GTspec_query' LIST_OF_GENES = ['P01106','P01229','P01374'] PDB_FILE_TYPE = 'mmtf' # Create the GEM-PRO project my_gempro = GEMPRO(gem_name=PROJECT, root_dir=ROOT_DIR, genes_list=LIST_OF_GENES, pdb_file_type=PDB_FILE_TYPE) # UniProt mapping my_gempro.uniprot_mapping_and_metadata(model_gene_source='ACC+ID') ``` fails and...

Issues running the tutorial

1

https://github.com/SBRG/ssbio/blob/6f41652f716681a64f2f57aa3cc47eb1953e4ae4/docs/tutorials.ipynb#L7 There are two issues I've found running this code: 1) I think ```shutil.which``` is only availible for python3 but the ipython notbook defaults to opening in python2. I switched...

tmscore issue

1

https://github.com/SBRG/ssbio/blob/6f41652f716681a64f2f57aa3cc47eb1953e4ae4/docs/notebooks/FATCAT%20-%20Structure%20Similarity.ipynb#L72 When I try to run parse_fatcat I get an error: ``` --------------------------------------------------------------------------- KeyError Traceback (most recent call last) in () ----> 1 fatcat.parse_fatcat(fatcat_outfile) /home/ben/anaconda2/lib/python2.7/site-packages/ssbio/protein/structure/properties/fatcat.pyc in parse_fatcat(fatcat_xml) 96 # Find...

Question: mouse reference docs?

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Hi, Just curious, I'm new to variant calling and I'm not so familiar with some of the references (e.g. vcfindicies) or the specific index preparation preferred by GATK. The pipeline...