| Previous changeset 22:386b975927dd (2021-04-09) Next changeset 24:6d529bf13e2e (2021-04-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb" |
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modified:
hyphy_sm19.xml macros.xml |
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added:
scripts/annotator.bf scripts/strike-ambigs.bf test-data/annotate-in1.fa.gz test-data/annotate-in1.nhx test-data/annotate-out1-clade.nhx test-data/annotate-out1-full.nhx test-data/annotate-out1-int.nhx test-data/cfel-out1.json test-data/conv-in1.fa test-data/conv-out1.nhx test-data/fubar-in1.fa.gz test-data/strike-ambigs-in1.fa test-data/strike-ambigs-in2.fa test-data/strike-ambigs-out1.fa test-data/strike-ambigs-out2.fa |
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removed:
test-data/fubar-in1.fa |
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| diff -r 386b975927dd -r f1261376fd4b hyphy_sm19.xml --- a/hyphy_sm19.xml Fri Apr 09 21:49:31 2021 +0000 +++ b/hyphy_sm19.xml Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -13,10 +13,11 @@ '${partition.regex}' #end for $replicates - --output '$sm19_output' + --output '$sm19_output' ; + @CATCH_ERROR@ ]]></command> <inputs> - <param name="input_file" type="data" format="nhx" label="Input tree"/> + <param name="input_file" type="data" format="nhx,newick,nexus" label="Input tree"/> <repeat name="partitions" min="2" max="50" title="Partitions"> <param name="label" type="text" label="Partition label"/> <param name="regex" type="text" label="Regular expression"> |
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| diff -r 386b975927dd -r f1261376fd4b macros.xml --- a/macros.xml Fri Apr 09 21:49:31 2021 +0000 +++ b/macros.xml Tue Apr 20 10:27:10 2021 +0000 |
| [ |
| @@ -1,8 +1,8 @@ <?xml version="1.0"?> <macros> <xml name="inputs"> - <param name="input_file" type="data" format="fasta" label="Input FASTA file"/> - <param name="input_nhx" type="data" format="nhx" label="Input newick file"/> + <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> + <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> </xml> <xml name="substitution"> <param name="model" type="select" label="Substitution model"> @@ -107,7 +107,7 @@ <yield/> </citations> </xml> - <token name="@VERSION@">2.5.30</token> + <token name="@VERSION@">2.5.31</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">hyphy</requirement> @@ -115,10 +115,14 @@ </requirements> </xml> <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> - <token name="@CATCH_MPIERR@"><![CDATA[ + <token name="@CATCH_ERROR@"><![CDATA[ EC=\$? ; if [ \$EC -ne 0 ] ; then - cat errors.log.mpinode0 >&2 ; + if [ -f errors.log.mpinode0 ] ; then + cat errors.log.mpinode0 >&2 ; + else + cat errors.log >&2 ; + fi ; fi ; exit \$EC ]]></token> @@ -129,4 +133,12 @@ <token name="@HYPHY_INVOCATION@"><![CDATA[ @HYPHY_ENVIRONMENT@ hyphy LIBPATH=\$HYPHY_LIB ]]></token> + <token name="@SYMLINK_FILES@"><![CDATA[ + ln -s '$input_file' input.$input_file.extension && + ln -s '$@operation@_output' input.${input_file.extension}.@OPERATION@.json && + #set $input_file = 'input.%s' % $input_file.extension + #if $input_nhx: + ln -s '$input_nhx' input.nhx && + #end if + ]]></token> </macros> |
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| diff -r 386b975927dd -r f1261376fd4b scripts/annotator.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/annotator.bf Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -0,0 +1,102 @@ +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/convenience/regexp.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); + +tags = { + "^Node" : "Internal" +}; + + + + +tree = trees.LoadAnnotatedTopology (TRUE); +ts = tree[^"terms.trees.newick_with_lengths"]; +root_node = io.PromptUserForString ("Root on this node"); + + + +Topology T = ts; +ts = RerootTree (T, root_node); +ACCEPT_ROOTED_TREES = FALSE; +Topology T = ts; +ACCEPT_ROOTED_TREES = TRUE; +Topology TR = ts; + + +NORMALIZE_SEQUENCE_NAMES = FALSE; +SetDialogPrompt ("File with the sequences to label as the in-clade"); +DataSet query = ReadDataFile (PROMPT_FOR_FILE); +GetString (seqNames,query,-1); + +label = io.PromptUserForString ("Use this label"); + + +for (s;in;seqNames) { + tags [s && 6] = label; +} + +reg_exp = Rows (tags); + + +node_labels = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labels[l] = tag; + } + } +} + +node_labelsR = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labelsR[l] = tag; + } + } +} + + +leaf_labels = node_labels; +node_labelsF = node_labels; +node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]); +node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]); +node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]); + +output_to = io.PromptUserForString ("Write output to this prefix"); + +fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels); +fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE)); +fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE)); +fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE)); + +function relabel_and_annotate (node_name) { + _label = ""; + if (node_labels / node_name && leaf_labels / node_name == FALSE) { + _label = "{" + node_labels[node_name] + "}"; + } + return node_name + _label; +} + +function relabel_and_annotate_full (node_name) { + _label = ""; + if (node_labelsR / node_name) { + _label = "{" + node_labelsR[node_name] + "}"; + } + return node_name + _label; +} |
