| Previous changeset 2:d8b6f0adaa79 (2021-07-09) Next changeset 4:a287431cdf4f (2021-10-05) |
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Commit message:
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit af3bfbbd3f1236bf96a25bcb8483f2889295ec0c" |
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modified:
bealign.xml macros.xml test-data/bealign-out1.bam test-data/bealign-out2.bam test-data/bealign-out3.bam |
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added:
bealign_selection.loc.sample copy_reference.py test-data/bam2msa-in1.bam test-data/bam2msa-in2.bam test-data/bealign-out3-background.bam test-data/bealign-out4.bam test-data/bealign_selection.loc test-data/nsp8.fa test-data/query.fa test-data/reference.fa tool_data_table_conf.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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removed:
test-data/bealign-in-ref-1.fa test-data/bealign-in-ref-2.fa test-data/bealign-in1.fa test-data/bealign-in2.fa |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 bealign.xml --- a/bealign.xml Fri Jul 09 15:19:05 2021 +0000 +++ b/bealign.xml Fri Aug 20 21:04:17 2021 +0000 |
| [ |
| b'@@ -3,9 +3,11 @@\n <description>to a reference using a codon alignment algorithm</description>\n <macros>\n <import>macros.xml</import>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n </macros>\n- <expand macro="requirements" />\n+ <expand macro="requirements">\n+ <requirement type="package" version="5.1.0">gawk</requirement>\n+ </expand>\n <version_command>bealign --version</version_command>\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -16,17 +18,41 @@\n ## and replace any unwanted characters in the sequence names with underscores.\n ## This should not affect the actual alignment, since any non-standard character\n ## in the sequences is already ignored, but the possibility remains.\n- cat \'$input\' | awk \'{ if (\\$0 ~ "^[^>]") {a = gensub(/[^ACGTURYKMSWBDHVNacgturykmswbdhvn?-]/, "", "g"); } else {a=gensub(/[^>A-Za-z0-9_]/, "_", "g"); }; print a } \' |\n- sed \'s,_\\\\+,_,g\' > reads.fa &&\n+ cat \'$input\' @SANITIZE@ reads.fa &&\n bealign --reference \'$select_reference.reference\' --alphabet $advanced.alphabet\n #if $advanced.expected_identity:\n --expected-identity $advanced.expected_identity\n #end if\n- --score-matrix $advanced.score_matrix $advanced.reverse_complement $advanced.keep_reference\n #if $advanced.discard:\n $advanced.discard \'$advanced.discarded_reads\'\n #end if\n- reads.fa alignment.bam\n+ --score-matrix $advanced.score_matrix\n+ $advanced.reverse_complement\n+ $advanced.keep_reference\n+ reads.fa \'$output\'\n+ #set $input_background = False\n+ #if $background_source.selection == \'history\':\n+ #if $background_source.sequences:\n+ #set $input_background = $background_source.sequences\n+ #end if\n+ #else:\n+ #if $background_source.sequences:\n+ #set $input_background = $background_source.sequences.fields.path\n+ #end if\n+ #end if\n+ #if $input_background:\n+ && cat \'$input_background\' @SANITIZE@ background.fa &&\n+ bealign --reference \'$select_reference.reference\' --alphabet $advanced.alphabet\n+ #if $advanced.expected_identity:\n+ --expected-identity $advanced.expected_identity\n+ #end if\n+ --keep-reference --score-matrix $advanced.score_matrix $advanced.reverse_complement \n+ background.fa \'$background\'\n+ #end if\n+ #set $reference_name = str($select_reference.reference)\n+ #if $select_reference.reference_type == \'preset\' and $select_reference.save_reference:\n+ && python \'$__tool_directory__/copy_reference.py\' --reference \'$reference_name\' --dataset \'$saved_reference\'\n+ #end if\n ]]>\n </command>\n <inputs>\n@@ -81,13 +107,28 @@\n <option value="CoV2-ORF10">SARS-CoV-2: ORF10</option>\n <option value="CoV2-RdRp">SARS-CoV-2: RNA-dependent RNA polymerase</option>\n </param>\n+ <param name="save_reference" type="boolean" display="radio" label="Save this reference to your history" />\n </when>\n <when value="dataset">\n <param argument="--reference" type="data" format="fasta" label="Reference sequences" />\n </when>\n </conditional>\n+ <conditional name="background_source">\n+ <param name="selection" type="select" label="Source for the background" help="You can use a predefined background cached on this Galaxy server or select a dataset from your history">\n+ <option value="data_table">Use a predefined