Mapping columns to residues

src/Pfam/pdb.jl

@@ -3,7 +3,16 @@
 
 const _regex_PDB_from_GS = r"PDB;\s+(\w+)\s+(\w);\s+\w+-\w+;" # i.e.: "PDB; 2VQC A; 4-73;\n"
 
-"Generates from a Pfam `msa` a `Dict{ASCIIString, Vector{Tuple{ASCIIString,ASCIIString}}}` with sequence ID as key and list of tuples of PDB code and chain as values."
+"""Generates from a Pfam `msa` a `Dict{ASCIIString, Vector{Tuple{ASCIIString,ASCIIString}}}`.
+Keys are sequence IDs and each value is a list of tuples containing PDB code and chain.
+
+```
+julia> getseq2pdb(msa)
+Dict{ASCIIString,Array{Tuple{ASCIIString,ASCIIString},1}} with 1 entry:
+  "F112_SSV1/3-112" => [("2VQC","A")]
+
+```
+"""
 function getseq2pdb(msa::AnnotatedMultipleSequenceAlignment)
     dict = Dict{ASCIIString, Vector{Tuple{ASCIIString,ASCIIString}}}()
     for (k, v) in getannotsequence(msa)
@@ -21,3 +30,37 @@ function getseq2pdb(msa::AnnotatedMultipleSequenceAlignment)
     end
     sizehint!(dict, length(dict))
 end
+
+# Mapping PDB/Pfam
+# ================
+
+function getcol2res(seqid::ASCIIString,
+    pdbid::ASCIIString,
+    chain::ASCIIString,
+    pfamid::ASCIIString,
+    msa::AnnotatedMultipleSequenceAlignment,
+    siftsfile::ASCIIString)
+    siftsmap = siftsmapping(siftsfile, dbPfam, pfamid, dbPDB, lowercase(pdbid), chain=chain, missings=false)
+    seqmap   = getsequencemapping(msa, seqid)
+    colmap   = getcolumnmapping(msa)
+    N = length(colmap)
+    m = Dict{Int,ASCIIString}()
+    sizehint!(m, N)
+    for i in 1:N
+      m[colmap[i]] = get(siftsmap, seqmap[i], "")
+    end
+    m
+end
+
+getcol2res(seqid::ASCIIString, pdbid::ASCIIString, chain::ASCIIString,
+           msa::AnnotatedMultipleSequenceAlignment, siftsfile::ASCIIString) = getcol2res(seqid, pdbid, chain,
+           ascii(split(getannotfile(msa, "AC"), '.')[1]), msa, siftsfile::ASCIIString)
+
+getcol2res(seqid::ASCIIString, pdbid::ASCIIString, chain::ASCIIString,
+           pfamid::ASCIIString, msa::AnnotatedMultipleSequenceAlignment) = getcol2res(seqid, pdbid, chain,
+           pfamid, msa, downloadsifts(pdbid))
+
+getcol2res(seqid::ASCIIString, pdbid::ASCIIString, chain::ASCIIString,
+           msa::AnnotatedMultipleSequenceAlignment) = getcol2res(seqid, pdbid, chain,
+           ascii(split(getannotfile(msa, "AC"), '.')[1]), msa)
+