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| diff -r 386b975927dd -r f1261376fd4b scripts/strike-ambigs.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/strike-ambigs.bf Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -0,0 +1,83 @@ +RequireVersion ("2.5.20"); + +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/UtilityFunctions.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); +LoadFunctionLibrary ("libv3/convenience/math.bf"); + + + +filter.analysis_description = {terms.io.info : + " + Read an alignment of coding sequences and replace any ambiguous codons with ---. Write results to a new file in FASTA format, and report changed sequences to stdout + ", + terms.io.version : "0.1", + terms.io.reference : "TBD", + terms.io.authors : "Sergei L Kosakovsky Pond", + terms.io.contact : "spond@temple.edu", + terms.io.requirements : "An MSA" + }; + + +io.DisplayAnalysisBanner (filter.analysis_description); + +utility.SetEnvVariable ("NORMALIZE_SEQUENCE_NAMES", FALSE); + +KeywordArgument ("code", "Which genetic code should be used", "Universal"); +KeywordArgument ("alignment", "An in-frame codon alignment in one of the formats supported by HyPhy"); + +filter.in = alignments.PromptForGeneticCodeAndAlignment ("filter.dataset", "filter.input"); + +KeywordArgument ("output", ".fasta for compressed data", None); +filter.out = io.PromptUserForFilePath(".fasta for filtered data"); +fprintf (filter.out, CLEAR_FILE, KEEP_OPEN); + +GetDataInfo (filter.site_patterns, filter.input); + +filter.patter2site = {}; + + +for (i,j,v; in; filter.site_patterns) { + index = i+j; + if (filter.patter2site / v == FALSE ) { + filter.patter2site [v] = {}; + } + filter.patter2site [v] + index; +} + +GET_DATA_INFO_RETURNS_ONLY_THE_INDEX = TRUE; +COUNT_GAPS_IN_FREQUENCIES = FALSE; +filter.unique_patterns = utility.Array1D (filter.input.site_freqs); + +for (seq = 0; seq < filter.input.species; seq += 1) { + io.ReportProgressBar ("filter","Processing sequence " + (1+seq)); + codons = {1, filter.input.sites}; + codons [0] = ""; + GetString (seq_name, filter.input, seq); + GetDataInfo (seq_chars, filter.input, seq); + + filter.ambigs = 0; + + for (pattern = 0; pattern < filter.unique_patterns; pattern += 1) { + GetDataInfo (pattern_info, filter.input, seq, pattern); + if (pattern_info >= 0) { + codon_start = (filter.patter2site[pattern])[0] * 3; + codon = seq_chars [codon_start][codon_start+2]; + } else { + codon = "---"; + filter.ambigs += Abs (filter.patter2site [pattern]) + } + for (c; in; filter.patter2site [pattern] ) { + codons[c] = codon; + } + } + if (filter.ambigs > 0) { + fprintf (stdout, "\nStriking ", filter.ambigs, " codons that are incompletely resolved from " + seq_name + "\n"); + } + fprintf (filter.out,">",seq_name,"\n",Join ("", codons), "\n"); +} + +fprintf (filter.out,CLOSE_FILE); + + |
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| diff -r 386b975927dd -r f1261376fd4b test-data/annotate-in1.fa.gz |
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| Binary file test-data/annotate-in1.fa.gz has changed |
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| diff -r 386b975927dd -r f1261376fd4b test-data/annotate-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-in1.nhx Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -0,0 +1,1 @@ +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1:0.000523,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021:0.000001):0.000001,REFERENCE:0.000262,(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4:0.001835,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3:0.000001,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1:0.000786,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1:0.000785,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021:0.823959):0.000001):0.000001):0.000262):0.000001); |
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| diff -r 386b975927dd -r f1261376fd4b test-data/annotate-out1-clade.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-clade.nhx Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -0,0 +1,1 @@ +(((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1{Annotated},epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated})Node2{Annotated},(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated},(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3{Annotated},(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated},(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated},epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated})Node11{Annotated})Node9{Annotated})Node7{Annotated})Node5{Annotated})Node1{Annotated},REFERENCE{Annotated})Node14 \ No newline at end of file |