background</option>\n+ <option value="history">Select a dataset from your history</option>\n+ </param>\n+ <when value="data_table">\n+ <param name="sequences" type="select" optional="true" label="Select sequences from data'..b'label="Discard sequences that are insufficiently identical to the reference" />\n <param argument="--alphabet" type="select" label="Alphabet to use for alignment">\n <option value="codon" selected="True">Codon</option>\n <option value="dna">DNA</option>\n@@ -110,33 +151,54 @@\n </section>\n </inputs>\n <outputs>\n- <data name="output" format="bam" from_work_dir="alignment.bam" />\n+ <data name="output" format="bam" label="${tool.name} on ${on_string} - Aligned Sequences" />\n+ <data name="background" format="bam" label="${tool.name} on ${on_string} - Background" >\n+ <filter>background_source[\'sequences\']</filter>\n+ </data>\n+ <data name="saved_reference" format="fasta" label="${tool.name} on ${on_string} - Reference" >\n+ <filter>select_reference[\'save_reference\']</filter>\n+ </data>\n <data name="discarded_reads" format="fasta">\n <filter>advanced[\'discard\']</filter>\n </data>\n </outputs>\n <tests>\n <test>\n- <param name="input" ftype="fasta" value="bealign-in1.fa" />\n+ <param name="input" ftype="fasta" value="query.fa" />\n <param name="reference_type" value="dataset" />\n <param name="score_matrix" value="HIV_BETWEEN_F" />\n- <param name="reference" ftype="fasta" value="bealign-in-ref-1.fa" />\n+ <param name="reference" ftype="fasta" value="reference.fa" />\n <output name="output" file="bealign-out1.bam" ftype="bam" lines_diff="2" />\n </test>\n <test>\n- <param name="input" ftype="fasta" value="bealign-in2.fa" />\n- <param name="reference_type" value="dataset" />\n- <param name="score_matrix" value="BLOSUM62" />\n- <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />\n+ <param name="input" ftype="fasta" value="query.fa" />\n+ <param name="reference_type" value="preset" />\n+ <param name="reference" value="CoV2-nsp8" />\n+ <param name="score_matrix" value="HIV_BETWEEN_F" />\n <output name="output" file="bealign-out2.bam" ftype="bam" lines_diff="2"/>\n </test>\n- <test>\n- <param name="input" ftype="fasta" value="bealign-in2.fa" />\n- <param name="reference_type" value="dataset" />\n- <param name="expected_identity" value="0.9" />\n- <param name="score_matrix" value="BLOSUM62" />\n- <param name="reference" ftype="fasta" value="bealign-in-ref-2.fa" />\n+ <test expect_num_outputs="2">\n+ <param name="input" ftype="fasta" value="query.fa" />\n+ <param name="reference_type" value="preset" />\n+ <param name="reference" value="CoV2-nsp8" />\n+ <param name="add_background" value="Yes" />\n+ <param name="background_source" value="data_table" />\n+ <param name="sequences" value="CoV2-nsp8" />\n+ <param name="alphabet" value="codon" />\n+ <param name="score_matrix" value="HIV_BETWEEN_F" />\n <output name="output" file="bealign-out3.bam" ftype="bam" lines_diff="2"/>\n+ <output name="background" file="bealign-out3-background.bam" ftype="bam" lines_diff="2"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="input" ftype="fasta" value="query.fa" />\n+ <param name="reference_type" value="preset" />\n+ <param name="reference" value="CoV2-nsp8" />\n+ <param name="save_reference" value="true" />\n+ <param name="add_background" value="No" />\n+ <param name="alphabet" value="codon" />\n+ <param name="score_matrix" value="HIV_BETWEEN_F" />\n+ <output name="output" file="bealign-out4.bam" ftype="bam" lines_diff="2"/>\n+ <output name="saved_reference" file="reference.fa" ftype="fasta"/>\n </test>\n </tests>\n <help>\n' |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 copy_reference.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/copy_reference.py Fri Aug 20 21:04:17 2021 +0000 |
