required=True,
dest='outFilePath',
help='Path of the output directory')
######### Recuperation arguments ###########
args = parser.parse_args()
directory = args.dirPath
outFile = args.outFilePath
########### Gestion directory ##############
directory = verifDir(directory, True)
############### start message ########################
print(
form("\n\t---------------------------------------------------------",
'yellow', 'bold'))
print("\t" + form("|", 'yellow', 'bold') +
form(" Welcome in Quality (Version " + version +
") ",
type='bold') + form("|", 'yellow', 'bold'))
print(
form("\t---------------------------------------------------------",
'yellow', 'bold') + '\n')
############# Main #########################
# listeID = []
# for ID in os.listdir(directory) :
# listeID.append(ID)
# listeID.sort()
with open(outFile, "w") as qualityR:
qualityR.write(
filesreq = parser.add_argument_group('Input mandatory infos for running')
filesreq.add_argument('-d', '--directory',type = str , required=True,dest = 'dir', help = 'Path of the gff2fasta.pl output directory')
filesreq.add_argument('-s', '--strain',type = str , required=True,dest = 'strain', help = 'Name of the strain')
######### Recuperation arguments ###########
args = parser.parse_args()
directory = os.path.abspath(args.dir)
folder= args.strain
############### start message ########################
print(form("\n\t---------------------------------------------------------",'yellow','bold'))
print("\t"+form("|",'yellow','bold')+form(" Welcome in renameFasta (Version " + version + ") ",type='bold')+form("|",'yellow','bold'))
print(form("\t---------------------------------------------------------",'yellow','bold')+'\n')
############## Main ##################################
dico_Gff = {}
cdsFile = directory +"/"+ folder + '_cds.fna'
protFile = directory +"/"+ folder + '_protein.faa'
gffFile = directory +"/"+ folder + '_merge.gff3'
f = open(gffFile,'r')
lines = f.readlines()
f.close()
print('Creation dico GFF')
for line in lines :
if 'mRNA' in line :
######### Recuperation arguments ###########
args = parser.parse_args()
brakerFile = os.path.abspath(args.BRAKER)
augustusFile = os.path.abspath(args.augustus)
outFile = os.path.abspath(args.outFile)
########### Gestion directory ##############
name = augustusFile.split('/')[-1].replace('.gff3', '')
brakerPath = brakerFile.replace(brakerFile.split('/')[-1], '')
augustusPath = augustusFile.replace(augustusFile.split('/')[-1], '')
############### start message ########################
print(
form("\n\t---------------------------------------------------------",
'yellow', 'bold'))
print("\t" + form("|", 'yellow', 'bold') +
form(" Welcome in mergeBraker_augustus (Version " + version +
") ",
type='bold') + form("|", 'yellow', 'bold'))
print(
form("\t---------------------------------------------------------",
'yellow', 'bold') + '\n')
####################### main #################"
nouveauGene = []
listeGene = []
liste = []
liste1 = []
nbAjout = 0
if nbAjout != 0:
args = parser.parse_args()
directory = os.path.abspath(args.dirPath)
genome = os.path.abspath(args.genome)
output = os.path.abspath(args.outfile)
########### Gestion directory ##############
directory = verifDir(directory, True)
if __name__ == "__main__":
version = "0.1"
############### start message ########################
print(
form("\n\t---------------------------------------------------------",
'yellow', 'bold'))
print("\t" + form("|", 'yellow', 'bold') +
form(" Welcome in RecupInfoGFF (Version " + version +
") ",
type='bold') + form("|", 'yellow', 'bold'))
print(
form("\t---------------------------------------------------------",
'yellow', 'bold') + '\n')
################## Main ################################
f = open(output, 'w')
f.write('%s\t%s\t%s\t%s\t%s\t%s\n' %
('Strain'.center(10), 'Augustus'.center(10), 'Braker'.center(10),
'nb Gene'.center(10), 'Length mean'.center(10),
'Length (mb)'.center(10)))