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| diff -r 386b975927dd -r f1261376fd4b test-data/annotate-out1-full.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-full.nhx Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -0,0 +1,1 @@ +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1{Annotated},epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021{Annotated})Node2{Annotated},(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4{Annotated},(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3{Annotated},(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1{Annotated},(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1{Annotated},epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021{Annotated})Node11{Annotated})Node9{Annotated})Node7{Annotated})Node5{Annotated},REFERENCE{Annotated})Node1{Annotated} \ No newline at end of file |
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| diff -r 386b975927dd -r f1261376fd4b test-data/annotate-out1-int.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-out1-int.nhx Tue Apr 20 10:27:10 2021 +0000 |
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| @@ -0,0 +1,1 @@ +((gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1,epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021)Node2{Annotated},(gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4,(gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3,(gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1,(gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1,epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021)Node11{Annotated})Node9{Annotated})Node7{Annotated})Node5{Annotated},REFERENCE)Node1{Annotated} \ No newline at end of file |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/cfel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cfel-out1.json Tue Apr 20 10:27:10 2021 +0000 |
| [ |
| b'@@ -0,0 +1,457 @@\n+{\n+ "MLE":{\n+ "content":{\n+ "0": [\n+[0.06119510183854701, 89.89195279268617, 0.0004623763636215286, 1, 0, 0.02604337408104318, 0.811685158859179, -1, 63.5934805540066],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 30.68649872459121, 0, 4, 0.09420783493835005, 0.60747810805074, -1, 17.97424403638481],\n+ [4.002735462744614, 1.681163962819147, 1.228805177498639, 2, 1, 0.8623362362181146, 1, -1, 3.706931649150397],\n+ [3.050065014123722, 3.059937797506153, 2.418613924712312, 4, 3, 0.8197206876541498, 1, -1, 4.950806946880908],\n+ [0, 24.69410076903886, 2.602816011187676, 6, 0, 0.2048204536099466, 0.7226683929256608, -1, 18.98662250194162],\n+ [0.7973929595981712, 0.56976393636776, 6.448137478127731, 2, 3, 0.06745323839043926, 0.5733525263187338, -1, 4.538073888148586],\n+ [0, 1.220294976236213, 1.931034796125328, 2, 1, 0.6817876981968, 1, -1, 1.993993062285827],\n+ [0, 0.7273121045548806, 0, 1, 0, 0.261419115100697, 0.7638339769348492, -1, 0.5143075999810249],\n+ [1.621724997367116, 0, 0, 1, 1, 0.9121485865111767, 1, -1, 0.7286149415473206],\n+ [0.5060806624687831, 1.999902075014571, 0, 3, 1, 0.0321757051476228, 0.752107107825683, -1, 1.641573976803133],\n+ [0.9420105153372681, 0.7146285434777966, 0, 2, 1, 0.2644815118797826, 0.7381797421122291, -1, 0.9285687782746239],\n+ [0, 1.987391099359683, 0, 3, 0, 0.3529798862703204, 0.7253542717862628, -1, 1.405353135379039],\n+ [8.244286695269041, 1.185994719868233, 0.6569566762624601, 3, 1, 0.6286360235526834, 1, -1, 4.927487703059774],\n+ [0.9500757632276707, 0, 0.5124208919340753, 1, 1, 0.2013061949629433, 0.7239280472705847, -1, 0.726998065759856],\n+ [0, 0.5627658928917045, 0, 1, 0, 0.268228707078901, 0.7376289444669777, -1, 0.3979512700416927],\n+ [0, 0.4711115774899237, 0.6829037036151366, 1, 1, 0.7990116922248531, 1, -1, 0.7331418792667797],\n+ [0.4167417817571659, 0, 0, 0, 1, 0.9206940254260957, 1, -1, 0.1872353755712544],\n+ [0, 0, 0.5212303676872864, 0, 1, 0.1996277088955986, 0.731968265950528, -1, 0.3053043591603385],\n+ [0.8675634762363731, 0, 0, 0, 1, 0.9661066726954236, 1, -1, 0.3897823074521307],\n+ [0.7210654427571777, 0, 0, 1, 0, 0.9836163243596738, 1, -1, 0.3239630987246734],\n+ [1.427522329748797, 1.811321397351979, 2.047657099183609, 3, 2, 0.9153591138659802, 1, -1, 3.121601237885459],\n+ [0, 1.169550303774839, 0, 2, 0, 0.1240860099621399, 0.6106337858663201, -1, 0.8270295599708779],\n+ [0, 0.5199246087354797, 0.6609898247714937, 1, 1, 0.8711034612935368, 1, -1, 0.7548234772115322],\n+ [15.62849382074995, 0.8354792436567606, 0.3568193143210429, 2, 1, 0.692201812400887, 1, -1, 7.821429665659478],\n+ [0, 2.048844622077364, 0.7034505168953565, 2, 1, 0.3378069542919415, 0.7097741623886861, -1, 1.86084665052398],\n+ [0, 1.700054129075257, 0, 2, 0, 0.04433653641539281, 0.5922094506913184, -1, 1.202167203717357],\n+ [1.996997597242381, 4.191343395708055, 0, 4, 1, 0.1469200405479562, 0.6541439900587571, -1, 3.861063080915803],\n+ [2.905972734304771, 