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| @@ -0,0 +1,59 @@ +import argparse +import os +import shutil + +from BioExt.references import cov2, hxb2, nl4_3 + + +references = { + 'HXB2_env': hxb2.env, + 'HXB2_gag': hxb2.gag, + 'HXB2_int': hxb2.int, + 'HXB2_nef': hxb2.nef, + 'HXB2_pol': hxb2.pol, + 'HXB2_pr': hxb2.pr, + 'HXB2_prrt': hxb2.prrt, + 'HXB2_rev': hxb2.rev, + 'HXB2_rt': hxb2.rt, + 'HXB2_tat': hxb2.tat, + 'HXB2_vif': hxb2.vif, + 'HXB2_vpr': hxb2.vpr, + 'HXB2_vpu': hxb2.vpu, + 'NL4-3_prrt': nl4_3.prrt, + 'CoV2-3C': cov2.threeC, + 'CoV2-E': cov2.E, + 'CoV2-endornase': cov2.endornase, + 'CoV2-exonuclease': cov2.exonuclease, + 'CoV2-helicase': cov2.helicase, + 'CoV2-leader': cov2.leader, + 'CoV2-methyltransferase': cov2.methyltransferase, + 'CoV2-M': cov2.M, + 'CoV2-N': cov2.N, + 'CoV2-nsp10': cov2.nsp10, + 'CoV2-nsp2': cov2.nsp2, + 'CoV2-nsp3': cov2.nsp3, + 'CoV2-nsp4': cov2.nsp4, + 'CoV2-nsp6': cov2.nsp6, + 'CoV2-nsp7': cov2.nsp7, + 'CoV2-nsp8': cov2.nsp8, + 'CoV2-nsp9': cov2.nsp9, + 'CoV2-ORF10': cov2.ORF10, + 'CoV2-ORF1a': cov2.ORF1a, + 'CoV2-ORF1b': cov2.ORF1b, + 'CoV2-ORF3a': cov2.ORF3a, + 'CoV2-ORF5': cov2.ORF5, + 'CoV2-ORF6': cov2.ORF6, + 'CoV2-ORF7a': cov2.ORF7a, + 'CoV2-ORF7b': cov2.ORF7b, + 'CoV2-ORF8': cov2.ORF8, + 'CoV2-RdRp': cov2.RdRp, + 'CoV2-S': cov2.S +} + +parser = argparse.ArgumentParser() +parser.add_argument('--reference', dest='reference', action='store', type=str) +parser.add_argument('--dataset', dest='dataset', action='store', type=str) +args = parser.parse_args() +reference = os.path.abspath(references[args.reference]._seqpath) + +shutil.copy(reference, os.path.abspath(args.dataset)) |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 macros.xml --- a/macros.xml Fri Jul 09 15:19:05 2021 +0000 +++ b/macros.xml Fri Aug 20 21:04:17 2021 +0000 |
| [ |
| @@ -2,6 +2,7 @@ <macros> <token name="@TOOL_VERSION@">0.20.1</token> <token name="@PROFILE@">20.05</token> + <token name="@SANITIZE@"><![CDATA[| gawk '{ if (\$0 ~ "^[^>]") {a = gensub(/[^ACGTURYKMSWBDHVNacgturykmswbdhvn?-]/, "", "g"); } else {a=gensub(/[^>A-Za-z0-9_]/, "_", "g"); }; print a } ' | sed 's,_\\+,_,g' >]]></token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">python-bioext</requirement> |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bam2msa-in1.bam |
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| Binary file test-data/bam2msa-in1.bam has changed |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bam2msa-in2.bam |
| b |
| Binary file test-data/bam2msa-in2.bam has changed |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-in-ref-1.fa --- a/test-data/bealign-in-ref-1.fa Fri Jul 09 15:19:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ ->CUSTOM_JP_REFERENCE -cctcaggtcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacagg -agcagatgatacagtattagaagaaatgagtttgccaggaagatggaaaccaaaaatgatagggggaattggaggtttta -tcaaagtaagacagtatgatcagatactcatagaaatctgtggacataaagctataggtacagtattagtaggacctaca -cctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagccctattgagactgt -accagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattag -tagaaatttgtacagagatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt -gccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg -ggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat -atttttcagttcccttagatgaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccaggg -attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatctt -agagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaa -tagggcagcatagaacaaaaatagaggagctgagacaacatctgttgaggtggggacttaccacaccagacaaaaaacat -cagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaga -aaaagacagctggactgtcaatgacatacagaagttagtggggaaattgaattgggcaagtcagatttacccagggatta -aagtaaggcaattatgtaaactccttagaggaaccaaagcactaacagaagtaataccactaacagaagaagcagagcta -gaactggcagaaaacagagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcaga -aatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatg -caagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagta -atatggggaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagc -cacctggattcctgagtgggagtttgttaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatag -taggagcagaaaccttc |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-in-ref-2.fa --- a/test-data/bealign-in-ref-2.fa Fri Jul 09 15:19:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ ->reference -CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGG -AGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTA -TCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACA -CCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGT -ACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAG -TAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTT -GCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTG -GGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCAT -ATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGG -ATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTT -AGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAA -TAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACAT -CAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGA -AAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTA -AAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTA -GAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGA -AATACAGAAGCAGGGGCAAGGC |
