Mercurial > repos > iuc > meningotype
changeset 0:b5f872c50249 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype commit b4e0bbb9a2a23cbac9137a96d59bc1775c23c8a5
| author | iuc |
|---|---|
| date | Tue, 13 Jun 2023 11:04:30 +0000 |
| parents | |
| children | 7f88b804fc0c |
| files | check_output.py meningotype.xml strip_header.py test-data/NHBA_seqs.fasta test-data/NadA_seqs.fasta test-data/fHbp_seqs.fasta test-data/fetA_seqs.fasta test-data/input.fasta.gz test-data/input2.fasta.gz test-data/output.tsv test-data/porA_seqs.fasta test-data/porB_seqs.fasta update_db.py |
| diffstat | 13 files changed, 421 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_output.py Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,12 @@ +#!/usr/bin/env python3 + +import argparse +import sys + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('meningotype_file', type=argparse.FileType()) + args = parser.parse_args() + for line in args.meningotype_file: + if 'ERROR:' in line: + sys.exit('Found error in meningotype output: ' + line.strip())
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meningotype.xml Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,233 @@ +<tool id="meningotype" name="Meningotype" version="@TOOL_VERSION@+galaxy0" profile="21.05"> + <description>assign sequence type to Neisseria meningitidis genome assemblies</description> + <macros> + <token name="@TOOL_VERSION@">0.8.5</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">meningotype</requirement> + <!-- coreutils dep added because of a bug in the meningotype 0.8.5 container - it doesn't have `file` --> + <requirement type="package" version="9.0">coreutils</requirement> + </requirements> + <version_command>meningotype --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + #if $db_source == 'network' + python3 '$__tool_directory__/update_db.py' && + #end if + #if $input.source == "single" + #set $input_data = "'" + $input.fasta.element_identifier.replace(' uncompressed', '') + "'" + ln -s '$input.fasta' $input_data && + #else + #set $input_data = "" + #for $el in $input.fastas + #set $name = $el.element_identifier.replace(' uncompressed', '') + ln -s '$el' '$name' && + + #set $input_data = $input_data + " '" + $name + "'" + #end for + #end if + meningotype + #if $db_source == "network" + --db ./db + #end if + $input_data + --cpus \${GALAXY_SLOTS:-1} + #if "mlst" in $typing + --mlst + #end if + #if "finetype" in $typing + --finetype + #end if + #if "porb" in $typing + --porB + #end if + #if "bast" in $typing + --bast + #end if + #if $write_allele_sequences + --printseq allele_sequences + #end if + #if not $include_header + | python3 '$__tool_directory__/strip_header.py' + #end if + >'$output_tsv' && + python3 '$__tool_directory__/check_output.py' '$output_tsv' + ]]></command> + <inputs> + <conditional name="input"> + <param type="select" name="source" label="Input