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* Update URL and function to fetch UniProt accession * Add function to fetch protein length * Fetch Pfam hits and protein features from InterPro * Get domain/motif featues from InterPro API * Update images * Remove unused functions/variables * Update README * Remove deleted options
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| // | ||
| // 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" | ||
| "os" | ||
| "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 SequenceFeaturesURL = "https://www.ebi.ac.uk/interpro/api/protein/UniProt/%s/?extra_features=true" | ||
|
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||
| func GetPfamProteinMatches(accession string) ([]GraphicFeature, error) { | ||
| queryURL := fmt.Sprintf(PfamURL, accession) | ||
| resp, err := httpGet(queryURL) | ||
| if err != nil { | ||
| if err, ok := err.(net.Error); ok && err.Timeout() { | ||
| fmt.Fprintf(os.Stderr, "Unable to connect to InterPro. 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("InterPro error: %s", resp.Status) | ||
| } | ||
|
|
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| r := InterProEntryResponse{} | ||
| err = json.Unmarshal(respBytes, &r) | ||
| if err != nil { | ||
| 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, | ||
| }, | ||
| } | ||
| gs = append(gs, gf) | ||
| } | ||
| } | ||
| } | ||
| } | ||
|
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| sort.Slice(gs, func(i, j int) bool { | ||
| start1, _ := gs[i].Start.Int64() | ||
| start2, _ := gs[j].Start.Int64() | ||
|
|
||
| if start1 != start2 { | ||
| return start1 < start2 | ||
| } | ||
|
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| end1, _ := gs[i].End.Int64() | ||
| end2, _ := gs[j].End.Int64() | ||
| return end1 < end2 | ||
| }) | ||
|
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| hexColors := [14]string{ | ||
| "#2DCF00", "#FF5353", "#5B5BFF", "#EBD61D", "#BA21E0", "#FF9C42", "#FF7DFF", | ||
| "#B9264F", "#BABA21", "#C48484", "#1F88A7", "#CAFEB8", "#4A9586", "#CEB86C", | ||
| } | ||
|
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||
| for i := 0; i < len(gs); i++ { | ||
| gs[i].Color = hexColors[i%len(hexColors)] | ||
| } | ||
|
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| return gs, nil | ||
| } | ||
|
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| func GetSequenceFeatures(accession string) ([]GraphicFeature, error) { | ||
| queryURL := fmt.Sprintf(SequenceFeaturesURL, accession) | ||
| resp, err := httpGet(queryURL) | ||
| if err != nil { | ||
| if err, ok := err.(net.Error); ok && err.Timeout() { | ||
| fmt.Fprintf(os.Stderr, "Unable to connect to InterPro. 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("InterPro error: %s", resp.Status) | ||
| } | ||
|
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| data := make(map[string]InterProFeature) | ||
|
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| err = json.Unmarshal(respBytes, &data) | ||
| if err != nil { | ||
| return nil, fmt.Errorf("InterPro error: %s", err) | ||
| } | ||
|
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| var gs []GraphicFeature | ||
| featureDatabases := map[string]string{ | ||
| "signalp_e": "sig_p", | ||
| "signalp_g+": "sig_p", | ||
| "signalp_g-": "sig_p", | ||
| "coils": "coiled_coil", | ||
| "tmhmm": "transmembrane", | ||
| } | ||
| for _, feature := range data { | ||
| if feature.Database == "mobidblt" { | ||
| for _, location := range feature.Locations { | ||
| for _, fragment := range location.Fragments { | ||
| if fragment.SeqFeature == "Consensus Disorder Prediction" { | ||
| gf := GraphicFeature{ | ||
| Color: "#CCCCCC", | ||
| Type: "disorder", | ||
| Start: fragment.Start, | ||
| End: fragment.End, | ||
| } | ||
| gs = append(gs, gf) | ||
| } | ||
| } | ||
| } | ||
|
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| continue | ||
| } | ||
|
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| for feature_db, feature_type := range featureDatabases { | ||
| if feature.Database == feature_db { | ||
|
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| for _, location := range feature.Locations { | ||
| for _, fragment := range location.Fragments { | ||
| gf := GraphicFeature{ | ||
| Color: "#CCCCCC", | ||
| Type: feature_type, | ||
| Start: fragment.Start, | ||
| End: fragment.End, | ||
| } | ||
| gs = append(gs, gf) | ||
| } | ||
| } | ||
|
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| break | ||
| } | ||
| } | ||
| } | ||
|
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| return gs, nil | ||
| } |
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