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 trapicalusage:
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
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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