refactor data package

Author: pbnjay

data/data.go

@@ -0,0 +1,80 @@
+//
+//    Lollipops diagram generation framework for genetic variations.
+//    Copyright (C) 2015 Jeremy Jay <[email protected]>
+//
+//    This program is free software: you can redistribute it and/or modify
+//    it under the terms of the GNU General Public License as published by
+//    the Free Software Foundation, either version 3 of the License, or
+//    (at your option) any later version.
+//
+//    This program is distributed in the hope that it will be useful,
+//    but WITHOUT ANY WARRANTY; without even the implied warranty of
+//    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//    GNU General Public License for more details.
+//
+//    You should have received a copy of the GNU General Public License
+//    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+package data
+
+import (
+	"encoding/json"
+	"os"
+	"strings"
+)
+
+// MotifNames has human-readable names
+//  - mostly from http://pfam.xfam.org/help#tabview=tab9
+var MotifNames = map[string]string{
+	"disorder":       "Disordered region",
+	"low_complexity": "Low complexity region",
+	"sig_p":          "Signal peptide region",
+	"coiled_coil":    "Coiled-coil motif",
+	"transmembrane":  "Transmembrane region",
+}
+
+// GraphicFeature is a generic representation of various feature responses
+type GraphicFeature struct {
+	Color    string          `json:"colour"`
+	Text     string          `json:"text"`
+	Type     string          `json:"type"`
+	Start    json.Number     `json:"start"`
+	End      json.Number     `json:"end"`
+	Link     string          `json:"href"`
+	Metadata GraphicMetadata `json:"metadata"`
+}
+
+type GraphicMetadata struct {
+	Description string `json:"description"`
+	Identifier  string `json:"identifier"`
+}
+
+type GraphicResponse struct {
+	Length   json.Number      `json:"length"`
+	Metadata GraphicMetadata  `json:"metadata"`
+	Motifs   []GraphicFeature `json:"motifs"`
+	Regions  []GraphicFeature `json:"regions"`
+}
+
+func GetLocalGraphicData(filename string) (*GraphicResponse, error) {
+	f, err := os.Open(filename)
+	if err != nil {
+		return nil, err
+	}
+	pf := &GraphicResponse{}
+	err = json.NewDecoder(f).Decode(pf)
+	f.Close()
+	for i, x := range pf.Motifs {
+		if x.Link != "" && !strings.Contains(x.Link, "://") {
+			x.Link = "http://pfam.xfam.org" + x.Link
+			pf.Motifs[i] = x
+		}
+	}
+	for i, x := range pf.Regions {
+		if x.Link != "" && !strings.Contains(x.Link, "://") {
+			x.Link = "http://pfam.xfam.org" + x.Link
+			pf.Regions[i] = x
+		}
+	}
+	return pf, err
+}

data/fetch_uniprot.go

@@ -0,0 +1,71 @@
+//
+//    Lollipops diagram generation framework for genetic variations.
+//    Copyright (C) 2015 Jeremy Jay <[email protected]>
+//
+//    This program is free software: you can redistribute it and/or modify
+//    it under the terms of the GNU General Public License as published by
+//    the Free Software Foundation, either version 3 of the License, or
+//    (at your option) any later version.
+//
+//    This program is distributed in the hope that it will be useful,
+//    but WITHOUT ANY WARRANTY; without even the implied warranty of
+//    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+//    GNU General Public License for more details.
+//
+//    You should have received a copy of the GNU General Public License
+//    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+package data
+
+import (
+	"encoding/json"
+	"fmt"
+	"io/ioutil"
+	"net"
+	"net/http"
+	"os"
+)
+
+const PfamGraphicURL = "http://pfam.xfam.org/protein/%s/graphic"
+
+func GetPfamGraphicData(accession string) (*GraphicResponse, error) {
+	queryURL := fmt.Sprintf(PfamGraphicURL, accession)
+	resp, err := http.Get(queryURL)
+	if err != nil {
+		if err, ok := err.(net.Error); ok && err.Timeout() {
+			fmt.Fprintf(os.Stderr, "Unable to connect to Pfam. Check your internet connection or try again later.")
+			os.Exit(1)
+		}
+		return nil, err
+	}
+	respBytes, err := ioutil.ReadAll(resp.Body)
+	if err != nil {
+		return nil, err
+	}
+	if resp.StatusCode != 200 {
+		return nil, fmt.Errorf("pfam error: %s", resp.Status)
+	}
+
+	data := []GraphicResponse{}
+	err = json.Unmarshal(respBytes, &data)
+	//if err != nil {
+	//	return nil, err
+	//}
+	if len(data) != 1 {
+		return nil, fmt.Errorf("pfam returned invalid result")
+	}
+	r := data[0]
+	for i, x := range r.Motifs {
+		if x.Link != "" {
+			x.Link = "http://pfam.xfam.org" + x.Link
+			r.Motifs[i] = x
+		}
+	}
+	for i, x := range r.Regions {
+		if x.Link != "" {
+			x.Link = "http://pfam.xfam.org" + x.Link
+			r.Regions[i] = x
+		}
+	}
+	return &r, nil
+}