INNER CODE UNIT · Python

n50_contig_index

PKU-EMBL/BASALT · Bin_quality_evaluation.py:41

                n50_contig_index=math.ceil(float(n)/2)

                x=0
                for item in bin_contig_rank:
                    x+=1
                    if x == n50_contig_index:
                        bin_n50_length[file]=str(n50_contig_index)+':'+str(item)
    os.chdir(pwd)
    
    for bins in bin_length.keys():
        bin_summary_file.write(str(bins)+'\t'+str(bin_length[bins])+'\t'+str(bin_contigs_n[bins])+'\t'+str(bin_contigs_5k[bins])+'\t'+str(bin_avg_length[bins])+'\t'+str(bin_n50_length[bins])+'\n')
    contig_file.close()
    bin_summary_file.close()
    return 'Total_contigs_'+bin_folder_name+'.fa', bin_length

def alignment_len_calc(blast_output, bin_length):
    vs_bins_contigs, aligned_length={}, {}
    standard_bin=str(blast_output).split('_vs_')[0].split('Filtrated_')[1]

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