pcalf 0.0.3

Search calcyanin in a set of amino acid sequences

pcalf stand for Python CALcyanin Finder.

pcalf pydoc is availbable here.

        _ (.".) _    
       '-'/. .\'-'   
         ( o o )     
          `"-"`  

Benzerara, K., Duprat, E., Bitard-Feildel, T., Caumes, G., Cassier-Chauvat, C., Chauvat, F., ... & Callebaut, I. (2022). A new gene family diagnostic for intracellular biomineralization of amorphous Ca carbonates by cyanobacteria. Genome Biology and Evolution, 14(3), evac026. DOI:https://doi.org/10.1093/gbe/evac026

Calcyanins are searched in a set of amino acid sequences using a weighted HMM profile specific of the glycine zipper triplication (aka GlyX3). Sequences with at least one hit against this profile are annotated with three HMM profiles specific of each Glycines zipper (Gly1, Gly2 and Gly3). A set of known calcyanins is used to infere the type of the N-ter extremity (X, Z, Y or CoBaHMA). Finally, a flag is assign to each calcyanin depending on its N-terminus type and its C-terminus modular organization.

Dependencies :

pyhmmer==0.7.1
biopython==1.81
numpy==1.22.4
pyyaml==6.0
snakemake==7.22
pandas==1.5.3
tqdm==4.64.1

External dependency :

blast

Input :

CDS in fasta format (faa) [gzip or not] or a tabular file with one "file designation\tpath/to/fasta/file" per line.

Output :

.
├── HMM/*.hmm (updated)
├── MSA/*.msa.fa (updated)
├── pcalf.features.tsv
├── pcalf.summary.tsv
└── N-ter-DB.tsv (updated)

INSTALLATION

mamba create -n pcalf -c bioconda blast pyhmmer pandas numpy biopython tqdm python=3.9 && conda activate pcalf;
pip3 install https://github.com/K2SOHIGH/pcalf.git

USAGE

pcalf -i fasta.cds.fa.gz -o pcalf_res