join_spades_fastg_by_blast.py 文件源码

def check_db():
    global options
    if options.reference_fa_base:
        time0 = time.time()
        ref_fasta = read_fasta(options.reference_fa_base)
        if len(ref_fasta[0]) > 1:
            options.reference_fa_base += '.1st.fasta'
            write_fasta(out_dir=options.reference_fa_base, matrix=[[ref_fasta[0][0]], [ref_fasta[1][0]], ref_fasta[2]], overwrite=True)
            sys.stdout.write('\nWarning: multi-seqs in reference file, only use the 1st sequence.')
        elif len(ref_fasta[0]) == 0:
            sys.stdout.write('\nError: illegal reference file!')
            exit()
        try:
            # python2
            makedb_result = subprocess.getstatusoutput('makeblastdb -dbtype nucl -in '+options.reference_fa_base+' -out '+options.reference_fa_base+'.index')
        except AttributeError:
            # python3
            makedb_result = commands.getstatusoutput('makeblastdb -dbtype nucl -in ' + options.reference_fa_base + ' -out ' + options.reference_fa_base + '.index')
        if 'Error' in str(makedb_result[1]) or 'error' in str(makedb_result[1]) or '?????????' in str(makedb_result[1]):
            os.system('makeblastdb -dbtype nucl -in '+options.reference_fa_base+' -out '+options.reference_fa_base+'.index')
            if not os.path.exists(options.reference_fa_base+'.index.nhr'):
                sys.stdout.write('Blast terminated with following info:\n'+str(makedb_result[1]))
                exit()
        in_index = options.reference_fa_base+'.index'
        sys.stdout.write('\nMaking BLAST db cost '+str(time.time()-time0))
    else:
        sys.stdout.write('\nError: No reference input!')
        exit()
    return in_index