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| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-in1.fa --- a/test-data/bealign-in1.fa Fri Jul 09 15:19:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,130 +0,0 @@\n->Z|JP|K03455|2036\n-aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag\n-gaatggatggcccaagggttaaacaatggccattgacagaagaaaaaataaaggcgttaacagaaatttgtacagaaatg\n-gaaagggaaggaaaaatttcaaaaattgggcctgaaaatccatacaatactccaatatttgccataaagaaaaaagatag\n-tactaaatggagaaaattagtagatttcagagaactcaataaaagaactcaagacttctgggaggtccaactaggaatac\n-ctcatcccgcgggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcatatttttcagttcccttagat\n-aaagactttagaaagcatactgcattcactatacctagtgtaaataatgaaacaccggggattagatatcagtacaatgt\n-gcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatcttagaaccctttagaacaaaca\n-atccagagatggtgatttaccaatatatggatgatttatatgtaggatctgacttagagataggacagcatagagaaaaa\n-atacaggagttgagagaacatctactgaaatggggatttaccacaccagataaaaaa\n->Z|JP|K03455|2036|DUPLICATE 2\n-cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n-agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta\n-tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacggtattaataggacctaca\n-cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt\n-accagtaaaattaaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa\n-cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt\n-gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg\n-ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat\n-atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg\n-attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n-agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n-tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n-cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n-aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n-aagtaaggcarctgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n-gaattagcagaaaacagagaaattctaaaagaacctgttcatggrgtatattatgatccattaaaagacctagtagcaga\n-aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg\n-caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta\n-atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca\n->Z|JP|K03455|2036|DUPLICATE 3\n-cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n-agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta\n-tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacggtattagtaggacctaca\n-cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt\n-accagtaaaattaaagccaggaatggatggcccgaaagttaaacaatggccattgacagaagaaaaaataaaagcattag\n-tagaaatttgtacagaaatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt\n-gccataaagaaaaaggacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg\n-ggaagttcaattagggataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat\n-atttttcagttcccttagataaagacttccggaagtatactgcattcactatacctagtacaaacaatgagacaccaggg\n-attagatatcaatacaatgtgctaccacagggctggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n-agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n-tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n-cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n-aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n-aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n-gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga\n-aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg\n-caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta\n-atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca\n->Z|JP|K03455|2036|DUPLICATE 4\n-cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n-a'..b'acctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat\n-atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg\n-attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n-agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n-tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n-cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n-aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n-aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n-gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga\n-aatacagaaacaagggcaagac\n->Z|JP|K03455|2036|DUPLICATE 