def parse_netmhcpan28_stdout(
        stdout,
        prediction_method_name="netmhcpan",
        sequence_key_mapping=None):
    """
    # Affinity Threshold for Strong binding peptides  50.000',
    # Affinity Threshold for Weak binding peptides 500.000',
    # Rank Threshold for Strong binding peptides   0.500',
    # Rank Threshold for Weak binding peptides   2.000',
    ----------------------------------------------------------------------------
    pos  HLA  peptide  Identity 1-log50k(aff) Affinity(nM)    %Rank  BindLevel
    ----------------------------------------------------------------------------
      0  HLA-A*02:03    QQQQQYFPE   id0         0.024     38534.25   50.00
      1  HLA-A*02:03    QQQQYFPEI   id0         0.278      2461.53   15.00
      2  HLA-A*02:03    QQQYFPEIT   id0         0.078     21511.53   50.00
      3  HLA-A*02:03    QQYFPEITH   id0         0.041     32176.84   50.00
      4  HLA-A*02:03    QYFPEITHI   id0         0.085     19847.09   32.00
      5  HLA-A*02:03    YFPEITHII   id0         0.231      4123.85   15.00
      6  HLA-A*02:03    FPEITHIII   id0         0.060     26134.28   50.00
      7  HLA-A*02:03    PEITHIIIA   id0         0.034     34524.63   50.00
      8  HLA-A*02:03    EITHIIIAS   id0         0.076     21974.48   50.00
      9  HLA-A*02:03    ITHIIIASS   id0         0.170      7934.26   32.00
     10  HLA-A*02:03    THIIIASSS   id0         0.040     32361.18   50.00
     11  HLA-A*02:03    HIIIASSSL   id0         0.515       189.74    4.00 <= WB
    """
    check_stdout_error(stdout, "NetMHCpan-2.8")
    return parse_stdout(
        stdout=stdout,
        prediction_method_name=prediction_method_name,
        sequence_key_mapping=sequence_key_mapping,
        key_index=3,
        offset_index=0,
        peptide_index=2,
        allele_index=1,
        ic50_index=5,
        rank_index=6,
        log_ic50_index=4)
def parse_netmhcpan28_stdout(
        stdout,
        prediction_method_name="netmhcpan",
        sequence_key_mapping=None):
    """
    # Affinity Threshold for Strong binding peptides  50.000',
    # Affinity Threshold for Weak binding peptides 500.000',
    # Rank Threshold for Strong binding peptides   0.500',
    # Rank Threshold for Weak binding peptides   2.000',
    ----------------------------------------------------------------------------
    pos  HLA  peptide  Identity 1-log50k(aff) Affinity(nM)    %Rank  BindLevel
    ----------------------------------------------------------------------------
      0  HLA-A*02:03    QQQQQYFPE   id0         0.024     38534.25   50.00
      1  HLA-A*02:03    QQQQYFPEI   id0         0.278      2461.53   15.00
      2  HLA-A*02:03    QQQYFPEIT   id0         0.078     21511.53   50.00
      3  HLA-A*02:03    QQYFPEITH   id0         0.041     32176.84   50.00
      4  HLA-A*02:03    QYFPEITHI   id0         0.085     19847.09   32.00
      5  HLA-A*02:03    YFPEITHII   id0         0.231      4123.85   15.00
      6  HLA-A*02:03    FPEITHIII   id0         0.060     26134.28   50.00
      7  HLA-A*02:03    PEITHIIIA   id0         0.034     34524.63   50.00
      8  HLA-A*02:03    EITHIIIAS   id0         0.076     21974.48   50.00
      9  HLA-A*02:03    ITHIIIASS   id0         0.170      7934.26   32.00
     10  HLA-A*02:03    THIIIASSS   id0         0.040     32361.18   50.00
     11  HLA-A*02:03    HIIIASSSL   id0         0.515       189.74    4.00 <= WB
