properly

in form
 - add space between ex: and the value

in reference to macsyfinder/view provide the 2 url
in reference to Txsscan remove text keep only the link

when the taxonomy ends with '.' or ';' the 'ast char must be removed
there was an error, only the last term was assigned to the taxonomy
which induce javascript error on the sever side
in the by_taxonomy view

taxonomy.join(', ') is not a function

when data are not valid a forbiden error is thrown and the message
was not clear.
know the 2 origin of erro data or credentials are treated separately and
an improved message is displayed to the user

so skip these systems and log them

replace namedtuple SystemInfo by an object
as we need to mutate it
some information (system_status, and predicted_system are
known after the creation of new system occurrence
when the parser encounter a gene belonging a system not neighbor genes

replace schema of T3SS system by schema of all secretion systems
and secreton logo of secreton by txssdb logo

instead for only T3SS genes

ncbi_id

replace all t3ss_family info and search by predicted_system

and add info ncbi_id and search system using ncbi_id

use argparse instead of optparse
raise error when system-id is not specify

the documents have not any longer fields:

gene.full_score
gene.evalue
gene.best_domain_score
gene.best_domain_evalue
gene.c_value
gene.coverage_profile

but there are now new fields:

replicon.ncbi_id
gene.score
gene.i_evalue
gene.coverage

GEM provide new data with some fields in plus and some have disapear
modification of the parser according to these new data