Alternative source of protein domains (#78)

* Add alternative source of of protein domains

* Defaults to UniProt accession for output file, if provided

* Do not return an error on 204

* Do not return an error on 204 (seq features)

README.md

@@ -79,6 +79,15 @@ the area is exponentially proportional to the count indicated. Examples:
   -dpi=300                set DPI (PNG output only)
 ```
 
+#### Domain sources:
+
+```
+  -D pfam                 set the source of protein domains
+                          pfam:     use Pfam domains only
+                          interpro: use representative domains 
+                                    from CDD, NCBIfam, Pfam, PROSITE, and SMART
+```
+
 ## Installation
 
 Head over to the [Releases](https://github.com/joiningdata/lollipops/releases) to

data/data.go

@@ -60,16 +60,18 @@ type InterProMetaData struct {
 	Accession string `json:"accession"`
 	Name      string `json:"name"`
 	Type      string `json:"type"`
+	Database  string `json:"source_database"`
 }
 
 type InterProExtraField struct {
 	ShortName string `json:"short_name"`
 }
 
 type InterProFragment struct {
-	Start      json.Number `json:"start"`
-	End        json.Number `json:"end"`
-	SeqFeature string      `json:"seq_feature"`
+	Start          json.Number `json:"start"`
+	End            json.Number `json:"end"`
+	SeqFeature     string      `json:"seq_feature"`
+	Representative bool        `json:"representative"`
 }
 
 type InterProLocation struct {

data/interpro.go

@@ -26,12 +26,20 @@ import (
 	"sort"
 )
 
-const PfamURL = "https://www.ebi.ac.uk/interpro/api/entry/pfam/protein/uniprot/%s/?extra_fields=short_name&page_size=100"
-const PfamLink = "https://www.ebi.ac.uk/interpro/entry/pfam/%s"
+const InterProURL = "https://www.ebi.ac.uk/interpro/api/entry/%s/protein/uniprot/%s/?extra_fields=short_name&page_size=100"
+const InterProLink = "https://www.ebi.ac.uk/interpro/entry/%s/%s"
 const SequenceFeaturesURL = "https://www.ebi.ac.uk/interpro/api/protein/UniProt/%s/?extra_features=true"
 
-func GetPfamProteinMatches(accession string) ([]GraphicFeature, error) {
-	queryURL := fmt.Sprintf(PfamURL, accession)
+func GetProteinMatches(database string, accession string) ([]GraphicFeature, error) {
+	var sourceDatabase string
+	filterDomains := false
+	if database == "interpro" {
+		sourceDatabase = "all"
+		filterDomains = true
+	} else {
+		sourceDatabase = "pfam"
+	}
+	queryURL := fmt.Sprintf(InterProURL, sourceDatabase, accession)
 	resp, err := httpGet(queryURL)
 	if err != nil {
 		if err, ok := err.(net.Error); ok && err.Timeout() {
@@ -44,7 +52,11 @@ func GetPfamProteinMatches(accession string) ([]GraphicFeature, error) {
 	if err != nil {
 		return nil, err
 	}
-	if resp.StatusCode != 200 {
+
+	var gs []GraphicFeature
+	if resp.StatusCode == 204 {
+		return gs, nil
+	} else if resp.StatusCode != 200 {
 		return nil, fmt.Errorf("InterPro error: %s", resp.Status)
 	}
 
@@ -54,23 +66,24 @@ func GetPfamProteinMatches(accession string) ([]GraphicFeature, error) {
 		return nil, err
 	}
 
-	var gs []GraphicFeature
 	for _, e := range r.Entries {
 		for _, m := range e.Matches {
 			for _, l := range m.Locations {
 				for _, f := range l.Fragments {
-					gf := GraphicFeature{
-						Text:  e.ExtraFields.ShortName,
-						Type:  e.Metadata.Type,
-						Start: f.Start,