    """
    check_stdout_error(stdout, "NetMHCpan-2.8")
    return parse_stdout(
        stdout=stdout,
        prediction_method_name=prediction_method_name,
        sequence_key_mapping=sequence_key_mapping,
        key_index=3,
        offset_index=0,
        peptide_index=2,
        allele_index=1,
        ic50_index=5,
        rank_index=6,
        log_ic50_index=4)
def parse_netmhcpan28_stdout ( stdout , prediction_method_name = "netmhcpan" , sequence_key_mapping = None ) : check_stdout_error ( stdout , "NetMHCpan-2.8" ) return parse_stdout ( stdout = stdout , prediction_method_name = prediction_method_name , sequence_key_mapping = sequence_key_mapping , key_index = 3 , offset_index = 0 , peptide_index = 2 , allele_index = 1 , ic50_index = 5 , rank_index = 6 , log_ic50_index = 4 )
# Affinity Threshold for Strong binding peptides  50.000',
    # Affinity Threshold for Weak binding peptides 500.000',
    # Rank Threshold for Strong binding peptides   0.500',
    # Rank Threshold for Weak binding peptides   2.000',
    ----------------------------------------------------------------------------
    pos  HLA  peptide  Identity 1-log50k(aff) Affinity(nM)    %Rank  BindLevel
    ----------------------------------------------------------------------------
      0  HLA-A*02:03    QQQQQYFPE   id0         0.024     38534.25   50.00
      1  HLA-A*02:03    QQQQYFPEI   id0         0.278      2461.53   15.00
      2  HLA-A*02:03    QQQYFPEIT   id0         0.078     21511.53   50.00
      3  HLA-A*02:03    QQYFPEITH   id0         0.041     32176.84   50.00
      4  HLA-A*02:03    QYFPEITHI   id0         0.085     19847.09   32.00
      5  HLA-A*02:03    YFPEITHII   id0         0.231      4123.85   15.00
      6  HLA-A*02:03    FPEITHIII   id0         0.060     26134.28   50.00
      7  HLA-A*02:03    PEITHIIIA   id0         0.034     34524.63   50.00
      8  HLA-A*02:03    EITHIIIAS   id0         0.076     21974.48   50.00
      9  HLA-A*02:03    ITHIIIASS   id0         0.170      7934.26   32.00
     10  HLA-A*02:03    THIIIASSS   id0         0.040     32361.18   50.00
     11  HLA-A*02:03    HIIIASSSL   id0         0.515       189.74    4.00 <= WB
# Affinity Threshold for Strong binding peptides 50 . 000 # Affinity Threshold for Weak binding peptides 500 . 000 # Rank Threshold for Strong binding peptides 0 . 500 # Rank Threshold for Weak binding peptides 2 . 000 ---------------------------------------------------------------------------- pos HLA peptide Identity 1 - log50k ( aff ) Affinity ( nM ) %Rank BindLevel ---------------------------------------------------------------------------- 0 HLA - A * 02 : 03 QQQQQYFPE id0 0 . 024 38534 . 25 50 . 00 1 HLA - A * 02 : 03 QQQQYFPEI id0 0 . 278 2461 . 53 15 . 00 2 HLA - A * 02 : 03 QQQYFPEIT id0 0 . 078 21511 . 53 50 . 00 3 HLA - A * 02 : 03 QQYFPEITH id0 0 . 041 32176 . 84 50 . 00 4 HLA - A * 02 : 03 QYFPEITHI id0 0 . 085 19847 . 09 32 . 00 5 HLA - A * 02 : 03 YFPEITHII id0 0 . 231 4123 . 85 15 . 00 6 HLA - A * 02 : 03 FPEITHIII id0 0 . 060 26134 . 28 50 . 00 7 HLA - A * 02 : 03 PEITHIIIA id0 0 . 034 34524 . 63 50 . 00 8 HLA - A * 02 : 03 EITHIIIAS id0 0 . 076 21974 . 48 50 . 00 9 HLA - A * 02 : 03 ITHIIIASS id0 0 . 170 7934 . 26 32 . 00 10 HLA - A * 02 : 03 THIIIASSS id0 0 . 040 32361 . 18 50 . 00 11 HLA - A * 02 : 03 HIIIASSSL id0 0 . 515 189 . 74 4 . 00 < = WB