Simplified names in parsers (#168)

* Simplified names

* Fixed up tests

Co-authored-by: Tim <[email protected]>

parsers/rebase/rebase.go

@@ -166,8 +166,8 @@ type Enzyme struct {
 	References             string   `json:"references"`
 }
 
-// ParseRebase parses the Rebase database into a map of enzymes
-func ParseRebase(file []byte) map[string]Enzyme {
+// Parse parses the Rebase database into a map of enzymes
+func Parse(file []byte) map[string]Enzyme {
 	// Setup some variables
 	var enzyme Enzyme
 	enzymeMap := make(map[string]Enzyme)
@@ -244,18 +244,18 @@ func ParseRebase(file []byte) map[string]Enzyme {
 	return enzymeMap
 }
 
-// ReadRebase returns an enzymeMap from a Rebase data dump
-func ReadRebase(path string) (map[string]Enzyme, error) {
+// Read returns an enzymeMap from a Rebase data dump
+func Read(path string) (map[string]Enzyme, error) {
 	file, err := ioutil.ReadFile(path)
 	if err != nil {
 		return map[string]Enzyme{}, err
 	}
-	enzymeMap := ParseRebase(file)
+	enzymeMap := Parse(file)
 	return enzymeMap, nil
 }
 
-// ExportRebase returns a json file of the Rebase database
-func ExportRebase(enzymeMap map[string]Enzyme) []byte {
+// Export returns a json file of the Rebase database
+func Export(enzymeMap map[string]Enzyme) []byte {
 	jsonRebase, _ := json.Marshal(enzymeMap)
 	return jsonRebase
 }

parsers/rebase/rebase_test.go

@@ -5,21 +5,21 @@ import (
 	"testing"
 )
 
-func ExampleReadRebase() {
-	enzymeMap, _ := ReadRebase("data/rebase_test.txt")
+func ExampleRead() {
+	enzymeMap, _ := Read("data/rebase_test.txt")
 	fmt.Println(enzymeMap["AarI"].MicroOrganism)
 	// Output: Arthrobacter aurescens SS2-322
 }
 
-func ExampleExportRebase() {
-	enzymeMap, _ := ReadRebase("data/rebase_test.txt")
-	enzymeJson := ExportRebase(enzymeMap)
+func ExampleExport() {
+	enzymeMap, _ := Read("data/rebase_test.txt")
+	enzymeJson := Export(enzymeMap)
 	fmt.Println(string(enzymeJson)[:100])
 	// Output: {"AaaI":{"name":"AaaI","isoschizomers":["XmaIII","BseX3I","BsoDI","BstZI","EagI","EclXI","Eco52I","S
 }
 
-func TestReadRebase(t *testing.T) {
-	_, err := ReadRebase("data/FAKE.txt")
+func TestRead(t *testing.T) {
+	_, err := Read("data/FAKE.txt")
 	if err == nil {
 		t.Errorf("Failed to error on fake file")
 	}

parsers/uniprot/uniprot.go

@@ -23,10 +23,10 @@ xml.go from uniprot.xsd
 
 Each protein in Uniprot is known as an "Entry" (as defined in xml.go).
 
-The function ParseUniprot stream-reads Uniprot into an Entry channel, from which
-you can use the entries however you want. ReadUniprot simplifies reading gzipped
+The function Parse stream-reads Uniprot into an Entry channel, from which
+you can use the entries however you want. Read simplifies reading gzipped
 files from a disk into an Entry channel, essentially just preparing the reader for
-ParseUniprot.
+Parse.
 
 Cheers,
 Keoni
@@ -37,10 +37,10 @@ Keoni
 
 ******************************************************************************/
 
-// ReadUniprot reads a gzipped Uniprot XML dump. Failing to open the XML dump
+// Read reads a gzipped Uniprot XML dump. Failing to open the XML dump
 // gives a single error, while errors encountered while decoding the XML dump
 // are added to the errors channel.
-func ReadUniprot(path string) (chan Entry, chan error, error) {
+func Read(path string) (chan Entry, chan error, error) {
 	entries := make(chan Entry, 100) // if you don't have a buffered channel, nothing will be read in loops on the channel.
 	decoderErrors := make(chan error, 100)
 	xmlFile, err := os.Open(path)
@@ -51,12 +51,12 @@ func ReadUniprot(path string) (chan Entry, chan error, error) {
 	if err != nil {
 		return entries, decoderErrors, err
 	}
-	go ParseUniprot(unzippedBytes, entries, decoderErrors)
+	go Parse(unzippedBytes, entries, decoderErrors)
 	return entries, decoderErrors, nil
 }
 
-// ParseUniprot parses Uniprot entries into a channel.
-func ParseUniprot(r io.Reader, entries chan<- Entry, errors chan<- error) {
+// Parse parses Uniprot entries into a channel.
+func Parse(r io.Reader, entries chan<- Entry, errors chan<- error) {
 	decoder := xml.NewDecoder(r)
 	for {
 		decoderToken, err := decoder.Token()

parsers/uniprot/uniprot_test.go

@@ -7,8 +7,8 @@ import (
 	"testing"
 )
 
-func ExampleReadUniprot() {
-	entries, _, _ := ReadUniprot("data/uniprot_sprot_mini.xml.gz")
+func ExampleRead() {
+	entries, _, _ := Read("data/uniprot_sprot_mini.xml.gz")
 
 	var entry Entry
 	for singleEntry := range entries {
@@ -18,13 +18,14 @@ func ExampleReadUniprot() {
 	// Output: O55723
 }
 
-func ExampleParseUniprot() {
+func ExampleParse() {
 	xmlFile, _ := os.Open("data/uniprot_sprot_mini.xml.gz")
 	unzippedBytes, _ := gzip.NewReader(xmlFile)
 
 	entries := make(chan Entry, 100) // if you don't have a buffered channel, nothing will be read in loops on the channel.
 	decoderErrors := make(chan error, 100)
-	go ParseUniprot(unzippedBytes, entries, decoderErrors)
+
+	go Parse(unzippedBytes, entries, decoderErrors)
 
 	var entry Entry
 	for singleEntry := range entries {
@@ -34,18 +35,18 @@ func ExampleParseUniprot() {
 	// Output: O55723
 }
 
-func TestReadUniprot(t *testing.T) {
-	_, _, err := ReadUniprot("data/test")
+func TestRead(t *testing.T) {
+	_, _, err := Read("data/test")
 	if err == nil {
 		t.Errorf("Failed to fail on non-gzipped file")
 	}
 
-	_, _, err = ReadUniprot("data/FAKE")
+	_, _, err = Read("data/FAKE")
 	if err == nil {
 		t.Errorf("Failed to fail on empty file")
 	}
 
-	_, errors, err := ReadUniprot("data/uniprot_sprot_mini.xml.gz")
+	_, errors, err := Read("data/uniprot_sprot_mini.xml.gz")
 	if err != nil {
 		t.Errorf("Failed on real file with error: %v", err)
 	}