0.5690151548622607, 0.8753525229497926, 2, 2, 0.7870098322033844, 1, -1, 2.22070423298495],\n+ [59.02352946734126, 0.9878963984643503, 0, 2, 2, 0.106227812438751, 0.6207687789389512, -1, 27.21689766175553],\n+ [0, 0.493823010263051, 0.5992185198004483, 1, 1, 0.8822938448128469, 1, -1, 0.700184340303363],\n+ [0.151693667651528, 0, 1.145340845562134, 0, 1, 0.1082039933982597, 0.6131559625901383, -1, 0.7390230172493181],\n+ [0, 2.787986645749746, 1.784950467476681, 4, 2, 0.6411055012556299, 1, -1, 3.01699506099285],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [385.3762662337238, 5.564044480778701, 0, 6, 1, 0.02371410328251622, 0.8869074627661065, -1, 177.0778829569787],\n+ [2.573452429663424, 0.5220696742903632, 0.713573878301312, 2, 1, 0.8351273640659775, 1, -1, 1.943351558242732],\n+ [0, 0, 0, 1, 1, 1, 1, 1, 0],\n+ [0, 0, 0, 1, 1, '..b'5003],\n+ [0.01837636270304883],\n+ [0.01541821854326533],\n+ [0.01892910005547028],\n+ [0.01545910240515689],\n+ [0.01921445878706794],\n+ [0.01612140169177368],\n+ [0.02829747763884322],\n+ [0.02311011106415996],\n+ [0.02872406592369408],\n+ [0.02410019507229243],\n+ [0.01663805943190806],\n+ [0.01358804506433061],\n+ [0.01688888041768248],\n+ [0.01417018446135155],\n+ [0.006177213955434187],\n+ [0.005044834822351987],\n+ [0.006270336287397383],\n+ [0.00526096577332031],\n+ [0.006458939937330408],\n+ [0.005274916061901906],\n+ [0.006556309326397028],\n+ [0.005500904159606446],\n+ [0.009655594186286731],\n+ [0.007885574003572761],\n+ [0.009801153568494354],\n+ [0.008223407979974132],\n+ [0.03327785448210915],\n+ [0.02717750758119989],\n+ [0.03377952261833742],\n+ [0.02834184710178207],\n+ [0.01235507229404208],\n+ [0.01009019590244688],\n+ [0.01254132667213156],\n+ [0.01052248035033209],\n+ [0.01291855364640413],\n+ [0.01055038238273567],\n+ [0.01311330258173711],\n+ [0.01100238215235291],\n+ [0.01931219560697892],\n+ [0.0157719705998612],\n+ [0.01960332955558842],\n+ [0.01644767379420349],\n+ [0.01965132601881859],\n+ [0.02049322866376102],\n+ [0.008933621043463411],\n+ [0.007295949736387736],\n+ [0.009068296583349953],\n+ [0.007608523013862737],\n+ [0.007628698224327205],\n+ [0.009481877006094248],\n+ [0.00795552712159237],\n+ [0.01396413011303752],\n+ [0.01140428846505027],\n+ [0.01417464125436193],\n+ [0.01189287130232129] \n+ ],\n+ "Log Likelihood":-3463.018342931476,\n+ "Rate Distributions":{\n+ "non-synonymous/synonymous rate ratio for *internal*": [\n+[0.6757243377045866, 1] \n+ ],\n+ "non-synonymous/synonymous rate ratio for *leaf*": [\n+[1.251739840537981, 1] \n+ ]\n+ },\n+ "display order":1,\n+ "estimated parameters":32\n+ },\n+ "Nucleotide GTR":{\n+ "AIC-c":7112.857310169033,\n+ "Equilibrium frequencies": [\n+[0.3592490842490842],\n+ [0.181959706959707],\n+ [0.240018315018315],\n+ [0.2187728937728937] \n+ ],\n+ "Log Likelihood":-3532.32122446679,\n+ "Rate Distributions":{\n+ "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087,\n+ "Substitution rate from nucleotide A to nucleotide G":1,\n+ "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847,\n+ "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032,\n+ "Substitution rate from nucleotide C to nucleotide T":1.02837595903795,\n+ "Substitution rate from nucleotide G to nucleotide T":0.304509117524575\n+ },\n+ "display order":0,\n+ "estimated parameters":24\n+ }\n+ },\n+ "input":{\n+ "file name":"/tmp/tmp29yw9zzo/job_working_directory/000/3/working/cfel_input.fa",\n+ "number of sequences":10,\n+ "number of sites":187,\n+ "partition count":1,\n+ "trees":{\n+ "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)"\n+ }\n+ },\n+ "tested":{\n+ "0":{\n+ "Baboon":"leaf",\n+ "Cat":"leaf",\n+ "Chimp":"leaf",\n+ "Cow":"leaf",\n+ "Horse":"leaf",\n+ "Human":"leaf",\n+ "Mouse":"leaf",\n+ "Node1":"internal",\n+ "Node12":"internal",\n+ "Node2":"internal",\n+ "Node3":"internal",\n+ "Node8":"internal",\n+ "Node9":"internal",\n+ "Pig":"leaf",\n+ "Rat":"leaf",\n+ "RhMonkey":"leaf"\n+ }\n+ },\n+ "timers":{\n+ "FEL analysis":{\n+ "order":2,\n+ "timer":180\n+ },\n+ "Model fitting":{\n+ "order":1,\n+ "timer":13\n+ },\n+ "Total time":{\n+ "order":0,\n+ "timer":193\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/conv-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-in1.fa Tue Apr 20 10:27:10 2021 +0000 |
| b |
| b'@@ -0,0 +1,22 @@\n+>epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGACG\n+>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021\n+------------------------------------------'..b'ATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+\n+>REFERENCE\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n\\ No newline at end of file\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/conv-out1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-out1.nhx Tue Apr 20 10:27:10 2021 +0000 |
| b |