type"> + <option value="collection" selected="true">Dataset collection</option> + <option value="single">Single dataset</option> + </param> + <when value="collection"> + <param name="fastas" type="data_collection" format="fasta" collection_type="list" label="N. meningtidis genomes in FASTA format" /> + </when> + <when value="single"> + <param type="data" format="fasta" name="fasta" label="Input FASTA" help="N. meningitidis genome in FASTA format" /> + </when> + </conditional> + <param type="select" name="db_source" label="Database source"> + <!-- the latest version of the DBs are stored on PubMLST. --> + <option value="network" selected="true">Network</option> + <option value="builtin">Built-in</option> + </param> + <param type="select" multiple="true" name="typing" label="Typing to perform"> + <option value="mlst" selected="true">MLST</option> + <option value="finetype" selected="true">porA and fetA fine typing</option> + <option value="bast" selected="true">Bexsero antigen sequence typing (BAST)</option> + <option value="porb" selected="true">porB (NEIS2020) sequence typing</option> + </param> + <param type="boolean" name="include_header" checked="false" label="Include header in output" /> + <param type="boolean" name="write_allele_sequences" checked="false" label="Output sequences of porA, fetA, portB and BAST alleles" /> + </inputs> + <outputs> + <data format="tabular" name="output_tsv" label="Meningotype on ${on_string}"> + <actions> + <action name="column_names" type="metadata" default="Sample_ID,Serogroup,ctrA,MLST,porA,fetA,porB,fHbp,NHBA,NadA,BAST" /> + </actions> + </data> + <collection format="fasta" type="list" name="output_allele_sequences" label="Meningotype allele sequences on ${on_string}"> + <discover_datasets pattern="__name_and_ext__" directory="allele_sequences" /> + <filter>write_allele_sequences</filter> + </collection> + </outputs> + <tests> + <test expect_num_outputs="1"> <!-- test1: basic functionality --> + <conditional name="input"> + <param name="source" value="single" /> + <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/> + </conditional> + <param name="db_source" value="builtin" /> + <param name="typing" value="mlst,finetype,bast,porb" /> + <output name="output_tsv"> + <assert_contents> + <has_n_columns n="11" /> + <has_text text="9367" /> + <has_text text="21-15,16" /> + <has_text text="F1-7" /> + <has_text text="NEIS2020_506" /> + <has_text text="27" /> + <has_text text="798" /> + <has_text text="0" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> <!-- test2: test with header included --> + <conditional name="input"> + <param name="source" value="single" /> + <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/> + </conditional> + <param name="db_source" value="builtin" /> + <param name="typing" value="mlst,finetype,bast,porb" /> + <param name="include_header" value="true" /> + <output name="output_tsv"> + <assert_contents> + <has_n_columns n="11" /> + <has_text text="SAMPLE_ID" /> <!