6\n-cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n-agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta\n-tcaaagtaagacaatatgatcagatacttatagaaatttgtgggaaaaaggctgtaggtacagtgttagtaggacctaca\n-cctgtcaacataattggacgaaatatgttgactcagattgggtgtactttaaattttccaattagtcctattgaaactgt\n-accagtaaaattgaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa\n-cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt\n-gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg\n-ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat\n-atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg\n-attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n-agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n-tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n-cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n-aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n-aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n-gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga\n-aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg\n-caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta\n-atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca\n->Z|JP|K03455|2036|DUPLICATE 7\n-cctcaggtcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacagg\n-agcagatgatacagtattagaagaaatgagtttgccaggaagatggaaaccaaaaatgatagggggaattggaggtttta\n-tcaaagtaagacagtatgatcagatactcatagaaatctgtggacataaagctataggtacagtattagtaggacctaca\n-cctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagccctattgagactgt\n-accagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattag\n-tagaaatttgtacagagatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt\n-gccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg\n-ggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat\n-atttttcagttcccttagatgaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccaggg\n-attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatctt\n-agagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaa\n-tagggcagcatagaacaaaaatagaggagctgagacaacatctgttgaggtggggacttaccacaccagacaaaaaacat\n-cagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaga\n-aaaagacagctggactgtcaatgacatacagaagttagtggggaaattgaattgggcaagtcagatttacccagggatta\n-aagtaaggcaattatgtaaactccttagaggaaccaaagcactaacagaagtaataccactaacagaagaagcagagcta\n-gaactggcagaaaacagagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcaga\n-aatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatg\n-caagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagta\n-atatggggaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagc\n-cacctggattcctgagtgggagtttgttaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatag\n-taggagcagaaaccttc\n' |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-in2.fa --- a/test-data/bealign-in2.fa Fri Jul 09 15:19:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ ->reads -CCTCAGATCACTCTTATGATGATGTGGCAACGACCCCTCGTCACAATAAAGGTAGGGGGGCAGCTAAAGGAAGCTCTATT -AGATACAGGAGCAGATGATACAGTATTAGAAGAAATAAATTTGCCAGGAAAATGGAAACCAAAAATGATAGGGGGAATTG -GAGGTTTTATCAAAGTAAGACAGTATGATCAGATACYTATAGAAATCWGYGGACATARAGCTATAGGTACAGTRTTAGTA -GGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTYCCCATTAGTCCTAT -TGAAACTGTACCAGTAAARTTAAAGCCAGGAATGGATGGCCCAAGAGTYAAACAATGGCCATTGACAGAAGAAAAAATAA -AAGCATTAGTAGAAATTTGTACAGAAATGGAAAARGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACT -CCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGARCTTAATAAGAGAACTCA -AGACTTCTGGGAAGTTCARTTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTRACAGTACTGGATGTAG -GTGATGCATACTTTTCAGTTCCCTTAGATGAAGAKTTCAGGAAGTATACTGCATTTACCATACCTAGTACAAACAATGAG -ACACCAGGGATTAGATAYCAGTACAATGTGCTYCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGAGTAGCATGAC -AAAAATCTTAGAGCCTTTTAGAAARCAAAATCCAGACATAGTKATYTATCAATACATGGATGATTTGTATGTAGGATCTG -ACTTAGAAATAGGGCAACATAGRGHAAAAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGAC -AARAAACATCAGAAAGAACCTCCATTYCTTTGGATGGGTTATGAACTCCATCCTGAYAAATGGACAGTACAGCCTATAAT -GCTGCCAGAAAAAGAAAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATG -CAGGGATTAAAGTAAAGCAATTATGTAAACTCCTTAGGGGRACCAAAGCAYTAACAGAAGTAGTACCACTAACAGCAGAA -GCAGAGCTAGAACTAGCAGAGAACAGGGARATTCTAAAAGAACCAGTACATGGAGTATATTATGACCCATCAAAAGACTT -AATAGCAGAAATACAGAAGCAGGGGCAAGGC |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-out1.bam |
