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

the user and the login are no longer option given on the commandline.
the program prompt for the logging and the password with no echoeing for the password.
the user have 3 attempt to give the right combination login/password
otherwise the program exit

change system_image (complet simple)
change gene (gene_SctJ gene_SctL  gene_SctK gene_SctN ) color 

remove rule for header svg from main.css as it not use anymore in main page and intefere with gene_shema in secretion_systeme page

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reorder the input fields

fix bug in taxidInput
a request is send only if the user data is an integer
if not display a warning message

 - allow only admin to create/update document
 - perform some basic checking on structure of newDocument

fix authentication problem, use restkit BasicAuth flter

fix parser 
taxonomy are not always ending by a dot. the I test the last char of taxonomy before remove the last char

Improvement
add field description in named tuple Gene

replace string passwd by variable passwd when update sha

add description in popup gene in genome schema
modify css to improved look of site

fix bug #917
the view was harcoded in pagination links
the "key" parameter was omitted in pagination links