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trapical: trapical rapidly aligns Pulsenet isolate core alleles

installation

Run the following commands to install trapical

git clone https://github.com/ncezid-biome/trapical.git
conda env create -f trapical/environment.yml
conda activate trapical

usage

usage:
    python3 trapical.py [-ifaocnvh]

required arguments:
    -i, --in            [directory] the directory containing the Pulsenet2.0 WGMLST results

optional arguments:
    -f, --fna_dir       [directory] the directory where locus fasta files should be written (default: ./loci_fastas)
    -a, --aln_dir       [directory] the directory where aligned locus files should be written (default: ./loci_alignments)
    -o, --out           [file] the name of the output alignment file (default: ./msa.aln)
    -c, --count         [file] the name of the file for conserved character counts (default: ./conserved_counts.csv)
    -n, --num_threads   [int] the number of processors for parallel processing (default: 1)
    -v, --version       prints the version
    -h, --help          prints this meessage
    --force             if specified, overwrite existing files and directories

workflow

flowchart TB
    %% variables
    input(["Pulsenet2.0 wgMLST results directory"])
    import1["import allele sequences"]
    import2["import core allele hashes"]
    count1["count conserved characters
            in loci with one allele"]
    write1[/"write a fasta for
             each core locus"/]
    align["align fastas with >1
           allele with clustalo"]
    extract["extract variable sites
             from each alignment"]
    concat["concatenate variable
            sites for each isolate"]
    count2["count conserved characters
           in each alignment"]
    write2[/"write concatenated
             alignment to file"/]
    write3[/"write conserved 
            character counts to file"/]
    
    %% workflow
    input --> import1
    input --> import2
    import1 --> write1
    import2 --> write1
    import1 --> count1
    write1 --> align
    align --> extract
    align --> count2
    extract --> concat
    concat --> write2
    count1 --> write3
    count2 --> write3
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