| b |
| Binary file test-data/bealign-out1.bam has changed |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-out2.bam |
| b |
| Binary file test-data/bealign-out2.bam has changed |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-out3-background.bam |
| b |
| Binary file test-data/bealign-out3-background.bam has changed |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-out3.bam |
| b |
| Binary file test-data/bealign-out3.bam has changed |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign-out4.bam |
| b |
| Binary file test-data/bealign-out4.bam has changed |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/bealign_selection.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bealign_selection.loc Fri Aug 20 21:04:17 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +CoV2-nsp8 SARS-CoV-2: nsp8 ${HERE}/nsp8.fa |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/nsp8.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nsp8.fa Fri Aug 20 21:04:17 2021 +0000 |
| b |
| b'@@ -0,0 +1,4279 @@\n+>gb_MW521761_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_OH_QDX_3423_2020_Segment_null_Host_Human\n+GCCATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MT928989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WI_UW_1035_2020_Segment_null_Host_Human\n+GCTACAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MT834339_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_WA_S1787_2020_Segment_null_Host_Human\n+GCTATAGCATCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW332218_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_BHR_341038078_S3_L001_2020_Segment_null_Host_Human\n+GCTATAGCCTCAGAATTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW522404_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_GA_QDX_3319_2020_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTATAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MT787747_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_TUR_Kafkas_SARSCoV2_0035_2020_Segment_null_Host_Human\n+GCTATAGCCTCAGAGTTTAATTCCCTTC'..b'TAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW550127_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4054_2021_Segment_null_Host_Human\n+GCTATAGCTTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCTTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW433763_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_LACPHL_AF00068_2020_Segment_null_Host_Human\n+GCTATAGCTTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTACTGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW596016_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_000007218_2021_Segment_null_Host_Human\n+GCTATAGCTTCAGAGTTTAGTTCCCTTTCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW560780_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_QDX_4372_2021_Segment_null_Host_Human\n+GCTATAGCTTCAGAGTTTAGTTCTCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n+>gb_MW424830_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_TX_DSHS_1732_2020_Segment_null_Host_Human\n+GCTGTAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAA\n+GCTTATGAGCAGGCTGTTGCTAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAG\n+TCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAGCCATGCAACGTAAGTTGGAA\n+AAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG\n+GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAAT\n+GATGCACTCAACAACATTATCAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATA\n+CCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAGACTATAACACATATAAAAAT\n+ACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA\n+GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTA\n+GCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG\n' |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/query.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query.fa Fri Aug 20 21:04:17 2021 +0000 |
| b |