-- the header --> + <has_text text="9367" /> + <has_text text="21-15,16" /> + <has_text text="F1-7" /> + <has_text text="NEIS2020_506" /> + <has_text text="27" /> + <has_text text="798" /> + <has_text text="0" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> <!-- test 3: test allele sequence output --> + <conditional name="input"> + <param name="source" value="single" /> + <param name="fasta" value="input.fasta.gz" ftype="fasta.gz"/> + </conditional> + <param name="db_source" value="builtin" /> + <param name="typing" value="mlst,finetype,bast,porb" /> + <param name="write_allele_sequences" value="true" /> + <output name="output_tsv"> + <assert_contents> + <has_n_columns n="11" /> + <has_text text="9367" /> + <has_text text="21-15,16" /> + <has_text text="F1-7" /> + <has_text text="NEIS2020_506" /> + <has_text text="27" /> + <has_text text="798" /> + <has_text text="0" /> + </assert_contents> + </output> + <output_collection name="output_allele_sequences"> + <element name="NHBA_seqs" file="NHBA_seqs.fasta" ftype="fasta" /> + <element name="NadA_seqs" file="NadA_seqs.fasta" ftype="fasta" /> + <element name="fHbp_seqs" file="fHbp_seqs.fasta" ftype="fasta" /> + <element name="fetA_seqs" file="fetA_seqs.fasta" ftype="fasta" /> + <element name="porA_seqs" file="porA_seqs.fasta" ftype="fasta" /> + <element name="porB_seqs" file="porB_seqs.fasta" ftype="fasta" /> + </output_collection> + </test> + <test expect_num_outputs="1"> <!-- test4: test input collection --> + <conditional name="input"> + <param name="source" value="collection" /> + <param name="fastas"> + <collection type="list"> + <element name="input1" value="input.fasta.gz" ftype="fasta.gz" /> + <element name="input2" value="input2.fasta.gz" ftype="fasta.gz" /> + </collection> + </param> + </conditional> + <param name="db_source" value="builtin" /> + <param name="typing" value="mlst,finetype,bast,porb" /> + <output name="output_tsv"> + <assert_contents> + <has_n_columns n="11" /> + <has_n_lines n="2" /> + <has_text text="9367" /> + <has_text text="21-15,16" /> + <has_text text="F1-7" /> + <has_text text="NEIS2020_506" /> + <has_text text="27" /> + <has_text text="798" /> + <has_text text="0" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + meningotype_: In silico typing of Neisseria meningitidis contigs + + * Serotyping + + * MLST + + * Finetyping (porA, fetA, porB) + + * Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA) + + The databases used in the tool are sourced from PubMLST_. The default behaviour is to download updated + copies of the databases before running the tool. While this can be ineffecient for e.g. typing a single + isolate, the databases built-in to the tool are not the most recent versions. + + If many isolates are being typed, they