Force sequence reading to produce lowercase sequences.

Adds two columns to the obiclean ratio csv file

pkg/obiformats/ecopcr_read.go

@@ -1,6 +1,7 @@
 package obiformats
 
 import (
+	"bytes"
 	"compress/gzip"
 	"encoding/csv"
 	"fmt"
@@ -67,7 +68,7 @@ func __read_ecopcr_bioseq__(file *__ecopcr_file__) (*obiseq.BioSequence, error)
 		comment = strings.TrimSpace(record[19])
 	}
 
-	bseq := obiseq.NewBioSequence(name, sequence, comment)
+	bseq := obiseq.NewBioSequence(name, bytes.ToLower(sequence), comment)
 	annotation := bseq.Annotations()
 
 	annotation["ac"] = name

pkg/obiformats/embl_read.go

@@ -128,7 +128,7 @@ func _ParseEmblFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
 				}
 			case line == "//":
 				sequence := obiseq.NewBioSequence(id,
-					seqBytes.Bytes(),
+					bytes.ToLower(seqBytes.Bytes()),
 					defBytes.String())
 
 				sequence.SetFeatures(featBytes.Bytes())

pkg/obiformats/fastseq_read.go

@@ -7,6 +7,7 @@ package obiformats
 import "C"
 
 import (
+	"bytes"
 	"fmt"
 	"os"
 	"unsafe"
@@ -38,7 +39,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 			comment = ""
 		}
 
-		rep := obiseq.NewBioSequence(name, sequence, comment)
+		rep := obiseq.NewBioSequence(name, bytes.ToLower(sequence), comment)
 
 		if s.qual.l > C.ulong(0) {
 			cquality := unsafe.Slice(s.qual.s, C.int(s.qual.l))

pkg/obiformats/genbank_read.go

@@ -84,7 +84,7 @@ func _ParseGenbankFile(input <-chan _FileChunk, out obiiter.IBioSequenceBatch) {
 
 			case line == "//":
 				sequence := obiseq.NewBioSequence(id,
-					seqBytes.Bytes(),
+					bytes.ToLower(seqBytes.Bytes()),
 					defBytes.String())
 				state = inHeader