| b'@@ -0,0 +1,130 @@\n+>Z|JP|K03455|2036\n+aaatatgttgactcagattggttgtactttaaattttccaattagtcctattgaaactgtaccagtaaaattgaagccag\n+gaatggatggcccaagggttaaacaatggccattgacagaagaaaaaataaaggcgttaacagaaatttgtacagaaatg\n+gaaagggaaggaaaaatttcaaaaattgggcctgaaaatccatacaatactccaatatttgccataaagaaaaaagatag\n+tactaaatggagaaaattagtagatttcagagaactcaataaaagaactcaagacttctgggaggtccaactaggaatac\n+ctcatcccgcgggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcatatttttcagttcccttagat\n+aaagactttagaaagcatactgcattcactatacctagtgtaaataatgaaacaccggggattagatatcagtacaatgt\n+gcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatcttagaaccctttagaacaaaca\n+atccagagatggtgatttaccaatatatggatgatttatatgtaggatctgacttagagataggacagcatagagaaaaa\n+atacaggagttgagagaacatctactgaaatggggatttaccacaccagataaaaaa\n+>Z|JP|K03455|2036|DUPLICATE 2\n+cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n+agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta\n+tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacggtattaataggacctaca\n+cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt\n+accagtaaaattaaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa\n+cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt\n+gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg\n+ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat\n+atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg\n+attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n+agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n+tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n+cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n+aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n+aagtaaggcarctgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n+gaattagcagaaaacagagaaattctaaaagaacctgttcatggrgtatattatgatccattaaaagacctagtagcaga\n+aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg\n+caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta\n+atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca\n+>Z|JP|K03455|2036|DUPLICATE 3\n+cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n+agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta\n+tcaaagtaagacagtatgatcagatacctatagaaatctgtggacataaaactataggtacggtattagtaggacctaca\n+cctgtcaacataattggaagaaatctgttgactcagcttggctgcactttaaattttcccattagccctattgaaaccgt\n+accagtaaaattaaagccaggaatggatggcccgaaagttaaacaatggccattgacagaagaaaaaataaaagcattag\n+tagaaatttgtacagaaatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt\n+gccataaagaaaaaggacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg\n+ggaagttcaattagggataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat\n+atttttcagttcccttagataaagacttccggaagtatactgcattcactatacctagtacaaacaatgagacaccaggg\n+attagatatcaatacaatgtgctaccacagggctggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n+agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n+tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n+cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n+aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n+aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n+gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga\n+aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg\n+caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta\n+atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca\n+>Z|JP|K03455|2036|DUPLICATE 4\n+cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n+a'..b'acctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat\n+atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg\n+attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n+agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n+tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n+cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n+aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n+aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n+gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga\n+aatacagaaacaagggcaagac\n+>Z|JP|K03455|2036|DUPLICATE 6\n+cctcaaatcactctttggcaacgacccttagttacagcaaaaataggggaacagctaatagaagccctattagacacagg\n+agcagatgatacagtattagaagaaataaatttaccagggaaatggaaaccaaaaatgatagggggaattggaggtttta\n+tcaaagtaagacaatatgatcagatacttatagaaatttgtgggaaaaaggctgtaggtacagtgttagtaggacctaca\n+cctgtcaacataattggacgaaatatgttgactcagattgggtgtactttaaattttccaattagtcctattgaaactgt\n+accagtaaaattgaagccaggaatggatggcccaaaggttaaacaatggccattgacagaagaaaaaataaaagcattaa\n+cagaaatttgtacagaaatggaaagggaaggaaaaatttcaaaaattgggcctgagaatccatacaatactccaatattt\n+gccataaagaaaaaagatggtactaaatggagaaaattagtagatttcagagaacttaataaaagaactcaagacttctg\n+ggaggtccaactaggaatacctcatcccgcaggattaaaaaagaaaaaatcagtaacagtactagatgtgggggatgcat\n+atttttcagttcccttagataaagactttagaaagtatactgcattcactatacctagtataaataatgaaacaccgggg\n+attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatatttcaggctagcatgacaaaaatctt\n+agagccctttagagcaaaaaatccagagatggtgatttaccaatacatggatgatttatatgtaggatctgacttagaga\n+tagggcagcatagaacaaaaatacaagagttgagagaacatctactgaagtggggattaaccacaccagataaaaaacat\n+cagaaagaacctccatttctttggatgggatatgaactccatcctgacaaatggacagtccagcctataaagctgccaga\n+aaaagacagctggactgtcaatgatatacagaaattagtgggaaagctaaattgggcaagtcagatttatgcaggaatta\n+aagtaaggcaactgtgtaaactcctcaggggagccaaagcactaacagagatagtaacactgactgaggaagcagaatta\n+gaattagcagaaaacagagaaattctaaaagaacctgttcatggagtatattatgatccatcaaaagacctagtagcaga\n+aatacagaaacaagggcaagaccaatggacatatcaaatttatcaagagccatttaaaaatttaaaaacaggaaaatatg\n+caaaaaagaagtctgcccacactaatgatgtaaaacaattaacagaggtagtgcaaaaggtgtctacagaaagcatagta\n+atatggggaaagacccctaaatttagactacccatacaaaaagaaacatgggaagca\n+>Z|JP|K03455|2036|DUPLICATE 7\n+cctcaggtcactctttggcaacgacccctcgtcacaataaagataggggggcaactaaaggaagctctattagatacagg\n+agcagatgatacagtattagaagaaatgagtttgccaggaagatggaaaccaaaaatgatagggggaattggaggtttta\n+tcaaagtaagacagtatgatcagatactcatagaaatctgtggacataaagctataggtacagtattagtaggacctaca\n+cctgtcaacataattggaagaaatctgttgactcagattggttgcactttaaattttcccattagccctattgagactgt\n+accagtaaaattaaagccaggaatggatggcccaaaagttaaacaatggccattgacagaagaaaaaataaaagcattag\n+tagaaatttgtacagagatggaaaaggaagggaaaatttcaaaaattgggcctgaaaatccatacaatactccagtattt\n+gccataaagaaaaaagacagtactaaatggagaaaattagtagatttcagagaacttaataagagaactcaagacttctg\n+ggaagttcaattaggaataccacatcccgcagggttaaaaaagaaaaaatcagtaacagtactggatgtgggtgatgcat\n+atttttcagttcccttagatgaagacttcaggaagtatactgcatttaccatacctagtataaacaatgagacaccaggg\n+attagatatcagtacaatgtgcttccacagggatggaaaggatcaccagcaatattccaaagtagcatgacaaaaatctt\n+agagccttttagaaaacaaaatccagacatagttatctatcaatacatggatgatttgtatgtaggatctgacttagaaa\n+tagggcagcatagaacaaaaatagaggagctgagacaacatctgttgaggtggggacttaccacaccagacaaaaaacat\n+cagaaagaacctccattcctttggatgggttatgaactccatcctgataaatggacagtacagcctatagtgctgccaga\n+aaaagacagctggactgtcaatgacatacagaagttagtggggaaattgaattgggcaagtcagatttacccagggatta\n+aagtaaggcaattatgtaaactccttagaggaaccaaagcactaacagaagtaataccactaacagaagaagcagagcta\n+gaactggcagaaaacagagagattctaaaagaaccagtacatggagtgtattatgacccatcaaaagacttaatagcaga\n+aatacagaagcaggggcaaggccaatggacatatcaaatttatcaagagccatttaaaaatctgaaaacaggaaaatatg\n+caagaatgaggggtgcccacactaatgatgtaaaacaattaacagaggcagtgcaaaaaataaccacagaaagcatagta\n+atatggggaaagactcctaaatttaaactgcccatacaaaaggaaacatgggaaacatggtggacagagtattggcaagc\n+cacctggattcctgagtgggagtttgttaatacccctcccttagtgaaattatggtaccagttagagaaagaacccatag\n+taggagcagaaaccttc\n' |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 test-data/reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference.fa Fri Aug 20 21:04:17 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +>NC_045512.2:nsp8:12092-12685 +GCTATAGCCTCAGAGTTTAGTTCCCTTCCATCATATGCAGCTTTTGCTACTGCTCAAGAAGCTTATGAGCAGGCTGTTGC +TAATGGTGATTCTGAAGTTGTTCTTAAAAAGTTGAAGAAGTCTTTGAATGTGGCTAAATCTGAATTTGACCGTGATGCAG +CCATGCAACGTAAGTTGGAAAAGATGGCTGATCAAGCTATGACCCAAATGTATAAACAGGCTAGATCTGAGGACAAGAGG +GCAAAAGTTACTAGTGCTATGCAGACAATGCTTTTCACTATGCTTAGAAAGTTGGATAATGATGCACTCAACAACATTAT +CAACAATGCAAGAGATGGTTGTGTTCCCTTGAACATAATACCTCTTACAACAGCAGCCAAACTAATGGTTGTCATACCAG +ACTATAACACATATAAAAATACGTGTGATGGTACAACATTTACTTATGCATCAGCATTGTGGGAAATCCAACAGGTTGTA +GATGCAGATAGTAAAATTGTTCAACTTAGTGAAATTAGTATGGACAATTCACCTAATTTAGCATGGCCTCTTATTGTAAC +AGCTTTAAGGGCCAATTCTGCTGTCAAATTACAG \ No newline at end of file |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 tool_data_table_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml Fri Aug 20 21:04:17 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of dbkeys and len files under genome directory --> + <table name="bealign_selection" comment_char="#"> + <columns>value, label, path</columns> + <file path="tool-data/bealign_selection.loc" /> + </table> +</tables> |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Aug 20 21:04:17 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of dbkeys and len files under genome directory --> + <table name="bealign_selection" comment_char="#"> + <columns>value, label, path</columns> + <file path="tool-data/bealign_selection.loc" /> + </table> +</tables> |
| b |
| diff -r d8b6f0adaa79 -r fb4975b507c6 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Aug 20 21:04:17 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of dbkeys and len files under genome directory --> + <table name="bealign_selection" comment_char="#"> + <columns>value, label, path</columns> + <file path="${__HERE__}/test-data/bealign_selection.loc" /> + </table> +</tables> |