From 926d9fe638217943fef37a26cafcfe3bf6128da5 Mon Sep 17 00:00:00 2001 From: Arjun Prasad Date: Mon, 5 Aug 2024 16:25:29 -0400 Subject: [PATCH] Updated tests to include AMBIGUOUS and na->NA PD-5064 and PD-5076 --- test/amrfinder_integration.expected | 14 +++++++------- test/amrfinder_integration2.expected | 14 +++++++------- test/cases.expected | 1 + test/cases.fa | 3 +++ 4 files changed, 18 insertions(+), 14 deletions(-) diff --git a/test/amrfinder_integration.expected b/test/amrfinder_integration.expected index 30a1982..0ddbf18 100644 --- 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 index 3d401de..9660200 100644 --- 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 index e39bc6d..fc788ba 100644 --- 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 index f6e5820..cca7ae9 100644 --- a/test/cases.fa +++ b/test/cases.fa @@ -433,3 +433,6 @@ GATTGTGCAAAAGGTAAAATTGAGTTCTCTAAGTATAATGAGAATGATACATTCACAGTAAAAGTGGCCG GGAAAGAGTACTGGACTAACCGCTGGAATCTGCAACCGCTACTGCAAAGCGCACAGTTAACAGGAATGAC GGTAACAATCAAATCAAATACCTGTGCGTCAGGTTCAGGATTTGCTGAAGTGCAGTTTAATTAATATCAG AAGCATTGCTGGTTTCGT + +>PD-5064_ambiguous_bases >contig204_denovo_2312W63683 +nnnnnnctggaaatatgcccatacgggcgaaaataacagaatcattcagataaaaagcccctccggagaggggctgacactgcgtatctgtatcatcatgtacatggtgccgggtgcctcccggtgagttcagtccggtgtccctgaacccgcgtatctcgctccaggttgtcgtcagagatgacaccttatacaccagtcgcccctccgcacagggggattcaccatgcgaatttttttaacgaatgctcagtctgacaggcaactgtcaactgactgaattgtgacacagattacacttgttacccacataccacgaatcaggttatgcctcagtcattattaaactgcacttcagcaaatccggagcctgattcacaggtactggatttgattgtgacagtcattcctgtcaactgagcactttgcagtaacggttgcagattccagcgactggtccagtaytctttcccgtcaaccttcactgtraatgtrtcatyctcattatacttggaaaactcaattttacctttagcrcaatccgccgccattgcattaacagaaactaatgcaaataaaaccgccataaacatcttcttcatacttaactcctttatttacccgttgtatataaaaactgtgactttctgttcagaaacgctgcagctgtattactttcccataatgtattgtttatttttataacgggcctgtcgccagttatctgacattctggttgactmtcttcattcacggcgcgaacagaacgcgccccctgatgatgrcaattcagtataacggccacagtrcccagtatcgcygatatattattaaaggatattctccccactctgacaccatcctctccccgatactccggaagcacattgctgattcgcccccagttcagagtgaggtccacgtctcccggcgtcatcgtatacacaggagcagtttcagacagtgcctgacgaaattctctctgtatctgcctgaagcgtaaggcttctgcygtgacagtgacaaaacgcagaactgctctggatgcatctctggtcattgtattaccactgaactccattaacgccagatatgatgaaaccagtgagtgacgactgatttgcattccggaacgttccagcgctgcgacacgttgcagagtggtataactgctgtccgttgtcatggaaaccgttgtcacaycgggcactgatatatgtgtaaaatctgaaaaacggtagaaagtatttgttgccgtattaacgaacccggccacatataaattattttgctcaataatcagacgaagatggtcaaaacgcgcctgatagacatcaagccctcgtatatccacagcaaaataactgcccggyggggtgtggttaataacagacaccgatgtggtcccctgagatatatgttcaagaggggtcgatatctctgtccgtatactatttaacgaagakacataactttgttgagtcgaaaagtctatcgtaaattcccgggaataggataccgaagaaaarcccagtaacaggcacagtacccatttaaataatatacacttcatatacaggtgttccttttggctgaagtaatcagcaccagacccggcgcagatataaaaaaggcccgcaaaagcgagcckggwaaataartrtggcgcgttgtactggattcgaaccagtgaccgattgcttagaaggcaattgctctgtcckgctgagctaacaacgc