Add missing regions to SARS-CoV-2, for #589.

cfe-lab · Jul 30, 2020 · 2115dc8 · 2115dc8
1 parent 5a9dee8
commit 2115dc8
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Showing 5 changed files with 163 additions and 52 deletions.
diff --git a/micall/project_scoring.json b/micall/project_scoring.json
@@ -4,17 +4,6 @@
       "max_variants": 0,
       "description": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)",
       "regions": [
-        {
-          "coordinate_region": "SARS-CoV-2-orf1ab",
-          "coordinate_region_length": 7096,
-          "key_positions": [],
-          "min_coverage1": 10,
-          "min_coverage2": 50,
-          "min_coverage3": 100,
-          "seed_region_names": [
-            "SARS-CoV-2-seed"
-          ]
-        },
         {
           "coordinate_region": "SARS-CoV-2-S",
           "coordinate_region_length": 1273,

diff --git a/micall/projects.json b/micall/projects.json
@@ -3,12 +3,6 @@
     "SARS-CoV-2": {
       "max_variants": 0,
       "regions": [
-        {
-          "coordinate_region": "SARS-CoV-2-orf1ab",
-          "seed_region_names": [
-            "SARS-CoV-2-seed"
-          ]
-        },
         {
           "coordinate_region": "SARS-CoV-2-S",
           "seed_region_names": [
@@ -4933,7 +4927,91 @@
     }
   },
   "regions": {
-    "SARS-CoV-2-orf1ab": {
+    "SARS-CoV-2-3'UTR": {
+      "is_nucleotide": true,
+      "reference": [
+        "CAATCTTTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCC",
+        "ACGCGGAGTACGATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCT",
+        "AATGTGTAAAATTAATTTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGA",
+        "CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-5'UTR": {
+      "is_nucleotide": true,
+      "reference": [
+        "ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCT",
+        "CTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTAT",
+        "AATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTT",
+        "ACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAG",
+        "GTAAG"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-1": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACGAACA"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-2": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACGAACTT"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-3": {
+      "is_nucleotide": true,
+      "reference": [
+        "GCACAAGCTGATGAGTACGAACTT"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-4": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCC"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-5": {
+      "is_nucleotide": true,
+      "reference": [
+        "GTGACAACAG"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-6": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACGAAC"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-7": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACGAAC"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-8": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACGAACAAACTAAA"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-TRS-B-9": {
+      "is_nucleotide": true,
+      "reference": [
+        "ACTCATGCAGACCACACAAGGCAG"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-ORF1a": {
       "is_nucleotide": false,
       "reference": [
         "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLE",
@@ -5003,7 +5081,14 @@
         "TACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKV",
         "KYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQP",
         "ITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTT",
-        "CANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCGVSAARLTPCGTGTST",
+        "CANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSADAQSFLNRVCGV"
+      ],
+      "seed_group": null
+    },
+    "SARS-CoV-2-ORF1b": {
+      "is_nucleotide": false,
+      "reference": [
+        "RVCGVSAARLTPCGTGTST",
         "DVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDC",
         "PAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFN",
         "KKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFI",
@@ -5045,7 +5130,7 @@
         "TLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFTYICGFI",
         "QQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFLIGCNYLGKPREQIDGY",
         "VMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNR",
-        "VVISSDVLVNN"
+        "VVISSDVLVNN*"
       ],
       "seed_group": null
     },
@@ -5071,7 +5156,7 @@
         "DFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVT",
         "QRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDIS",
         "GINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLC",
-        "CMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT"
+        "CMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*"
       ],
       "seed_group": null
     },
@@ -5082,15 +5167,15 @@
         "KKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLC",
         "WKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWES",
         "GVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVM",
-        "EPIYDEPTTTTSVPL"
+        "EPIYDEPTTTTSVPL*"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-E": {
       "is_nucleotide": false,
       "reference": [
         "MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNL",
-        "NSSRVPDLLV"
+        "NSSRVPDLLV*"
       ],
       "seed_group": null
     },
@@ -5100,37 +5185,37 @@
         "MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACF",
         "VLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILT",
         "RPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAA",
-        "YSRYRIGNYKLNTDHSSSSDNIALLVQ"
+        "YSRYRIGNYKLNTDHSSSSDNIALLVQ*"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-ORF6": {
       "is_nucleotide": false,
       "reference": [
-        "MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEID"
+        "MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEID*"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-ORF7a": {
       "is_nucleotide": false,
       "reference": [
         "MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFST",
-        "QFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE"
+        "QFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFITLCFTLKRKTE*"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-ORF7b": {
       "is_nucleotide": false,
       "reference": [
-        "MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA"
+        "MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA*"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-ORF8": {
       "is_nucleotide": false,
       "reference": [
         "MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIELC",
