INNER CODE UNIT · Python
cat_contigs
PKU-EMBL/BASALT · Bin_quality_evaluation.py:10
def cat_contigs(bin_folder, pwd):
bin_length, bin_contigs_n, bin_contigs_5k, bin_avg_length, bin_n50_length, bin_contigs_position_list={}, {}, {}, {}, {}, {}
try:
bin_folder_name=bin_folder.replace(' ','_')
except:
bin_folder_name=bin_folder
contig_file=open('Total_contigs_'+bin_folder_name+'.fa','w')
bin_summary_file=open(bin_folder_name+'_basic_information_of_bins.txt','w')
bin_summary_file.write('Bin'+'\t'+'Bin total length (bp)'+'\t'+'NO. contigs'+'\t'+'NO. contigs with than 5kbp'+'\t'+'Bin avg. length (bp)'+'\t'+'Bin N50 contig\'s length (bp)'+'\n')
os.chdir(pwd+'/'+bin_folder)
for root, dirs, files in os.walk(pwd+'/'+bin_folder):
for file in files:
hz=str(file).split('.')[-1]
if 'fa' in hz or 'fna' in hz:
bin_contig_rank=[]
bin_length[file]=0
bin_contigs_n[file]=0