Add Closest reference name back in

Also some cosmetic changes to test_stxtyper.sh

stxtyper.cpp

@@ -32,6 +32,7 @@
 * Dependencies: NCBI BLAST, gunzip (optional)
 *
 * Release changes:
+*  1.0.31 01/14/2025 PD-5215  "re-enable reporting Name of closest sequence"
 *  1.0.30 01/14/2025 PD-5215  "Closest reference accession" field should have two accessions separated by "," for two-subunit operons
 *  1.0.29 01/10/2025 PD-6215  "Name of closest sequence": na for two-subunit operons
 *  1.0.28 01/10/2025 PD-5215  blanks fields -> na; "Closest reference accession" is na for two-subunit operons
@@ -605,7 +606,7 @@ struct Operon
              << refIdentity       //17 "% Identity to reference sequence"
              << alignmentLen      //18 "Alignment length"
              << refAccessions     //19 "Accession of closest sequence"
-             << na /*"Shiga toxin " + genesymbol*/ //20 "Name of closest sequence"
+             << "Shiga toxin " + genesymbol //20 "Name of closest sequence"
              << na                //21 "HMM id"
              << na                //22 "HMM description"
              ;

test/amrfinder_integration.expected

@@ -1,8 +1,8 @@
 #Protein id	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Type	Subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference	% Identity to reference	Alignment length	Closest reference accession	Closest reference name	HMM accession	HMM description
-NA	partial	27	1048	+	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL	1022	NA	NA	99.41	337	NA	Shiga toxin stx2	NA	NA
-NA	partial_contig_end	3	661	-	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL_CONTIG_END	659	NA	NA	100.00	216	NA	Shiga toxin stx2	NA	NA
-NA	stx1a	218	1444	+	stx1a_operon	stx1a operon	plus	VIRULENCE	STX_TYPE	STX1	STX1A	COMPLETE	1227	NA	NA	100.00	406	NA	Shiga toxin stx1a	NA	NA
-NA	stx2_fs	2165	3232	+	stx2_operon	stx2 operon with frameshift	plus	VIRULENCE	STX_TYPE	STX2	STX2	FRAMESHIFT	1068	NA	NA	99.15	355	NA	Shiga toxin stx2c	NA	NA
-NA	stx2_novel	216	1456	+	stx2_operon	Novel stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	COMPLETE_NOVEL	1241	NA	NA	99.76	410	NA	Shiga toxin stx2c	NA	NA
+NA	partial	27	1048	+	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL	1022	NA	NA	99.41	337	AAA16362.1,AAS07607.1	Shiga toxin stx2	NA	NA
+NA	partial_contig_end	3	661	-	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL_CONTIG_END	659	NA	NA	100.00	216	AAM70046.1,AAA16362.1	Shiga toxin stx2	NA	NA
+NA	stx1a	218	1444	+	stx1a_operon	stx1a operon	plus	VIRULENCE	STX_TYPE	STX1	STX1A	COMPLETE	1227	NA	NA	100.00	406	AAA98347.1,AAA71894.1	Shiga toxin stx1a	NA	NA
+NA	stx2_fs	2165	3232	+	stx2_operon	stx2 operon with frameshift	plus	VIRULENCE	STX_TYPE	STX2	STX2	FRAMESHIFT	1068	NA	NA	99.15	355	AAG01033.1,AAA16363.1	Shiga toxin stx2c	NA	NA
+NA	stx2_novel	216	1456	+	stx2_operon	Novel stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	COMPLETE_NOVEL	1241	NA	NA	99.76	410	AAA19623.1,AAA16363.1	Shiga toxin stx2c	NA	NA
 NA	stx2_stop	694	1653	+	stx2_operon	stx2 operon with internal stop	plus	VIRULENCE	STX_TYPE	STX2	STX2	INTERNAL_STOP	960	NA	NA	91.25	320	AUM09788.1	Shiga toxin stx2h subunit A	NA	NA
-NA	stx2c	1298	2538	-	stx2c_operon	stx2c operon	plus	VIRULENCE	STX_TYPE	STX2	STX2C	COMPLETE	1241	NA	NA	100.00	410	NA	Shiga toxin stx2c	NA	NA
+NA	stx2c	1298	2538	-	stx2c_operon	stx2c operon	plus	VIRULENCE	STX_TYPE	STX2	STX2C	COMPLETE	1241	NA	NA	100.00	410	AAA16363.1,AAS07596.1	Shiga toxin stx2c	NA	NA

