Phage Hosts

Aims:

• make a master bacterial database file that has accurate Gram status information
• isolate refseqs of phages in Myoviridae and Siphoviridae
• determine the bacterial host of each phage and determine the Gram status of each host (using bacterial db)
• isolate annotated tape measure proteins from each phage
• analyze motifs for each annotated tape measure protein (TMP)
• find the TMP in phages with no annotated TMP

Data flow (so far)

Fetch ids for phages

Export list of ids (accession numbers) from NCBI

Get genbank files for this list of ids

Use efetch to get genbank files (TODO: comment on this process)

Output name, id, and gram status of the host for each phage in the gbk file

$ python assign_phages.py multi_gbk_file.gbk bacterial_host_file.json