can be provided as a dataset collection. The output of the tool + will contain one line of data for each isolate. + + By default the header line is not included in the tool output (to make concatenation of results easier). + + If output of matched alleles is requested, FASTA files are produced for each matching allele, with information + on which dataset was matched in the FASTA header. + + .. _meningotype: https://github.com/MDU-PHL/meningotype + .. _PubMLST: https://pubmlst.org/ + ]]></help> + <citations> + <citation type="bibtex"> + <![CDATA[ + @misc{Kwong2018, + author = {Kwong, J.C. and Gonçalves da Silva, A. and Stinear, T. P. and Howden, B. P. and Seemann, T.}, + title = {meningotype: in silico typing for Neisseria meningitidis.}, + year = {2018}, + publisher = {GitHub}, + journal = {GitHub repository}, + howpublished = {\url{https://github.com/MDU-PHL/meningotype}}, + commit = {aece5c9851c7ffc8357306a33a369307dddb726f} + } + ]]> + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/strip_header.py Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,8 @@ +#!/usr/bin/env python3 + +import sys + +if __name__ == '__main__': + next(sys.stdin) # skip first line + for line in sys.stdin: + sys.stdout.write(line)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NHBA_seqs.fasta Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,26 @@ +>input.fasta NHBA +GGCGTTCAGACGGCATATTTTTACAATTTTATGGGCATATGGCGGAAACAATACCGGCTG +CCTTGAATATGAAGGGGATGATGATGTTTGAACGCAGTGTGATTGCAATGGCTTGTATTT +TTGCCCTTTCAGCCTGCGGGGGCGGCGGTGGCGGATCGCCCGATGTTAAATCGGCGGACA +CGCTGTCAAAACCGGCCGCTCCTGTTGTTGCTGAAAAAGAGACAGAGGTAAAAGAAGATG +CGCCACAGGCAGGTTCTCAAGGACAGGGCGCGCCATCCACACAAGGCAGCCAAGATATGG +CGGCAGTTTCGGCAGAAAATACAGGCAATGGCGGTGCGGCAACAACGGACAAACCCAAAA +ATGAAGACGAGGGACCGCAAAATGATATGCCGCAAAATTCCGCCGAATCCGCAAATCAAA +CAGGGAACAACCAACCCGCCGATTCTTCAGATCCCATCCCCGCGTCAAACCCTGCCACTA +CGAATAGCGGCGGCGATTTTGGAAGGACGAACGTGGCTAATGGCATCAAACTTGACGGGC +CGTCGCAAAATATAACCTTGACCCATTGTAAAGACACAGTATGCGGTAGCAATTTCTTAG +CTGAAGAAGCACCGTCAAAATCAGAATTTGAATCGTTAGATGATTCTGGGCGAATTAATA +AATATAAAAAAGATGGACAGGATAAATTTACTAATTTGGTTGCGACAGAAGTTAAAGCTA +ATGGAACTAACAAATATGTCATCATTTATAAAGACAAGTCCACTTCATCTGCGCGAGTTA +GGCGTTCTGCACGGTCGAGGAGGTCGCTTCCCGCCGAGATGCCGCTGATCCCCGTCAATC +AGGCGGATACGCTGATTGTCGATGGGGAAGCGGTCAGCCTGACAGGGCACTCCGGCAATA +TCTTCGCGCCCGAAGGAAATTACCGGTATCTGACTTACGGGGCGGAAAAATTGTCCGGCG +GATCGTATGCCCTCCGTGTGCAAGGCGAACCTTCAAAAGGCGAAATGCTTGCGGGCGCGG +CCGTGTACAACGGCGAAGTGCTGCATTTCCATACGGAAAACGGCCGCTCGTACCCGACCA +GGGGCAGGTTTGCCGCAAAAGTCGATTTCGGCAGCAAATCTGTGGACGGCATTATCGACA +GCGGCGATGGTTTGCATATGGGTAAGCAAAAATTCAAAGCCGTTATCGATGGAAACGGCT +TTAAGGGGACTTGGACGGAAAATGGCGGCGGGGATGTTTCCGGAAGGTTTTACGGCCCGG +CCGGCGAGGAAGTGGCGGGAAAATACAGCTATCGCCCGACAGATGCGGAAAAGGGCGGAT +TCGGCGTGTTTGCCGGCAAAAAAGAGCAGGATTGATGCTGATGCCGCCCGAAGCGGGGGC +GTTCAGACGGCATTGTGATGTTTGGGGTGGGGTCCGGTTCAAGTCCGCATCAGTTGATAA +ACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NadA_seqs.fasta Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,9 @@ +>input.fasta NadA +GTGGACGTACTCGACTACGAAGGCAAAAAACTCATCGTCCACCATATCTGAAGCTCAAAA +AGAAAATGCCGTCTGAAAGGCTTTCAGACGGCATTTCCATTCCAAACGCTCAAACCGCCG +CGTCCGCACGTTCGCCCGTGCGGATACGGATTGCCTCCTCGACCGGCAGCACAAAAATCT +TGCCGTCGCCGATTTTTCCCGAACGCGCCACCTCGACAATCACGTCAATCGCGCGTTCCA +CAGCGTCATCCGCCAACACCAGCTCGATTTTGACCTTGGGCAGGAAATCGACGGCGTATT +CCGCACCGCGATAGATTTCCGTATGCCCCTTCTGCCTGCCGAACCCTTTGACCTCGCTGA +CGGTCATGCCCGTAATGCCGATTTCCGTCAACGCCTCGCGCACGTCGTCGAGTTTGAACG +GTTTGACAATCGCCTCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fHbp_seqs.fasta Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,78 @@ +>input.fasta fHbp +GACCTGCCTCATTGATGCGGTATGTAAAAAAAGATACAATAACTAGGGCGTGTCCTCAAT +TTAACTTAGCATGAATAATAGAGCAAGCCAAGTAAAGCATCGATTTAAAATTACGAGCTA +ATTTCTCATAGCGAGTAGCAATACTACGAAACTGCTTTAATCGTGCAAATGCATTCTCGA +CTAAGTGGCGTAATTTATAAAGGTAGCTATCAAAATCAGGGTTAGGTTTCTTGGCATTTT +TACGCTTTGGTATAATAGCTTTCATACCGTGTTCTATCGCTTTATCTCTGATTTCTTGCG +AGTCATACCCTTTGTCAGCGATAAAATACTGGGCTTCTTGTATGACTTCTATCAAGTCGT +TTGCAACTTGACCGTCGTGCACGTTACCCCCAGTGACTTTAAAATCGAGCGGATTTCCAT +GCGAGTCCACACATAGGTGTATTTTTGTCGTGTTTCCGCCACGGCTTTGTCCAATTGCTC +TATCGAAACCACGCCGAGCTCCACTTGCATGTTGATGACACCGTACATAACTTCCGTCGA +TGAATACCCATTCTTTGTCAATTTCTTTTCGTAGATCAAAAAAAAATTCTGCCACAAGCC +TTTTTTAGACCATCGGTTAAAGCGGTTATAAGCGGTTTTCCATGACCCTAGCTCAATAGG +TATGTCTCGCCATGGTGCACCTGTTCTTAGCTTCCATAGTATGGCTTCCATCACGGTACG +GTCGTTCTTCCATTGATGACAGCCGTGCGCTTTCATGGTTGTTTGTAATTGTTCCCATAT +GTTGTCAGTTATTGCGGTTCTCGCCATTGTTTGTGTTTGCCTATATTTCGTTGGAATATA +GGGTTAAAATAGGGCTCTTTTGGGCTTATTCAAATTAGGGACACGCCCTAGGGTGTTTAT +ATATTATCTATATCTGCGTATGACTAGGAGTAAACCTGTGAACCGAACTGCCTTCTGCTG +CTTTTCTCTGACCGCCGCCCTGATTCTGACCGCCTGCAGCAGCGGAGGGGGCGGTGTCGC +CGCCGACATCGGTGCGGGGCTTGCCGATGCACTAACCGCACCGCTCGACCATAAAGACAA +AGGTTTGCAGTCTTTAACGCTGGATCAGTCCGTCAGGAAAAACGAGAAACTGAAGCTGGC +GGCACAAGGTGCGGAAAAAACTTATGGAAACGGCGACAGCCTTAATACGGGCAAATTGAA +GAACGACAAGGTCAGCCGTTTCGACTTTATCCGTCAAATCGAAGTGGACGGGCAGCTCAT +TACCTTGGAGAGCGGAGAGTTCCAAATATACAAACAGGACCACTCCGCCGTCGTTGCCCT +ACAGATTGAAAAAATCAACAACCCCGACAAAATCGACAGCCTGATAAACCAACGCTCCTT +CCTTGTCAGCGGTTTGGGCGGAGAACATACCGCCTTCAACCAACTGCCTGACGGCAAAGC +CGAGTATCACGGCAAAGCATTCAGCTCCGACGATGCTGGCGGAAAACTGACCTATACCAT +AGATTTCGCCGCCAAACAGGGACACGGCAAAATCGAACACCTGAAAACACCCGAGCAAAA +TGTCGAGCTTGCCGCCGCCGAACTCAAAGCAGATGAAAAATCACACGCCGTCATTTTGGG +CGACACGCGCTACGGCAGCGAAGAAAAAGGCACTTACCACCTCGCCCTTTTCGGCGACCG +CGCCCAAGAAATCGCCGGCTCGGCAACCGTGAAGATAGGGGAAAAGGTTCACGAAATCGG +CATCGCCGGCAAACAGTAGCATTTGAAAAATGCCGTCCGAACACGATAATTTACCG +>input.fasta fHbp +GACCTGCCTCATTGATGCGGTATGTAAAAAAAGATACAATAACTAGGGCGTGTCCTCAAT +TTAACTTAGCATGAATAATAGAGCAAGCCAAGTAAAGCATCGATTTAAAATTACGAGCTA +ATTTCTCATAGCGAGTAGCAATACTACGAAACTGCTTTAATCGTGCAAATGCATTCTCGA +CTAAGTGGCGTAATTTATAAAGGTAGCTATCAAAATCAGGGTTAGGTTTCTTGGCATTTT +TACGCTTTGGTATAATAGCTTTCATACCGTGTTCTATCGCTTTATCTCTGATTTCTTGCG +AGTCATACCCTTTGTCAGCGATAAAATACTGGGCTTCTTGTATGACTTCTATCAAGTCGT +TTGCAACTTGACCGTCGTGCACGTTACCCCCAGTGACTTTAAAATCGAGCGGATTTCCAT +GCGAGTCCACACATAGGTGTATTTTTGTCGTGTTTCCGCCACGGCTTTGTCCAATTGCTC +TATCGAAACCACGCCGAGCTCCACTTGCATGTTGATGACACCGTACATAACTTCCGTCGA +TGAATACCCATTCTTTGTCAATTTCTTTTCGTAGATCAAAAAAAAATTCTGCCACAAGCC +TTTTTTAGACCATCGGTTAAAGCGGTTATAAGCGGTTTTCCATGACCCTAGCTCAATAGG +TATGTCTCGCCATGGTGCACCTGTTCTTAGCTTCCATAGTATGGCTTCCATCACGGTACG +GTCGTTCTTCCATTGATGACAGCCGTGCGCTTTCATGGTTGTTTGTAATTGTTCCCATAT +GTTGTCAGTTATTGCGGTTCTCGCCATTGTTTGTGTTTGCCTATATTTCGTTGGAATATA +GGGTTAAAATAGGGCTCTTTTGGGCTTATTCAAATTAGGGACACGCCCTAGGGTGTTTAT +ATATTATCTATATCTGCGTATGACTAGGAGTAAACCTGTGAACCGAACTGCCTTCTGCTG +CTTTTCTCTGACCGCCGCCCTGATTCTGACCGCCTGCAGCAGCGGAGGGGGCGGTGTCGC +CGCCGACATCGGTGCGGGGCTTGCCGATGCACTAACCGCACCGCTCGACCATAAAGACAA +AGGTTTGCAGTCTTTAACGCTGGATCAGTCCGTCAGGAAAAACGAGAAACTGAAGCTGGC +GGCACAAGGTGCGGAAAAAACTTATGGAAACGGCGACAGCCTTAATACGGGCAAATTGAA +GAACGACAAGGTCAGCCGTTTCGACTTTATCCGTCAAATCGAAGTGGACGGGCAGCTCAT +TACCTTGGAGAGCGGAGAGTTCCAAATATACAAACAGGACCACTCCGCCGTCGTTGCCCT +ACAGATTGAAAAAATCAACAACCCCGACAAAATCGACAGCCTGATAAACCAACGCTCCTT +CCTTGTCAGCGGTTTGGGCGGAGAACATACCGCCTTCAACCAACTGCCTGACGGCAAAGC +CGAGTATCACGGCAAAGCATTCAGCTCCGACGATGCTGGCGGAAAACTGACCTATACCAT +AGATTTCGCCGCCAAACAGGGACACGGCAAAATCGAACACCTGAAAACACCCGAGCAAAA +TGTCGAGCTTGCCGCCGCCGAACTCAAAGCAGATGAAAAATCACACGCCGTCATTTTGGG +CGACACGCGCTACGGCAGCGAAGAAAAAGGCACTTACCACCTCGCCCTTTTCGGCGACCG +CGCCCAAGAAATCGCCGGCTCGGCAACCGTGAAGATAGGGGAAAAGGTTCACGAAATCGG +CATCGCCGGCAAACAGTAGCATTTGAAAAATGCCGTCCGAACACGATAATTTACCGTTCG +GACGGCATTTTTGCGCCATACCGCCCTAGGATACGACGGCACGGCAGGCAAGCCGGTTTC +ACTATATAATGCCGTCTGAACCAACGAGAACCACACCATGCAAGCCGATTTCAACCGCCC +CGTCCTCGCCGTCGATACCGGAACTTCCTATTTATCGCTCGCGCTGCGCGCCGACGGCGA +AACCCTCCTGTTCCATCAGGAGGCCGGCAGCCGCCAGTCCGAACTGATCCTGCCGGAAAT +CCGCACCCTATTCCGAAATGCGGGCATTACCGCCGCCGATTTGGGGGCGATTGTTTATGC +GAAAGGTCCCGGCGCGTTTACGGGACTGCGTATCGGCATCGGCGTGGCGCAAGGTTTGGC +AACGCCGTTTGATACGCCTTTAATCGGCATCCCCACGCTCGATGCCGCCGCCTCGCTGCC +GCCGCCGCAAAGCTGCATACTCGCCGCTGCGGACGCGCGTATGGGCGAAGTGTTTTATGC +GTGGTTCGACACGCTGAACCGCCGCCGTTTGAGCGGTTATCAAGTCGGTAGGGCGGCAGA +CATTGCCCTTCCCGAGGGACACGTCTTTTCAGACGGCATCGGCAATGCGTTCGCGCTGGA +AAACCGTCCGCCCTTCACAGGCAAACCCGATATGCCGACTGCCGCCGATTTTCTCAATCT +GGCGGAAGAAGGCGGTTTTCCCGCCGTCGCTGCGGCACACGCCGAGCTGCTCTACGTCCG +CAACAAAATCGCCTTGACTGCCAAAGAACAGGCGGAACGGAAAGCCCGAACATGAACATC +CGCCGCGCCTCACCGTCCGACTGCGCCGCACTCGCCGCGCTCGATGCCGTCTGCAACCCG +TCCGCGTGGACGCAACGCCAATTTGAGTCCGCATTGGTTTCGCCGTCCGAACAGGTTTTC +CTCGCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fetA_seqs.fasta Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,9 @@ +>input.fasta FetA +TTCAACTTCGACAGCCGCCTTGCCGAACAAACCCTGCTGAAATACGGTATCAACTACCGC +CATCAGGAAATCAAACCGCAAGCATTTTTGAATTCACAATTTAAAATTGAAGATAAAAAA +GATGCAACTGATGAAGAGAAAAAGAAGAACCGTGACAATGAAAACATTGCCAAAGCCTAC +CGTCTGACCAACCCGACCAAAACCGATACCGGCGCGTATATCGAAGCCATTCACGAGATT +GACGGCTTTACCCTGACCGGCGGGCTGCGTTACGACCGCTTCAAGGTGAAAACCCATGAC +GGCAAAACCGTTTCAAGCAGCAACCTTAACCCGAGTTTCGGTGTGATTTGGCAGCCGCAC +GAACACTGGAGCTTCAGCGCGAGCCACAACTACGCCAGCCGCAGCCCGCGCCTGTATGAC +GCGCTGCAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tsv Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,1 @@ +input.fasta - - - 21-15,16/21-15,16 F1-7/F1-7 new 27 798 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/porA_seqs.fasta Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,13 @@ +>input.fasta PorA +TTACCGCCCTCGTATTGTCCGCACTGCCGCTTGCGGCCGTTGCCGATGTCAGCCTGTACG +GCGAAATCAAAGCCGGCGTGGAAGGCAGGAACATCCAGGCGCAATTGACCGAGCAGCCCC +AAGTAACTAACGGTGTGCAAGGCAAGCAGGTAAAAGTTACTAAGGCCAAAAGCCGCATCA +GGACGAAAATCAGTGATTTCGGCTCGTTTATCGGCTTTAAGGGGAGCGAGGATTTGGGCG +AAGGTCTGAAGGCTGTTTGGCAGCTTGAGCAAGACGTATCCGTTGCCGGCGGCGGCGCGA +CCCAGTGGGGTAACAGGGAATCCTTTATCGGCTTGGCAGGCGAATTCGGCACGCTGCGCA +CCGGCCGCGTTGCAAATCAGTTTGACGATGCCAGCCAAGCCATTGATCCTTGGGACAGCA +ATAATGATGTGGCTTCGCAATTGGGTATTTTCAAACGCCACGACGATATGCCGGTTTCCG +TACGCTACGATTCTCCGGAATTTTCCGGTTTCAGCGGCAGCGTCCAATTCGTTCCGGCTC +AAAACAGCAAGTCCGCCTATAAGCCGGCTTATTATACTAAGGATACAAACAATAATCTTA +CTCTCGTTCCGGCTGTTGTCGGCAAGCCCGGATCGGATGTGTATTATGCCGGTCTGAATT +AC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/porB_seqs.fasta Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,18 @@ +>input.fasta PorB +ATGAAAAAATCCCTGATTGCCCTGACTTTGGCAGCCCTTCCTGTTGCAGCAATGGCTGAC +GTTACCCTGTACGGCACCATCAAAGCCGGCGTAGAAACTTCCCGCTCCGTAGCTCACAAT +GGAGCTCAGGCGGCTAGCGTTGAAACCGGTACCGGCATCGTTGATTTGGGTTCGAAAATC +GGCTTCAAAGGCCAAGAAGACCTCGGTAACGGTCTGAAAGCCATTTGGCAGGTTGAGCAA +AAGGCATCTATCGCCGGTACTGACTCCGGTTGGGGCAACCGCCAATCCTTCATCGGTTTG +AAAGGCGGCTTCGGTAAATTGCGCGTCGGCCGTTTGAACAGCGTCCTGAAAGACACCGGC +GACATCAATCCTTGGGATAGCAAAAGCGACTATTTGGGTGTAAACAAAATTGCCGAACCC +GAAGCACGCCTCATTTCCGTACGCTACGATTCTCCCGAATTTGCCGGCCTCAGCGGCAGC +GTACAATACGCGCTTAACGACAATGCAGGCAGACATAACAGCGAATCTTACCACGCCGGC +TTCAACTACAAAAACGGCGGCTTCTTCATGCAATATGGCGGTGCCTATAAAAGACATCAG +AATGTGGATGACGTGAAGATTGAGAAATACCAGATTCACCGTTTGGTCAGCGGTTACGAC +AATGATGCCCTGTACGCTTCCGTAGCCGTACAGCAACAAGACGCGAAACTGGTTGAAGAC +AATTCGCACAACTCTCAAACCGAAGTTGCCGCTACCTTGGCATACCGCTTCGGCAACGTA +ACGCCCCGCGTTTCTTACGCCCACGGCTTCAAAGGCTCGTTTGATGATGCAAACTACACC +AACGATTACGACCAAGTGGTTGTCGGTGCGGAATACGACTTCTCCAAACGCACTTCTGCC +TTGGTTTCTGCCGGTTGGTTGCAAGAAGGCAAAGGCGAAAGCAAATTCGTATCGACTGCC +GGCGGTGTCGGTCTGCGCCACAAATTCTAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update_db.py Tue Jun 13 11:04:30 2023 +0000 @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 + +import pathlib +import shutil +import subprocess + +import meningotype + +if __name__ == '__main__': + db_path = 'db' + original_db_path = pathlib.Path(meningotype.__file__).parent / 'db' + shutil.copytree(original_db_path, db_path) + cmd = ["meningotype", "--updatedb", "--db", db_path] + subprocess.run(cmd)