-						End:   f.End,
-						Link:  fmt.Sprintf(PfamLink, e.Metadata.Accession),
-						Metadata: GraphicMetadata{
-							Description: e.Metadata.Name,
-							Identifier:  e.Metadata.Accession,
-						},
+					if !filterDomains || f.Representative {
+						gf := GraphicFeature{
+							Text:  e.ExtraFields.ShortName,
+							Type:  e.Metadata.Type,
+							Start: f.Start,
+							End:   f.End,
+							Link:  fmt.Sprintf(InterProLink, e.Metadata.Database, e.Metadata.Accession),
+							Metadata: GraphicMetadata{
+								Description: e.Metadata.Name,
+								Identifier:  e.Metadata.Accession,
+							},
+						}
+						gs = append(gs, gf)
 					}
-					gs = append(gs, gf)
 				}
 			}
 		}
@@ -115,7 +128,11 @@ func GetSequenceFeatures(accession string) ([]GraphicFeature, error) {
 	if err != nil {
 		return nil, err
 	}
-	if resp.StatusCode != 200 {
+
+	var gs []GraphicFeature
+	if resp.StatusCode == 204 {
+		return gs, nil
+	} else if resp.StatusCode != 200 {
 		return nil, fmt.Errorf("InterPro error: %s", resp.Status)
 	}
 
@@ -126,7 +143,6 @@ func GetSequenceFeatures(accession string) ([]GraphicFeature, error) {
 		return nil, fmt.Errorf("InterPro error: %s", err)
 	}
 
-	var gs []GraphicFeature
 	featureDatabases := map[string]string{
 		"signalp_e":  "sig_p",
 		"signalp_g+": "sig_p",

main.go

@@ -36,6 +36,7 @@ import (
 var (
 	queryDB = flag.String("Q", "GENENAME", "Uniprot query database when -U not used")
 	uniprot = flag.String("U", "", "Uniprot accession instead of GENE_SYMBOL")
+	domains = flag.String("D", "pfam", "source of protein domains (defaults to pfam)")
 	output  = flag.String("o", "", "output SVG/PNG file (default GENE_SYMBOL.svg)")
 	width   = flag.Int("w", 0, "output width (default automatic fit labels)")
 	dpi     = flag.Float64("dpi", 72, "output DPI for PNG rasterization")
@@ -92,6 +93,11 @@ Protein changes:
 
   (N.B. color must come before count in tags)
 
+Protein domains:
+  -D pfam				  set the source of protein domains
+						    "pfam"     = use domains from Pfam
+							"interpro" = use domains from CDD, NCBIfam, Pfam, PROSITE, and SMART
+
 Diagram generation options:
   -legend                 draw a legend for colored regions
   -syn-color="#0000ff"    color to use for synonymous mutation markers
@@ -123,6 +129,7 @@ Output options:
 	drawing.DefaultSettings.SynonymousColor = *synColor
 	drawing.DefaultSettings.MutationColor = *mutColor
 	drawing.DefaultSettings.GraphicWidth = float64(*width)
+	domainsDatabase := strings.ToLower(*domains)
 
 	if *fontPath == "" {
 		err := drawing.LoadDefaultFont()
@@ -142,6 +149,11 @@ Output options:
 		}
 	}
 
+	if domainsDatabase != "pfam" && domainsDatabase != "interpro" {
+		fmt.Fprintln(os.Stderr, "ERROR: Invalid source of protein domains (available: InterPro, Pfam).")
+		os.Exit(1)
+	}
+
 	var err error
 	varStart := 0
 	acc := ""
@@ -168,6 +180,9 @@ Output options:
 
 	if *uniprot != "" {
 		acc = *uniprot
+		if geneSymbol == "" {
+			geneSymbol = acc
+		}
 	}
 
 	if flag.NArg() == 0 && *uniprot == "" {
@@ -195,7 +210,7 @@ Press Enter/Ctrl-C to quit.`)
 
 	d.Length = json.Number(fmt.Sprint(length))
 
-	regions, err := data.GetPfamProteinMatches(acc)
+	regions, err := data.GetProteinMatches(domainsDatabase, acc)
 	if err != nil {
 		fmt.Fprintln(os.Stderr, err)
 		os.Exit(1)