Updated tests to include AMBIGUOUS and na->NA

PD-5064 and PD-5076
ncbi · Aug 5, 2024 · 926d9fe · 926d9fe
1 parent 62b3d0c
commit 926d9fe
Show file tree

Hide file tree

Showing 4 changed files with 18 additions and 14 deletions.
diff --git a/test/amrfinder_integration.expected b/test/amrfinder_integration.expected
@@ -1,8 +1,8 @@
 #Protein identifier	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	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			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
diff --git a/test/amrfinder_integration2.expected b/test/amrfinder_integration2.expected
@@ -1,8 +1,8 @@
 #Protein identifier	Contig id	Start	Stop	Strand	Element symbol	Element name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	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			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
diff --git a/test/cases.expected b/test/cases.expected
@@ -3,4 +3,5 @@ A2l_a2e_equidistant	stx2l	COMPLETE	99.02	14780	16020	+	CAP17609.1	stxA2l	98.75	1
 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-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
diff --git a/test/cases.fa b/test/cases.fa
@@ -433,3 +433,6 @@ GATTGTGCAAAAGGTAAAATTGAGTTCTCTAAGTATAATGAGAATGATACATTCACAGTAAAAGTGGCCG
 GGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGCGCACAGTTAACAGGAATGAC
 GGTAACAATCAAATCAAATACCTGTGCGTCAGGTTCAGGATTTGCTGAAGTGCAGTTTAATTAATATCAG
 AAGCATTGCTGGTTTCGT
+
+>PD-5064_ambiguous_bases >contig204_denovo_2312W63683
+nnnnnnctggaaatatgcccatacgggcgaaaataacagaatcattcagataaaaagcccctccggagaggggctgacactgcgtatctgtatcatcatgtacatggtgccgggtgcctcccggtgagttcagtccggtgtccctgaacccgcgtatctcgctccaggttgtcgtcagagatgacaccttatacaccagtcgcccctccgcacagggggattcaccatgcgaatttttttaacgaatgctcagtctgacaggcaactgtcaactgactgaattgtgacacagattacacttgttacccacataccacgaatcaggttatgcctcagtcattattaaactgcacttcagcaaatccggagcctgattcacaggtactggatttgattgtgacagtcattcctgtcaactgagcactttgcagtaacggttgcagattccagcgactggtccagtaytctttcccgtcaaccttcactgtraatgtrtcatyctcattatacttggaaaactcaattttacctttagcrcaatccgccgccattgcattaacagaaactaatgcaaataaaaccgccataaacatcttcttcatacttaactcctttatttacccgttgtatataaaaactgtgactttctgttcagaaacgctgcagctgtattactttcccataatgtattgtttatttttataacgggcctgtcgccagttatctgacattctggttgactmtcttcattcacggcgcgaacagaacgcgccccctgatgatgrcaattcagtataacggccacagtrcccagtatcgcygatatattattaaaggatattctccccactctgacaccatcctctccccgatactccggaagcacattgctgattcgcccccagttcagagtgaggtccacgtctcccggcgtcatcgtatacacaggagcagtttcagacagtgcctgacgaaattctctctgtatctgcctgaagcgtaaggcttctgcygtgacagtgacaaaacgcagaactgctctggatgcatctctggtcattgtattaccactgaactccattaacgccagatatgatgaaaccagtgagtgacgactgatttgcattccggaacgttccagcgctgcgacacgttgcagagtggtataactgctgtccgttgtcatggaaaccgttgtcacaycgggcactgatatatgtgtaaaatctgaaaaacggtagaaagtatttgttgccgtattaacgaacccggccacatataaattattttgctcaataatcagacgaagatggtcaaaacgcgcctgatagacatcaagccctcgtatatccacagcaaaataactgcccggyggggtgtggttaataacagacaccgatgtggtcccctgagatatatgttcaagaggggtcgatatctctgtccgtatactatttaacgaagakacataactttgttgagtcgaaaagtctatcgtaaattcccgggaataggataccgaagaaaarcccagtaacaggcacagtacccatttaaataatatacacttcatatacaggtgttccttttggctgaagtaatcagcaccagacccggcgcagatataaaaaaggcccgcaaaagcgagcckggwaaataartrtggcgcgttgtactggattcgaaccagtgaccgattgcttagaaggcaattgctctgtcckgctgagctaacaacgc