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03 Mar 2017 16:23:59 UTC
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- License: gpl_3
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Andrew J. Page
- Dependencies
- Bio::AlignIO
- Bio::Perl
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- Bio::SimpleAlign
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Documentation
Downloads all the MLST databases to disk. It requires access to the Internet.Downloads all the MLST databases to disk. It requires access to the Internet.Given an assembly find the MLST sequence type of the emm gene from the CDC.Given an assembly find the MLST sequence type.Modules
Wrapper around NCBI BlastNWrapper around NCBIs makeblastdb commandTake in a fasta file of emmST sequences and convert it into an MLST formatMultilocus sequence type checking using blastHigh throughput multilocus sequence typing (MLST) checking against several MLST databases.Get a list of matching alleles between the sequence and databaseRead in an XML file of settings and return a hash with the values.List available MLST databasesRepresents a single genus-species database on a single speciesRepresents multiple databases of speciesMoose Role to download everything dataFilter AllelesTake in a Fasta file, check for invalid characters and build a corrected file if needed.Take in two hashes, both containing sequence names and sequences and output fasta files.Take in a fasta file, lookup the MLST database and create relevant files.Take in a species name and get the allele and profile files.Take in a list of matched alleles and look up the sequence type from the profile.Create a file representation of the ST results for multiple fasta files.Create a row representation of the ST results for a single fasta file.Moose types to use for validation.Validates the executable is available in the path before running it.Check to see if a file exists. For validation when classes have input files.Check to see if a file exists or if a uri is valid. For validation when classes have input files which may be local or on the web.Examples
- example/README.md
- example/expected_output_data/concatenated_alleles.fa
- example/expected_output_data/mlst_results.allele.csv
- example/expected_output_data/mlst_results.genomic.csv
- example/input_data/Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1.fa
- example/input_data/Salmonella_enterica_subsp_enterica_serovar_Typhimurium_DT104_v1.fa
- example/input_data/Salmonella_enterica_subsp_enterica_serovar_Weltevreden_str_10259_v0.2.fa
- example/mlst_databases/Salmonella_enterica/alleles/aroC.tfa
- example/mlst_databases/Salmonella_enterica/alleles/dnaN.tfa
- example/mlst_databases/Salmonella_enterica/alleles/hemD.tfa
- example/mlst_databases/Salmonella_enterica/alleles/hisD.tfa
- example/mlst_databases/Salmonella_enterica/alleles/purE.tfa
- example/mlst_databases/Salmonella_enterica/alleles/sucA.tfa
- example/mlst_databases/Salmonella_enterica/alleles/thrA.tfa
- example/mlst_databases/Salmonella_enterica/profiles/senterica.txt
Module Install Instructions
To install Bio::MLST::Check, copy and paste the appropriate command in to your terminal.
cpanm Bio::MLST::Check
perl -MCPAN -e shell install Bio::MLST::Check
For more information on module installation, please visit the detailed CPAN module installation guide.