Hello ! :)

Thank you very much !

I'm late for the answer, because I writting and testing a script to download the genome in Python from PATRIC and the time to understand your answer and learn more about that :).

import requests
import json
import math
import time
import os
import sys
import subprocess

#function

def execute(command,path):
    """
    print the command line output in the console
    """
    process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=path)

    # Poll process for new output until finished
    while True:
        nextline = process.stdout.readline()
        if nextline == '' and process.poll() != None:
            break
        sys.stdout.write(nextline)
        sys.stdout.flush()

    output = process.communicate()[0]
    exitCode = process.returncode

    if (exitCode == 0):
        return output
    else:
        raise ProcessException(command, exitCode, output)

#commands

requests.get('https://guest.ulg.ac.be/welcome',verify=True)

taxonID = str(input('Give the NCBI Tax ID of your rank or taxon : '))
limit = '10000'
print "Make POST Request to PATRIC Server to have the number of genome"
r = requests.post('https://www.patricbrc.org/portal/portal/patric/GenomeFinder/GenomeFinderWindow?action=b&cacheability=PAGE&need=0&taxonId='+taxonID+'&keyword=*:*&facet={"facet":"public,genome_status,reference_genome,antimicrobial_resistance,antimicrobial_resistance_evidence,isolation_country,host_name,disease,collection_date,completion_date","facet_text":"Public,Genome Status,Reference Genome,Antimicrobial Resistance,Antimicrobial Resistance Evidence,Isolation Country,Host Name,Disease,Collection Date,Completion Date","field_facets":"genome_status,reference_genome,antimicrobial_resistance,antimicrobial_resistance_evidence,isolation_country,host_name,disease,collection_date,public","date_range_facets":"completion_date"}&sort=[{"property":"genome_name","direction":"ASC"}]',verify=False)
genomeNumber = r.json()[u'total']
print "Number of genome found : ", genomeNumber
if genomeNumber < int(limit):
    pageNumber = 1
else:
    pageNumber = int(math.ceil(genomeNumber/int(limit)))

dicoFTP = dict()
with open("patricGenome_"+taxonID+".txt","w") as f:
    pageList = list()
    for page in range(pageNumber):
        start = page*int(limit)+1
        page+=1
        print "page ",page,"/",pageNumber
        t0 = time.time()
        req = requests.post('https://www.patricbrc.org/portal/portal/patric/GenomeFinder/GenomeFinderWindow?action=b&cacheability=PAGE&need=0&taxonId='+taxonID+'&keyword=*:*&facet={"facet":"public,genome_status,reference_genome,antimicrobial_resistance,antimicrobial_resistance_evidence,isolation_country,host_name,disease,collection_date,completion_date","facet_text":"Public,Genome Status,Reference Genome,Antimicrobial Resistance,Antimicrobial Resistance Evidence,Isolation Country,Host Name,Disease,Collection Date,Completion Date","field_facets":"genome_status,reference_genome,antimicrobial_resistance,antimicrobial_resistance_evidence,isolation_country,host_name,disease,collection_date,public","date_range_facets":"completion_date"}&page='+str(page)+'&start='+str(start)+'&limit='+limit+'&sort=[{"property":"genome_name","direction":"ASC"}]',verify=False)
        pageList.append(req)
        t1 = time.time()
        t = t1-t0
        print t,"seconds"
    cpt = 0
    for page in pageList:
        cpt +=1
        t0 = time.time()
        nbGenome = len(req.json()[u'results'])
        for i in range(nbGenome):
            t1 = time.time()
            dico = req.json()[u'results'][i]
            taxID, genomeName, genomeID = dico[u'taxon_id'],dico[u'genome_name'],dico[u'genome_id']
            dicoFTP[genomeID]="ftp://ftp.patricbrc.org/patric2/genomes/"+str(genomeID)+"/"+str(genomeID)+".PATRIC.faa"
            f.write(str(taxID)+"\t"+str(genomeName)+"\t"+str(genomeID)+"\n")
            t2 = time.time()
            print "parsed genome",genomeName,"in",t2-t1,"seconds"
        t3 = time.time()
        print "parsed page",cpt,"in",t3-t0,"seconds"

#download founded genome
patricDir = os.getcwd()+"/patricGenome"
if os.path.isdir(patricDir) == False:
    os.mkdir(patricDir)
#logFile
with open("logFilePatric.txt","w") as log:
    #download genome
    for key in dicoFTP.keys():
        print dicoFTP[key]
        name = os.path.split(dicoFTP[key])[1]
        call = 'wget '+dicoFTP[key]
        execute(call,patricDir)
        #process = subprocess.Popen(call, shell=True, cwd=patricDir)
        #process.communicate()
        if os.path.isfile(name) == False:
            print name," not found"
            log.write(dicoFTP[key]+"\n")

Maybe this code can help someone :)

Thank you !