Merge branch 'master' of github.com:pjotrp/bioruby-rdf

pjotrp · Jul 26, 2014 · eccc96e · eccc96e
2 parents b089e83 + 47b72eb
commit eccc96e
Showing 1 changed file with 39 additions and 27 deletions.
diff --git a/lib/bio-rdf/extra/gwp.rb b/lib/bio-rdf/extra/gwp.rb
@@ -49,35 +49,47 @@ def Blast::parse(name,cluster,buf)
 
               r = {}
               r[:id] = name + '_' + cluster + '_' + gene
-              r[:cluster] = ('gwp:'+clusterid).to_sym
-              r['a'] = :blast_match
-              # r[:species] = species
-              # r[:source] = type
-              hfull = a[0]
-              if hfull !~ /_(DNA|CDS|EST)/
-                hfull = /\[(\S+_(CDS|DNA|EST))\]/.match(buf)[1]
+              r["gwp:cluster"] = ('gwp:'+clusterid).to_sym
+              species_match = (buf =~ /\S+_(CDS|DNA|EST)/)
+              if species_match 
+                r['a'] = :species_match
+              else
+                r['a'] = :refseq_match
               end
-              raise "Expected Ss_TYPE (e.g., Mi_CDS) instead of #{hfull} for "+buf if hfull !~ /\S\S_(CDS|DNA|EST)/
-              r[:homolog_species] = hfull.split.map { |w| w[0] }.join('')
-              r[:homolog_gene] = gene
-              hcluster = /(cluster\d+)/.match(descr)[1]
-              # $stderr.print hcluster,"\n"
-              raise "Missing cluster for "+buf if not hcluster
-              r[:homolog_cluster] = ('gwp:'+hfull+'_'+hcluster).to_sym
-              raise "Illegal hcluster <#{r[:homolog_cluster]}> for "+buf if r[:homolog_cluster] =~ /\s/
-              r[:descr] = descr
-              r[:e_value] = a[4].to_f
-              # p "HERE",descr
-              if descr =~ /(\[(\w+)_(DNA|CDS|EST)\])/ or hfull =~ /((\w+)_(DNA|CDS|EST))/
-                r[:homolog_species_full] = $1
-                r[:homolog_species] = $2
-                r[:homolog_source] = $3
+              hfull = a[0]
+              if species_match
+                if hfull !~ /_(DNA|CDS|EST)/
+                  hfull = /\[(\S+_(CDS|DNA|EST))\]/.match(buf)[1]
+                end
+                raise "Expected Ss_TYPE (e.g., Mi_CDS) instead of #{hfull} for "+buf if hfull !~ /\S\S_(CDS|DNA|EST)/
+                r[:homolog_species] = hfull.split.map { |w| w[0] }.join('')
+                r[:homolog_gene] = gene
+                hcluster = /(cluster\d+)/.match(descr)[1]
+                # $stderr.print hcluster,"\n"
+                raise "Missing cluster for "+buf if not hcluster
+                r[:homolog_cluster] = ('gwp:'+hfull+'_'+hcluster).to_sym
+                raise "Illegal hcluster <#{r[:homolog_cluster]}> for "+buf if r[:homolog_cluster] =~ /\s/
+                r[:descr] = descr
+                r[:e_value] = a[4].to_f
+                # p "HERE",descr
+                if descr =~ /(\[(\w+)_(DNA|CDS|EST)\])/ or hfull =~ /((\w+)_(DNA|CDS|EST))/
+                  r[:homolog_species_full] = $1
+                  r[:homolog_species] = $2
+                  r[:homolog_source] = $3
+                end
+                r[:homolog_species_full] = hfull.sub(/\[|\]/,"") # remove brackets
+                # assertions
+                raise "Error <#{r[:homolog_source]}> "+buf if not /(CDS|DNA|EST)$/.match(r[:homolog_source])
+                raise "Error <#{r[:homolog_species_full]}> "+buf if not /\w+_(CDS|DNA|EST)$/.match(r[:homolog_species_full])
+                raise "Error "+buf if not /\S\S_(CDS|DNA|EST)_cluster\d+$/.match(r[:homolog_cluster])
+              else
+                # refseq match
+                r[:homolog_species] = hfull.split.map { |w| w[0] }.join('')
+                r[:homolog_gene] = gene
+                r[:descr] = descr
+                r[:e_value] = a[4].to_f
+                r[:homolog_species_full] = hfull.sub(/\[|\]/,"") # remove brackets
               end
-              r[:homolog_species_full] = hfull.sub(/\[|\]/,"") # remove brackets
-              # assertions
-              raise "Error <#{r[:homolog_source]}> "+buf if not /(CDS|DNA|EST)$/.match(r[:homolog_source])
-              raise "Error <#{r[:homolog_species_full]}> "+buf if not /\w+_(CDS|DNA|EST)$/.match(r[:homolog_species_full])
-              raise "Error "+buf if not /\S\S_(CDS|DNA|EST)_cluster\d+$/.match(r[:homolog_cluster])
               # override species
               recs << r
             end