batch MLST of species

Purpose: to get allele (nucleotide) sequences according to multi-locus sequence types (STs)

Input

• a tab-delimited file (despite its extension enigmatically being TXT) from PubMLST, labeled as a 'profile' for a particular species database
• all multi-FastA formatted files of alleles for the specified profile in the cwd; default file extension is TFA as PubMLST uses, however any extension can be specified with the --ext opt

Output

• multi-FastA format file of each allele for a ST (ST-##.fas)
• a FastA file of the concatenated alleles for a ST (concat_ST-##.fas)

Usage

python get_allele_seqs_from_PubMLST_db.py -p profile.txt

Example Install

cd $HOME
pip install biopython numpy
git clone https://github.com/chrisgulvik/batch_MLST_of_species.git
echo 'export PATH="$PATH:$HOME/batch_MLST_of_species"' >> $HOME/.bash_profile
chmod u+x ~/batch_MLST_of_species/get_allele_seqs_from_PubMLST_db.py

Example Usage

Step 1 - Download profile and corresponding alleles:

mkdir ~/Cdiff_MLST && cd ~/Cdiff_MLST
for f in {profiles/cdifficile.txt,alleles/cdifficile/adk.tfa,alleles/cdifficile/atpA.tfa,alleles/cdifficile/dxr.tfa,alleles/cdifficile/glyA.tfa,alleles/cdifficile/recA.tfa,alleles/cdifficile/sodA.tfa,alleles/cdifficile/tpi.tfa};
    do wget http://pubmlst.org/data/"$f";
done

Step 2 - Get all allele sequences for each ST

get_allele_seqs_from_PubMLST_db.py -p cdifficile.txt
ls concat_ST-*.fas | xargs cat > 351_Cdiff_concat_MLSTs.fa
rm *.fas

Step 3 - Align and infer phylogeny

muscle -in 351_Cdiff_concat_MLSTs.fa -out 351_Cdiff_concat_MLSTs.fa.aln
python ~/scripts/fasta2phylip.py 351_Cdiff_concat_MLSTs.fa.aln 351_Cdiff_concat_MLSTs.aln.phy
# collapse invariant sites
raxmlHPC-PTHREADS -T 30 -f a -s 351_Cdiff_concat_MLSTs.aln.phy -n Cdiff_concat_MLSTs -p 654321 -x 54321 -N 100 -m GTRGAMMA