Major changes. Added additional command line functionality, fixed dynamic gi sequence extraction, altered loop structure so that top x hits are taken from each query, additional term currently commented out to add query ids to be retrieved (may not be necessary, lines 93-95). Works with multiple query .xml output. Appears stable. Type $ python quickOrtho.py --help for intructions.
retrieving any changes to quickOrtho.py and merging before pushing new version
Edited text feedback. Fixed bug that would mean that unpublished queries (ie those with no gid) would result in an error during xml data retrieval. Changed Exception handler so that errors in retrieval from entrez break the script with more useful feedback.