Support new sequence file formats and improve error handling

Add support for .gbff and .gbff.gz file extensions in sequence reader.

Update the logic to return an error instead of using NilIBioSequence when no sequence files are found, improving the error handling and user feedback.

obitests/obitools/obisuperkmer/test.sh

@@ -4,8 +4,8 @@
 # Here give the name of the test serie
 #
 
-TEST_NAME=obisuperkmer
+TEST_NAME=obik-super
-CMD=obisuperkmer
+CMD=obik
 
 ######
 #
@@ -16,7 +16,7 @@ TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
 OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
 export PATH="${OBITOOLS_DIR}:${PATH}"
 
-MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
+MCMD="OBIk-super"
 
 TMPDIR="$(mktemp -d)"
 ntest=0
@@ -65,31 +65,10 @@ log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
 ####
 #### Below are the tests
 ####
-#### Before each test :
-####  - increment the variable ntest
-####
-#### Run the command as the condition of an if / then /else
-####  - The command must return 0 on success
-####  - The command must return an exit code different from 0 on failure
-####  - The datafiles are stored in the same directory than the test script
-####  - The test script directory is stored in the TEST_DIR variable
-####  - If result files have to be produced they must be stored
-####    in the temporary directory (TMPDIR variable)
-####
-#### then clause is executed on success of the command
-####  - Write a success message using the log function
-####  - increment the variable success
-####
-#### else clause is executed on failure of the command
-####  - Write a failure message using the log function
-####  - increment the variable failed
-####
 ######################################################################
 
-
-
 ((ntest++))
-if $CMD -h > "${TMPDIR}/help.txt" 2>&1
+if $CMD super -h > "${TMPDIR}/help.txt" 2>&1
 then
     log "$MCMD: printing help OK"
     ((success++))
@@ -100,7 +79,7 @@ fi
 
 # Test 1: Basic super k-mer extraction with default parameters
 ((ntest++))
-if obisuperkmer "${TEST_DIR}/test_sequences.fasta" \
+if $CMD super "${TEST_DIR}/test_sequences.fasta" \
     > "${TMPDIR}/output_default.fasta" 2>&1
 then
     log "$MCMD: basic extraction with default parameters OK"
@@ -148,7 +127,7 @@ fi
 
 # Test 5: Extract super k-mers with custom k and m parameters
 ((ntest++))
-if obisuperkmer -k 15 -m 7 "${TEST_DIR}/test_sequences.fasta" \
+if $CMD super -k 15 -m 7 "${TEST_DIR}/test_sequences.fasta" \
     > "${TMPDIR}/output_k15_m7.fasta" 2>&1
 then
     log "$MCMD: extraction with custom k=15, m=7 OK"
@@ -172,7 +151,7 @@ fi
 
 # Test 7: Test with different output format (FASTA output explicitly)
 ((ntest++))
-if obisuperkmer --fasta-output -k 21 -m 11 \
+if $CMD super --fasta-output -k 21 -m 11 \
     "${TEST_DIR}/test_sequences.fasta" \
     > "${TMPDIR}/output_fasta.fasta" 2>&1
 then
@@ -209,7 +188,7 @@ fi
 
 # Test 10: Test with output file option
 ((ntest++))
-if obisuperkmer -o "${TMPDIR}/output_file.fasta" \
+if $CMD super -o "${TMPDIR}/output_file.fasta" \
     "${TEST_DIR}/test_sequences.fasta" 2>&1
 then
     log "$MCMD: output to file with -o option OK"

pkg/obioptions/version.go

@@ -3,7 +3,7 @@ package obioptions
 // Version is automatically updated by the Makefile from version.txt
 // The patch number (third digit) is incremented on each push to the repository
 
-var _Version = "Release 4.4.12"
+var _Version = "Release 4.4.14"
 
 // Version returns the version of the obitools package.
 //

pkg/obitools/obiconvert/sequence_reader.go

@@ -68,6 +68,8 @@ func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
 						strings.HasSuffix(path, "seq.gz") ||
 						strings.HasSuffix(path, "gb") ||
 						strings.HasSuffix(path, "gb.gz") ||
+						strings.HasSuffix(path, "gbff") ||
+						strings.HasSuffix(path, "gbff.gz") ||
 						strings.HasSuffix(path, "dat") ||
 						strings.HasSuffix(path, "dat.gz") ||
 						strings.HasSuffix(path, "ecopcr") ||
@@ -204,7 +206,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 					iterator = iterator.PairTo(ip)
 				}
 			} else {
-				iterator = obiiter.NilIBioSequence
+				return obiiter.NilIBioSequence, fmt.Errorf("no sequence files found in the provided paths")
 			}
 		}
 

version.txt

@@ -1 +1 @@
-4.4.12
+4.4.14