Deal with None in SIFTS

[diegozea]

Example:

shell> zgrep "None" /home/diego/SIFTS/3cx5.sifts.xml.gz | head -3
          <crossRefDb dbSource="NCBI" dbCoordSys="UniProt" dbAccessionId="10090" dbResNum="None" dbResName="None"/>
          <crossRefDb dbSource="InterPro" dbCoordSys="UniProt" dbAccessionId="IPR013783" dbResNum="None" dbResName="None" dbEvidence="G3DSA:2.60.40.10"/>
          <crossRefDb dbSource="InterPro" dbCoordSys="UniProt" dbAccessionId="IPR007110" dbResNum="None" dbResName="None" dbEvidence="PS50835"/>

This causes:

ArgumentError("invalid base 10 digit 'N' in \"None\"")

[diegozea]

This error is solved in MITOS 2.0, where "None" values are stored as "".

        <residue dbSource="PDBe" dbCoordSys="PDBe" dbResNum="107" dbResName="LYS">
          <crossRefDb dbSource="PDB" dbCoordSys="PDBresnum" dbAccessionId="3cx5" dbResNum="107" dbResName="LYS" dbChainId="V"/>
          <crossRefDb dbSource="CATH" dbCoordSys="PDBresnum" dbAccessionId="2.60.40.10" dbResNum="107" dbResName="LYS" dbChainId="V"/>
          <crossRefDb dbSource="SCOP" dbCoordSys="PDBresnum" dbAccessionId="157107" dbResNum="107" dbResName="LYS" dbChainId="V"/>
          <crossRefDb dbSource="NCBI" dbCoordSys="UniProt" dbAccessionId="10090" dbResNum="None" dbResName="None"/>
          <crossRefDb dbSource="InterPro" dbCoordSys="UniProt" dbAccessionId="IPR013783" dbResNum="None" dbResName="None" dbEvidence="G3DSA:2.60.40.10"/>
          <crossRefDb dbSource="InterPro" dbCoordSys="UniProt" dbAccessionId="IPR003599" dbResNum="None" dbResName="None" dbEvidence="SM00409"/>
          <residueDetail dbSource="PDBe" property="codeSecondaryStructure">T</residueDetail>
          <residueDetail dbSource="PDBe" property="nameSecondaryStructure">loop</residueDetail>
        </residue>

julia> file = downloadsifts("3cx5");

julia> res = read(file, SIFTSXML);

julia> r = filter(r -> r.PDBe.number == "107" && r.PDBe.name == "LYS" && get(get(r, dbPDB, :chain)) == "V", res)[1]
SIFTSResidue with secondary structure code (sscode): "T" and name (ssname): "loop"
  PDBe:
    number: 107
    name: LYS
  NCBI (Nullable) :
    id: 10090
    number: 
    name: 
  PDB (Nullable) :
    id: 3cx5
    number: 107
    name: LYS
    chain: V
  SCOP (Nullable) :
    id: 157107
    number: 107
    name: LYS
    chain: V
  CATH (Nullable) :
    id: 2.60.40.10
    number: 107
    name: LYS
    chain: V
  InterPro: MIToS.SIFTS.dbInterPro[MIToS.SIFTS.dbInterPro("IPR013783", "", "", "G3DSA:2.60.40.10"), MIToS.SIFTS.dbInterPro("IPR003599", "", "", "SM00409")]


julia> get(r, dbNCBI)
Nullable{MIToS.SIFTS.dbNCBI}(MIToS.SIFTS.dbNCBI("10090", "", ""))