Approving tests for gpipe compatible version

PD-5215

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			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			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			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			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			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			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			100.00	410	AAA16363.1, AAS07596.1	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	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	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

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			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			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			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			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			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			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			100.00	410	AAA16363.1, AAS07596.1	Shiga toxin stx2c	NA	NA	stxB2c::stxA2a
+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	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

test/basic.expected

@@ -4,5 +4,5 @@ partial_contig_end	stx2	PARTIAL_CONTIG_END	100.00	3	661	-	AAA16362.1	stxA2c	100.
 stx1a	stx1a	COMPLETE	100.00	218	1444	+	AAA98347.1	stxA1a	100.00	100.00	AAA71894.1	stxB1a	100.00	100.00
 stx2_fs	stx2	FRAMESHIFT	99.15	2165	3232	+	AAG01033.1	stxA2c	98.87	82.19	AAA16363.1	stxB2c	100.00	100.00
 stx2_novel	stx2	COMPLETE_NOVEL	99.76	216	1456	+	AAA19623.1	stxA2	99.69	100.00	AAA16363.1	stxB2c	100.00	100.00
-stx2_stop	stx2	INTERNAL_STOP		694	1653	+	AUM09788.1	stxA2h	91.25	100.00				
+stx2_stop	stx2	INTERNAL_STOP	NA	694	1653	+	AUM09788.1	stxA2h	91.25	100.00	NA	NA	NA	NA
 stx2c	stx2c	COMPLETE	100.00	1298	2538	-	AAS07596.1	stxA2	100.00	100.00	AAA16363.1	stxB2c	100.00	100.00

test/cases.expected

@@ -1,7 +1,7 @@
 #target_contig	stx_type	operon	identity	target_start	target_stop	target_strand	A_reference	A_reference_subtype	A_identity	A_coverage	B_reference	B_reference_subtype	B_identity	B_coverage
 A2l_a2e_equidistant	stx2l	COMPLETE	99.02	14780	16020	+	CAP17609.1	stxA2l	98.75	100.00	CAP17610.1	stxB2	100.00	100.00
 PD-4797_multirow	stx1	PARTIAL	100.00	1625	2852	-	AAA98347.1	stxA1a	100.00	100.00	AAA71894.1	stxB1a	100.00	86.67
-PD-4897_multirow_contig_end	stx2	PARTIAL_CONTIG_END		11	274	+					AAA16361.1	stxB2b	100.00	100.00
+PD-4897_multirow_contig_end	stx2	PARTIAL_CONTIG_END	NA	11	274	+	NA	NA	NA	NA	AAA16361.1	stxB2b	100.00	100.00
 PD-4898_A2a_B2l	stx2a	COMPLETE	100.00	718	1958	+	QZL10984.1	stxA2a	100.00	100.00	QZL10985.1	stxB2	100.00	100.00
 PD-5064_ambiguous_bases	stx2	AMBIGUOUS	99.27	333	1573	-	AAA19623.1	stxA2	99.38	100.00	AAM90978.1	stxB2a	98.89	100.00
 stx2d_better_stxB2k	stx2d	COMPLETE	100.00	3	1243	+	AAM22256.1	stxA2	100.00	100.00	MCW3229578.1	stxB2d	100.00	100.00

test/virulence_ecoli.expected

@@ -11,12 +11,12 @@ stx1a-O157-GPU96MM:7:AB035142	stx1a	COMPLETE	100.00	1	1227	+	AAA98347.1	stxA1a	1
 stx1a-O165-HI-2:14:AB048232	stx1a	COMPLETE	100.00	1	1227	+	AAA98347.1	stxA1a	100.00	100.00	AAA71894.1	stxB1a	100.00	100.00
 stx1a-O48-94C:11:Z36899	stx1a	COMPLETE	100.00	1	1227	+	CAA85366.1	stxA1a	100.00	100.00	AAA71894.1	stxB1a	100.00	100.00
 stx1a-ONT-HI-A:15:AB071620	stx1a	COMPLETE	99.51	1	1227	+	UIU88878.1	stxA1a	99.37	100.00	BAC10988.1	stxB1a	100.00	100.00
-stx1c-O174-DG131-3:20:Z36901	stx1	PARTIAL_CONTIG_END		1	948	+	CAA85370.1	stxA1c	100.00	100.00				
-stx1c-ONT-BCN26:19:DQ449666	stx1	PARTIAL_CONTIG_END		1	948	+	CAA85370.1	stxA1c	100.00	100.00				
-stx1c-ONT-HI-B:17:AB071622	stx1	PARTIAL_CONTIG_END		1	948	+	CAA85370.1	stxA1c	98.73	100.00				
-stx1c-ONT-HI-C:18:AB071624	stx1	PARTIAL_CONTIG_END		1	948	+	CAA85370.1	stxA1c	100.00	100.00				
+stx1c-O174-DG131-3:20:Z36901	stx1	PARTIAL_CONTIG_END	NA	1	948	+	CAA85370.1	stxA1c	100.00	100.00	NA	NA	NA	NA
+stx1c-ONT-BCN26:19:DQ449666	stx1	PARTIAL_CONTIG_END	NA	1	948	+	CAA85370.1	stxA1c	100.00	100.00	NA	NA	NA	NA
+stx1c-ONT-HI-B:17:AB071622	stx1	PARTIAL_CONTIG_END	NA	1	948	+	CAA85370.1	stxA1c	98.73	100.00	NA	NA	NA	NA
+stx1c-ONT-HI-C:18:AB071624	stx1	PARTIAL_CONTIG_END	NA	1	948	+	CAA85370.1	stxA1c	100.00	100.00	NA	NA	NA	NA
 stx1c-Out-HI-N:16:AB048237	stx1c	COMPLETE	100.00	1	1228	+	BAB83022.1	stxA1c	100.00	100.00	BAB83023.1	stxB1c	100.00	100.00
-stx1d-ONT-92-1251:21:AB050958	stx1	PARTIAL_CONTIG_END		1	948	+	AAO19475.1	stxA1d	100.00	100.00				
+stx1d-ONT-92-1251:21:AB050958	stx1	PARTIAL_CONTIG_END	NA	1	948	+	AAO19475.1	stxA1d	100.00	100.00	NA	NA	NA	NA
 stx1d-ONT-92-1252:22:AB050959	stx1d	COMPLETE	100.00	1	1227	+	AAO19475.1	stxA1d	100.00	100.00	AAO19476.1	stxB1d	100.00	100.00
 stx1d-ONT-AB8SF:23:AY986980	stx1d	COMPLETE	100.00	1	1227	+	AAO19475.1	stxA1d	100.00	100.00	AAO19476.1	stxB1d	100.00	100.00
 stx1d-ONT-MHI813:24:AY170851	stx1d	COMPLETE	100.00	1	1227	+	AAO19475.1	stxA1d	100.00	100.00	AAO19476.1	stxB1d	100.00	100.00