comparison graphprot_predict_wrapper.py @ 2:4cebb3439e1a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit afbe0da7a518d6fc60ea066917b1e567c8c42391"

1:adcc4c457c3c

    assert c_in_fa, "input .fa file \"%s\" no headers found" %(args.in_fa)
    print("# input .fa sequences:   %i" %(c_in_fa))
    # Read in FASTA sequences to check for uppercase sequences.
    seqs_dic = gplib.read_fasta_into_dic(args.in_fa)
    c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic)
    assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept))"
    if not args.ws_pred:
        # Check for lowercase sequences.
        c_lc_nt = gplib.seqs_dic_count_lc_nts(seqs_dic)
        assert not c_lc_nt, "lowercase nucleotides not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept))"
    # Check .bed.
    if args.genomic_sites_bed:
        # An array of checks, marvelous.
        assert os.path.exists(args.genomic_sites_bed), "genomic .bed file \"%s\" not found" %(args.genomic_sites_bed)
        # Check .bed for content.

2:4cebb3439e1a

    assert c_in_fa, "input .fa file \"%s\" no headers found" %(args.in_fa)
    print("# input .fa sequences:   %i" %(c_in_fa))
    # Read in FASTA sequences to check for uppercase sequences.
    seqs_dic = gplib.read_fasta_into_dic(args.in_fa)
    c_uc_nt = gplib.seqs_dic_count_uc_nts(seqs_dic)
    assert c_uc_nt, "no uppercase nucleotides in input .fa sequences. Please change sequences to uppercase (keep in mind GraphProt only scores uppercase regions (according to its viewpoint concept)"
    if not args.ws_pred:
        # Check for lowercase sequences.
        c_lc_nt = gplib.seqs_dic_count_lc_nts(seqs_dic)
        assert not c_lc_nt, "lowercase nucleotides in input .fa not allowed in profile predictions, since GraphProt only scores uppercase regions (according to its viewpoint concept)"
    # Check .bed.
    if args.genomic_sites_bed:
        # An array of checks, marvelous.
        assert os.path.exists(args.genomic_sites_bed), "genomic .bed file \"%s\" not found" %(args.genomic_sites_bed)
        # Check .bed for content.