def main():
os.chdir(wdir)
file_list = glob.glob(os.path.join(wdir,'cluster_NSR','*.fasta'))
save=open('all.fasta','w')
for file1 in file_list:
fasta = trile.read_fasta(file1)
for head in fasta.keys():
save.write('>'+head+'\n')
save.write(fasta.get(head)+'\n')
save.close()
file1 = 'all.fasta'
name = 'all'
cmd = uclust+' --sort '+file1
cmd+= ' --output '+file1+'.tmp'
os.system(cmd)
cmd = uclust+' --input '+file1+'.tmp'
cmd+= ' --uc '+name+'.uc'
os.system(cmd)
cmd = uclust+' --input '+name+'.fasta --uc2fasta '
cmd+= name+'.uc --output '
cmd+= name+'.fasta.tmp2'
os.system(cmd)
os.system('mv '+name+'.fasta.tmp2 '+name+'.fasta')
os.system('rm '+name+'.uc '+name+'.fasta.tmp')
def main():
try:
os.mkdir(os.path.join(wdir,'cluster_NSR'))
except:
pass
os.chdir(os.path.join(wdir,'cluster_NSR'))
file_list = glob.glob(os.path.join(wdir,'format_NSR','*.fasta'))
for file1 in file_list:
name = os.path.basename(file1).split('.fasta')[0]
cmd = uclust+' --sort '+file1
cmd+= ' --output '+os.path.basename(file1)
os.system(cmd)
cmd = uclust+' --input '+os.path.basename(file1)
cmd+= ' --uc '+name+'.uc'
os.system(cmd)
cmd = uclust+' --input '+name+'.fasta --uc2fasta '
cmd+= name+'.uc --types S --output '
cmd+= name+'.fasta.tmp'
os.system(cmd)
os.system('mv '+name+'.fasta.tmp '+name+'.fasta')
os.system('rm '+name+'.uc')
fasta = trile.read_fasta(name+'.fasta')
save = open(name+'.fasta','w')
count = 0
for head in fasta.keys():
count+=1
save.write('>'+name+'.'+str(count)+'\n')
save.write(fasta.get(head)+'\n')
save.close()
def main():
try:
os.mkdir(os.path.join(wdir,'format_NSR'))
except:
pass
file_list = glob.glob(os.path.join(wdir,'NSR','*.fasta'))
for file1 in file_list:
name = os.path.basename(file1).split('.fasta')[0]
fasta = trile.read_fasta(file1)
save = open(os.path.join(wdir,'format_NSR',name+'.fasta'),'w')
count = 0
for head in fasta.keys():
count+=1
save.write('>'+name+'.'+str(count)+'\n')
save.write(fasta.get(head)+'\n')
save.close()
def main():
os.chdir(wdir)
save = open('epidemic.fasta','w')
read = open('heatmap.tsv')
head = next(read).split()
seq_dict = trile.read_fasta('all.fasta')
bool_dict = dict()
for line in read:
col = line.split()
name = col[0]
col = col[1:]
for i in range(len(col)):
if float(col[i])>20.0:
if head[i] not in bool_dict.keys():
bool_dict[head[i]]=name
else:
bool_dict[head[i]]+='.'+name
count = 1
for key in bool_dict.keys():
val = bool_dict.get(key)
if val.count('O')==7 and 'N' not in val:
save.write('>E'+str(count)+'\n')
save.write(seq_dict.get(key)+'\n')
count+=1
