comparison graphprot_predict_wrapper.py @ 4:2d6de5b769e6 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit 15c382f71f1984aecff67ef9d268b992528996b2"

3:9a83a84a25a7

    c_in_fa = gplib.count_fasta_headers(args.in_fa)
    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)"

4:2d6de5b769e6

    c_in_fa = gplib.count_fasta_headers(args.in_fa)
    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)
    # Check for lowercase only sequences, which cause GP to crash.
    error_mess = "input sequences encountered containing "\
        "only lowercase characters or lowercase characters in between "\
        "uppercase characters. Please provide either all uppercase "\
        "sequences or sequences containing uppercase regions surrounded "\
        "by lowercase context regions for structure calculation (see "\
        "viewpoint concept in original GraphProt publication "\
        "for more details)"
    if args.ws_pred:
        bad_ids = gplib.check_seqs_dic_format(seqs_dic)
        assert not bad_ids, "%s" % (error_mess)

    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)"