| b"@@ -0,0 +1,27 @@\n+#NEXUS\n+\n+BEGIN TAXA;\n+\tDIMENSIONS NTAX = 8;\n+\tTAXLABELS\n+\t\t'epi_isl_1041406_hCoV_19_USA_NY_PRL_2021_02_08_05H12_2021' 'epi_isl_1041403_hCoV_19_USA_NY_PRL_2021_02_08_05H08_2021' 'gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4' 'gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1' 'gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3' 'gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1' 'gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1' 'REFERENCE' ;\n+END;\n+\n+BEGIN CHARACTERS;\n+\tDIMENSIONS NCHAR = 1273;\n+\tFORMAT\n+\t\tDATATYPE = PROTEIN\n+\t\tGAP=-\n+\t\tMISSING=?\n+\t\tNOLABELS\n+\t;\n+\n+MATRIX\n+ ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ET\n+ ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????\n+ LVFFFVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGLSPTKLNDLCFTNVYADSFVI"..b'DPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n+ MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFYNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n+ MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTLFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNHPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT\n+ MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT;\n+END;\n\\ No newline at end of file\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/fubar-in1.fa --- a/test-data/fubar-in1.fa Fri Apr 09 21:49:31 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,326 +0,0 @@\n->KF789585\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCCCAAAAACTTCCTGGAAATGACAATAGCACGGCAACGCTGTGCCTTGGACACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCGAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAATTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTTCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGGCTGGAGTCACTCAAAACGGAACAAGTTCTGCTTGCATAAGGGGATCTAATAGTAGTTTCTTTAGTAGATTAAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAACAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAAGGACCAAATCTTCCTGTATGCTCAATCATCAGGAAGAATCACAGTATCTACCAAAAGAAGCCAACAAGCTGTAATCCCGAATATCGGATCTAGACCCAGAATAAGGAATATCCCTAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAAGTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAGCACTCTGAAATTGGCAACAGGAATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATAGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n->CY025485\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCATCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAGTGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAATTCCTCAATAGGTGGAATCTGCAACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAATTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAATGGAACAAGCTCTGCTTGCAAAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAGAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAATCAGCCTATATGCTCAAGCACCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCCGAGTAAGGGATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGACAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATATGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGCTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGACCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAGGACACTAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGACCTAACTGACTCAGAAATGAACAAATTGTTTGAAAGAACAAAAAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n->KC535396\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGAAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAATAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAACTTCAAATACCCAGCATTGAACGTGA'..b'GAGGGAAGAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATCGATTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACAAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGGGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGAGTTGAGCTGAAGTCAGGGTACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAGGGCAACATTAGGTGCAACATTTGCATT\n->CY012232\n-ATGAAGACTATCATTGCTTTGAGCTACATTTTATGTCTGGTTTTCGCTCAAAAACTTCCCGGAAATGACAACAGCACAGCAACGCTGTGCCTGGGACACCATGCAGTGCCAAACGGAACGCTAGTGAAAACAATCACGAATGATCAAATTGAAGTGACTAATGCTACTGAGCTGGTTCAGAGTTCCCCAACAGGTAGAATATGCGACAGTCCTCACCGAATCCTTGATGGAAAGAACTGCACACTGATAGATGCTCTATTGGGAGACCCTCATTGTGATGGCTTCCAAAATAAGGAATGGGACCTTTTTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCAGGCACCCTGGAGTTTACCAACGAAAACTTCAATTGGACTGGAGTCGCTCAGGATGGGAAAAGCTATGCTTGCAAAAGGGGATCTGTTAACAGTTTCTTTAGTAGATTGAATTGGTTGCACAAATTAGAATACAAATATCCAGCGCTGAACGTGACTATGCCAAACAATGGCAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGAGCACGGACAGTGACCAAACCAGCCTATATGTCCGAGCATCAGGGAAAGTCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGGATATCGGGTATAGACCATGGGTAAGGGGTCTTTCCAGTAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAATAGCACAGGGAATCTAATTGCTCCTCGGGGTTACTTCAAAATACGAAATGGGAAAAGCTCAATAATGAGGTCAGATGCACCCATTGGCAACTGCAGTTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCTTTTCAAAATGTAAACAGGATCACATATGGGGCCTGCCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGGAATGTACCAGAGAAACAAACTAGAGGCATATTCGGCGCAATCGCAGGTTTCATAGAGAATGGTTGGGAGGGAATGGTAGACGGTTGGTACGGTTTCAGGCATCAGAATTCTGAGGGCACAGGACAAGCTGCAGATCTTAAAAGCACTCAAGCAGCAATCGACCAAATCAACGGGAAACTGAATAGGTTAGTCGAGAAAACGAACGAGAAATTCCATCAAATCGAAAAAGAATTCTCAGAAGTAGAAGGGAGAATTCAGGACCTCGAGAAATATGTTGAAGACACTAAAATAGATCTCTGGTCTTACAATGCGGAGCTTCTTGTTGCTCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTATTTGAAAGAACAAGGAAGCAACTGAGGGAAAATGCTGAGGACATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGGTCAATCAGAAATGGAACTTATGACCATGATGTATACAGAGACGAAGCATTAAACAACCGGTTCCAGATCAAAGGTGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGCTTTTTGCTTTGTGTTGTTTTGCTTGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n->EU199367\n-ATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAACTTCCTGGAAATGACAACAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACGAATGACCAAATTGAAGTTACTAATGCTACTGAGCTGGTTCAGAGTTCCTCAACAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCCTCAGTGTGATGGCTTCCAAAATAAGAAATGGGACCTTTTTGTTGAACGCAGCAAAGCCTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCTCCCTTAGGTCACTAGTTGCCTCATCCGGCACACTGGAGTTTAACAATGAAAGCTTCAATTGGACTGGAGTCACTCAAAACGGAACAAGCTCTGCTTGCATAAGGAGATCTAATAACAGTTTCTTTAGTAGATTGAATTGGTTGACCCACTTAAAATTCAAATACCCAGCATTGAACGTGACTATGCCAAACAATGAAAAATTTGACAAATTGTACATTTGGGGGGTTCACCACCCGGGTACGGACAATGACCAAGTCTTCCTGTATGCTCAAGCATCAGGAAGAATCACAGTCTCTACCAAAAGAAGCCAACAAACTGTAATCCCGAATATCGGATCTAGACCCAGAGTAAGGAATATCCCCAGCAGAATAAGCATCTATTGGACAATAGTAAAACCGGGAGACATACTTTTGATTAACAGCACAGGGAATCTAATTGCTCCTAGGGGTTACTTCAAAATACGAAGTGGGAAAAGCTCAATAATGAGATCAGATGCACCCATTGGCAAATGCAATTCTGAATGCATCACTCCAAATGGAAGCATTCCCAATGACAAACCATTCCAAAATGTAAACAGGATCACATACGGGGCCTGTCCCAGATATGTTAAGCAAAACACTCTGAAATTGGCAACAGGGATGCGAAATGTACCAGAGAAACAAACTAGAGGCATATTTGGCGCAATCGCGGGTTTCATAGAAAATGGTTGGGAGGGAATGGTGGATGGTTGGTACGGTTTCAGGCATCAAAATTCTGAGGGAATAGGACAAGCAGCAGATCTCAAAAGCACTCAAGCAGCAATCGATCAAATCAATGGGAAGCTGAATAGGTTGATCGGGAAAACCAACGAGAAATTCCATCAGATTGAAAAAGAATTCTCAGAAGTCGAAGGGAGAATTCAGGACCTTGAGAAATATGTTGAGGACACCAAAATAGATCTCTGGTCATACAACGCGGAGCTTCTTGTTGCCCTGGAGAACCAACATACAATTGATCTAACTGACTCAGAAATGAACAAACTGTTTGAAAAAACAAAGAAGCAACTGAGGGAAAATGCTGAGGATATGGGCAATGGTTGTTTCAAAATATACCACAAATGTGACAATGCCTGCATAGGATCAATCAGAAATGGAACTTATGACCACGATGTATACAGAGATGAAGCATTAAACAACCGGTTCCAGATCAAGGGCGTTGAGCTGAAGTCAGGATACAAAGATTGGATCCTATGGATTTCCTTTGCCATATCATGTTTTTTGCTTTGTGTTGCTTTGTTGGGGTTCATCATGTGGGCCTGCCAAAAAGGCAACATTAGGTGCAACATTTGCATT\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/fubar-in1.fa.gz |
| b |
| Binary file test-data/fubar-in1.fa.gz has changed |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/strike-ambigs-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in1.fa Tue Apr 20 10:27:10 2021 +0000 |
| b |
| b'@@ -0,0 +1,260 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC\n+AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC\n+AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC\n+AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT\n+AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA\n+ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT\n+AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT\n+TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT\n+TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA\n+GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT\n+TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT\n+TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT\n+TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT\n+GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT\n+GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG\n+TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC\n+CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA\n+GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC\n+TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT\n+GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT\n+GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT\n+TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT\n+CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT\n+CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT\n+AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT\n+AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA\n+CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT\n+TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG\n+CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG\n+ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA\n+GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTC\n+CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT\n+AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT\n+GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT\n+CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT\n+GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT\n+AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG\n+TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT\n+ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA\n+GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT\n+AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT\n+CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC\n+CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT\n+TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT\n+ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG\n+CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA\n+AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC\n+ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC\n+ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC\n+CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA\n+CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT\n+TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT\n+GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA\n+GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC\n+ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA\n+CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA\n+TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT\n+TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA\n+TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA\n+AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC\n+CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT\n+ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC\n+TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC\n+TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>epi_is'..b'sl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+------------------------------------------------------------\n+--------------------------------------A\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/strike-ambigs-in2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in2.fa Tue Apr 20 10:27:10 2021 +0000 |
| b |
| b'@@ -0,0 +1,455 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC\n+AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC\n+AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC\n+AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT\n+AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA\n+ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT\n+AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT\n+TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT\n+TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA\n+GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT\n+TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT\n+TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT\n+TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT\n+GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT\n+GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG\n+TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC\n+CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA\n+GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC\n+TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT\n+GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT\n+GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT\n+TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT\n+CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT\n+CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT\n+AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT\n+AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA\n+CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT\n+TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG\n+CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG\n+ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA\n+GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTC\n+CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT\n+AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT\n+GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT\n+CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT\n+GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT\n+AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG\n+TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT\n+ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA\n+GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT\n+AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT\n+CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC\n+CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT\n+TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT\n+ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG\n+CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA\n+AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC\n+ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC\n+ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC\n+CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA\n+CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT\n+TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT\n+GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA\n+GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC\n+ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA\n+CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA\n+TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT\n+TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA\n+TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA\n+AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC\n+CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT\n+ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC\n+TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC\n+TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>gb_MW5'..b'_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1\n+ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC\n+AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC\n+AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC\n+AATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT\n+AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA\n+ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT\n+AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTT\n+TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT\n+TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA\n+GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT\n+TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT\n+TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT\n+TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT\n+GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT\n+GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG\n+TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC\n+CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA\n+GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC\n+TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT\n+GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT\n+GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT\n+TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT\n+CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT\n+CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT\n+AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT\n+AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA\n+CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT\n+TTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG\n+CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG\n+ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA\n+GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC\n+CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT\n+AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT\n+GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT\n+CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT\n+GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT\n+AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG\n+TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT\n+ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA\n+GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT\n+AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT\n+CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC\n+CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT\n+TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT\n+ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG\n+CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA\n+AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC\n+ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC\n+ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC\n+CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA\n+CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT\n+TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT\n+GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA\n+GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC\n+ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA\n+CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA\n+TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT\n+TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA\n+TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA\n+AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC\n+CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT\n+ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC\n+TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC\n+TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/strike-ambigs-out1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out1.fa Tue Apr 20 10:27:10 2021 +0000 |
| b |
| b'@@ -0,0 +1,8 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021\n+----------------------------------------------------------------------------'..b'----------------------------------------------------------------------------------------------------------------------\n+>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021\n+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n' |
| b |
| diff -r 386b975927dd -r f1261376fd4b test-data/strike-ambigs-out2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out2.fa Tue Apr 20 10:27:10 2021 +0000 |
| b |
| b'@@ -0,0 +1,14 @@\n+>NC_045512.2:21563-25384\n+ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_nu'..b'CTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n+>gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1\n+ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA\n' |