Adding phamerator_manage_db2.py for testing to not remove results in score_summary
Updated phamerator_manage_db.py

phamerator_manage_db.py no longer deletes the scores_summary table
(BLAST and ClustalW scores) when phages are added or removed
Revert "Updated phamerator_manage_db.py"

This reverts commit 26685fa21d3ab47a44eb8b4f102b99916df821a9.
Revert "Revert "Updated phamerator_manage_db.py""

This reverts commit 86256cbd8ce794c2b85259ece11357714462968e.

Sorry, just trying to figure this out.
Added comments for circle location

Added comments describing where numbers are changed to move pham circle
and the label around
Revert "Added comments for circle location"

This reverts commit 6438103abc5a883ac86bc8d53d1311be62aeb6a3.
Updated to match latest changes

Rotated phage name labels on pham circle, added cluster designations to
pham circles.
Disabled automatic updates in Phamerator

Phamerator no longer updates databases automatically from
phamerator.csm.jmu.edu/sea/. To update databases from this server, run
phamerator.release instead. This resolves issue #15.
phamerator_manage_db.py prompts to delete scores

When adding or removing phages in the database, a prompt appears
allowing the user to either delete BLAST and ClustalW scores or keep
them. This resolves issue #4.
added phamServer_progress.py

This script will allow you to see how many genes have been processed in
the BLAST and ClustalW steps. Type ./phamServer_progress.py -h for
usage.
updated to show usage with incorrect # of opts

Usage is now displayed when the incorrect number of options are given
when running this script.
added 'Refreshing in # seconds...' back
updated script to remove deprecation warning

This script now uses SeqIO.read to parse GenBank files instead of the
deprecated gb_iterator.next().
This resolves issue #12.
Adding caching function to phams tab - testing

This is still being tested.
caching function is now functional for phams tab

Related to issue #13
added code for reading cached geneIDs
added "domains" column to pham and cluster tables

Added a concatenated list of all conserved domains found in genes in a
pham under the column header "domains" to the left side of both the pham
table and the cluster table. This resolves issue #14.
changed deprecated my_seq.tostring()

my_seq.tostring() is deprecated, so changed all instances to
str(my_seq).
fixed deprecated BLAST scripts

clicking on genes in "phams" tab used deprecated NCBIStandalone script.
Updated to use NcbiblastpCommandline and StringIO. Fixes issue #16.
Added User Manual to Phamerator user interface

Added Help files, user manual (quick start guide) to Phamerator.