-        "VDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDFI"
+        "VDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRCSFYEDFLEYHDVRVVLDFI*"
       ],
       "seed_group": null
     },
@@ -5143,14 +5228,14 @@
         "NSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQ",
         "KRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVT",
         "PSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQ",
-        "TVTLLPAADLDDFSKQLQQSMSSADSTQA"
+        "TVTLLPAADLDDFSKQLQQSMSSADSTQA*"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-ORF10": {
       "is_nucleotide": false,
       "reference": [
-        "MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT"
+        "MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT*"
       ],
       "seed_group": null
     },
@@ -5159,7 +5244,7 @@
       "reference": [
         "MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLE",
         "QPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNGNKG",
-        "AGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNG"
+        "AGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG"
       ],
       "seed_group": null
     },
@@ -5175,7 +5260,7 @@
         "DGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKLKPVLDWLEEKF",
         "KEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLVNKFLALCADSIIIGGAKL",
         "KALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEIIFLEGETLPTEVLTEEVVLKTGDLQP",
-        "LEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKG"
+        "LEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEKYCALAPNMMVTNNTFTLKGG"
       ],
       "seed_group": null
     },
@@ -5211,7 +5296,7 @@
         "GQKTYERHSLSHFVNLDNLRANNTKGSLPINVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLD",
         "QALVSDVGDSAEVAVKMFDAYVNTFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAAR",
         "QGFVDSDVETKDVVECLKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQV",
-        "AKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKG"
+        "AKSHNIALIWNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGG"
       ],
       "seed_group": null
     },
@@ -5225,7 +5310,7 @@
         "VNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCLAYYFMRFRRAFGEYSHVVAFNTLLFLMS",
         "FTVLCLTPVYSFLPGVYSVIYLYLTFYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHF",
         "YWFFSNYLKRRVVFNGVSFSTFEEAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFS",
-        "GAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVL"
+        "GAMDTTSYREAACCHLAKALNDFSNSGSDVLYQPPQTSITSAVLQ"
       ],
       "seed_group": null
     },
@@ -5236,7 +5321,7 @@
         "FLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAM",
         "RPNFTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAG",
         "TDTTITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIA",
-        "VLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTF"
+        "VLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQ"
       ],
       "seed_group": null
     },
@@ -5247,15 +5332,15 @@
         "FLCLFLLPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTART",
         "VYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLARGIVFMCVE",
         "YCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYLVSTQEFRYMNSQGLL",
-        "PPKNSIDAFKLNIKLLGVGGKPCIKVATV"
+        "PPKNSIDAFKLNIKLLGVGGKPCIKVATVQ"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-nsp7": {
       "is_nucleotide": false,
       "reference": [
         "SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGA",
-        "VDINKLCEEMLDNRATL"
+        "VDINKLCEEMLDNRATLQ"
       ],
       "seed_group": null
     },
@@ -5265,15 +5350,15 @@
         "AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQ",
         "AMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMV",
         "VIPDYNTYKNTCDGTTFTYASALWEIQQVVDADSKIVQLSEISMDNSPNLAWPLIVTALRANSAV",
-        "KL"
+        "KLQ"
       ],
       "seed_group": null
     },
     "SARS-CoV-2-nsp9": {
       "is_nucleotide": false,
       "reference": [
         "NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTI",
-        "YTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRL"
+        "YTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ"
       ],
       "seed_group": null
     },
@@ -5282,7 +5367,7 @@
       "reference": [
         "AGNATEVPANSTVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQ",
         "ESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSC",
-        "DQLREPML"
+        "DQLREPMLQ"
       ],
       "seed_group": null
     },
@@ -5303,7 +5388,7 @@
         "ADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIK",
         "NFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVD",
         "DIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTND",
-        "NTSRYWEPEFYEAMYTPHTVL"
+        "NTSRYWEPEFYEAMYTPHTVLQ"
       ],
       "seed_group": null
     },
@@ -5319,7 +5404,7 @@
         "LRAKHYVYIGDPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSAL",
         "VYDNKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNA",
         "VASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSDRDLYDKL",
-        "QFTSLEIPRRNVATL"
+        "QFTSLEIPRRNVATLQ"
       ],
       "seed_group": null
     },
@@ -5334,7 +5419,7 @@
         "FPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVD",
         "RYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESH",
         "GKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLW",
-        "NTFTRL"
+        "NTFTRLQ"
       ],
       "seed_group": null
     },
@@ -5346,7 +5431,7 @@
         "VDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFT",
         "QSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKE",
         "SPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYT",
-        "EISFMLWCKDGHVETFYPKL"
+        "EISFMLWCKDGHVETFYPKLQ"
       ],
       "seed_group": null
     },
@@ -5357,7 +5442,7 @@
         "RVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISD",
         "MYDPKTKNVTKENDSKEGFFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVT",
         "NVNASSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVM",
-        "SLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVN"
+        "SLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN"
       ],
       "seed_group": null
     },

diff --git a/micall/tests/microtest/README.md b/micall/tests/microtest/README.md
@@ -51,3 +51,6 @@ The scenarios that each file tests are:
   details.
 * 2170A-HCV - a mixed infection of HCV-1a and HCV-2a, each about 3000 bases
   long, with enough coverage to assemble two contigs.
+* 2180A-HIV - random reads from GP120 that can be assembled. See the
+  `make_sample.py` script for details.
+* 2190A-SARS - amplicon from the start of nsp12.