From b47988f15a1b2b2569d32a153118cfe7a358b82c Mon Sep 17 00:00:00 2001 From: Arjun Prasad Date: Fri, 10 Jan 2025 14:23:16 -0500 Subject: [PATCH] Approving tests for gpipe compatible version PD-5215 --- test/amrfinder_integration.expected | 14 +++++++------- test/amrfinder_integration2.expected | 14 +++++++------- test/basic.expected | 2 +- test/cases.expected | 2 +- test/virulence_ecoli.expected | 10 +++++----- 5 files changed, 21 insertions(+), 21 deletions(-) diff --git a/test/amrfinder_integration.expected b/test/amrfinder_integration.expected index 4e96184..5274b4a 100644 --- a/test/amrfinder_integration.expected +++ b/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 diff --git a/test/amrfinder_integration2.expected b/test/amrfinder_integration2.expected index 320ccc2..d8c69fc 100644 --- a/test/amrfinder_integration2.expected +++ b/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 diff --git a/test/basic.expected b/test/basic.expected index d5d165c..1bf953e 100644 --- a/test/basic.expected +++ b/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 diff --git a/test/cases.expected b/test/cases.expected index fc788ba..a9cd674 100644 --- a/test/cases.expected +++ b/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 diff --git a/test/virulence_ecoli.expected b/test/virulence_ecoli.expected index 48fa9cc..9563d52 100644 --- a/test/virulence_ecoli.expected +++ b/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