test/amrfinder_integration2.expected

@@ -1,8 +1,8 @@
 #Protein id	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Type	Subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference	% Identity to reference	Alignment length	Closest reference accession	Closest reference name	HMM accession	HMM description	Hierarchy node
-NA	partial	27	1048	+	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL	1022	NA	NA	99.41	337	NA	Shiga toxin stx2	NA	NA	stxA2c::stxB2a
-NA	partial_contig_end	3	661	-	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL_CONTIG_END	659	NA	NA	100.00	216	NA	Shiga toxin stx2	NA	NA	stxB2a::stxA2c
-NA	stx1a	218	1444	+	stx1a_operon	stx1a operon	plus	VIRULENCE	STX_TYPE	STX1	STX1A	COMPLETE	1227	NA	NA	100.00	406	NA	Shiga toxin stx1a	NA	NA	stxA1a::stxB1a
-NA	stx2_fs	2165	3232	+	stx2_operon	stx2 operon with frameshift	plus	VIRULENCE	STX_TYPE	STX2	STX2	FRAMESHIFT	1068	NA	NA	99.15	355	NA	Shiga toxin stx2c	NA	NA	stxA2c::stxB2c
-NA	stx2_novel	216	1456	+	stx2_operon	Novel stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	COMPLETE_NOVEL	1241	NA	NA	99.76	410	NA	Shiga toxin stx2c	NA	NA	stxA2c::stxB2c
+NA	partial	27	1048	+	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL	1022	NA	NA	99.41	337	AAA16362.1,AAS07607.1	Shiga toxin stx2	NA	NA	stxA2c::stxB2a
+NA	partial_contig_end	3	661	-	stx2_operon	Partial stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	PARTIAL_CONTIG_END	659	NA	NA	100.00	216	AAM70046.1,AAA16362.1	Shiga toxin stx2	NA	NA	stxB2a::stxA2c
+NA	stx1a	218	1444	+	stx1a_operon	stx1a operon	plus	VIRULENCE	STX_TYPE	STX1	STX1A	COMPLETE	1227	NA	NA	100.00	406	AAA98347.1,AAA71894.1	Shiga toxin stx1a	NA	NA	stxA1a::stxB1a
+NA	stx2_fs	2165	3232	+	stx2_operon	stx2 operon with frameshift	plus	VIRULENCE	STX_TYPE	STX2	STX2	FRAMESHIFT	1068	NA	NA	99.15	355	AAG01033.1,AAA16363.1	Shiga toxin stx2c	NA	NA	stxA2c::stxB2c
+NA	stx2_novel	216	1456	+	stx2_operon	Novel stx2 operon	plus	VIRULENCE	STX_TYPE	STX2	STX2	COMPLETE_NOVEL	1241	NA	NA	99.76	410	AAA19623.1,AAA16363.1	Shiga toxin stx2c	NA	NA	stxA2c::stxB2c
 NA	stx2_stop	694	1653	+	stx2_operon	stx2 operon with internal stop	plus	VIRULENCE	STX_TYPE	STX2	STX2	INTERNAL_STOP	960	NA	NA	91.25	320	AUM09788.1	Shiga toxin stx2h subunit A	NA	NA	stxA2h
-NA	stx2c	1298	2538	-	stx2c_operon	stx2c operon	plus	VIRULENCE	STX_TYPE	STX2	STX2C	COMPLETE	1241	NA	NA	100.00	410	NA	Shiga toxin stx2c	NA	NA	stxB2c::stxA2a
+NA	stx2c	1298	2538	-	stx2c_operon	stx2c operon	plus	VIRULENCE	STX_TYPE	STX2	STX2C	COMPLETE	1241	NA	NA	100.00	410	AAA16363.1,AAS07596.1	Shiga toxin stx2c	NA	NA	stxB2c::stxA2a

test_stxtyper.sh

@@ -38,10 +38,10 @@ FAILURES=0
 TESTS=0
 TEST_TEXT=''
 
-echo "TERM=$TERM"
+# echo "TERM=$TERM"
 
 # some color macros
-if [ "$TERM" == "" ] || [ "$TERM" == "dumb" ]
+if [ "$TERM" == "" ] || [ "$TERM" == "dumb" ] || [ ! -t 1 ]
 then
     green='' # no colors
     red=''
@@ -62,7 +62,7 @@ function test_input_file {
     then
         echo "${red}not ok: $STXTYPER returned a non-zero exit value indicating a failure of the software${reset}"
         echo "#  $STXTYPER $options -n test/$test_base.fa > test/$test_base.got"
-        TEST_TEXT="$TEST_TEXT"$'\n'"Failed $test_base"
+        TEST_TEXT="$TEST_TEXT"$'\n'"${red}Failed $test_base${reset}"
         return 1
     else
         if ! diff -q "test/$test_base.expected" "test/$test_base.got"
@@ -73,7 +73,7 @@ function test_input_file {
             diff "test/$test_base.expected" "test/$test_base.got"
             echo "#  To approve run:"
             echo "#     mv test/$test_base.got test/$test_base.expected "
-            TEST_TEXT="$TEST_TEXT"$'\n'"Failed $test_base"
+            TEST_TEXT="$TEST_TEXT"$'\n'"${red}Failed $test_base${reset}"
             return 1
         else
             echo "${green}ok:${reset} test/$test_base.fa"
@@ -95,7 +95,7 @@ then
     diff "test/basic.nuc_out.expected" "test/basic.nuc_out.got"
     echo "#  To approve run:"
     echo "#     mv test/basic.nuc_out.got test/basic.nuc_out.expected "
-    TEST_TEXT="$TEST_TEXT"$'\n'"Failed basic --nucleotide_output test"
+    TEST_TEXT="$TEST_TEXT"$'\n'"${red}Failed basic --nucleotide_output test${reset}"
     FAILURES=$(( $FAILURES + 1 ))
 else 
     echo "${green}ok:${reset} --nucleotide_output test/basic.nuc_out.got options worked"

version.txt

@@ -1 +1 @@
-1.0.30
+1.0.31