Scripts are grouped in folders depending on the purpose the were used for.
We create eda_r conda environment , to work with traits_eda.Rmd script
mamba env create --file envs/eda_r.yaml
We dowonload Newick tree (with PHAST estimated branch lengths from 241-way Zoonomia mammalian alignment, update V2 ):
wget https://cgl.gi.ucsc.edu/data/cactus/241-mammalian-2020v2.phast-242.nh
We have followed the instructions on https://github.com/linudz/caastools to intall it.
We create conda environment with dependencies needed by CAAStools
mamba env create --file envs/caast_test.yaml
We can run localy the example provided with:
bash scripts/local_caas_test.sh
Commands for running internal covariation in all contrasts:
python scripts/internal_validation.py "functional/df_byFGN.txt" "functional/4fam_other_spp.txt"
python scripts/internal_validation.py "functional/cebi_atel_byFGN.txt" "functional/cebi_atel_other_spp.txt"
python scripts/internal_validation.py "functional/lemu_atel_byFGN.txt" "functional/lemu_atel_other_spp.txt"
python scripts/internal_validation.py "functional/cerco_atel_byFGN.txt" "functional/cerco_atel_other_spp.txt"
python scripts/internal_validation.py "functional/cerco_lemu_byFGN.txt" "functional/cerco_lemu_other_spp.txt"
python scripts/internal_validation.py "functional/cerco_cebi_byFGN.txt" "functional/cerco_cebi_other_spp.txt"
python scripts/internal_validation.py "functional/cebi_lemu_byFGN.txt" "functional/cebi_lemu_other_spp.txt"
To obtain protein location of our detected CAAS:
We run first Alejandro's file
python DATA_RAW_ALIGNMENTS_AND_POSITIONS/Extract_genomic_coordinates.py DATA_RAW_ALIGNMENTS_AND_POSITIONS/selected_cds_files DATA_RAW_ALIGNMENTS_AND_POSITIONS/Homo_sapiens.cds.fa.gz DATA_RAW_ALIGNMENTS_AND_POSITIONS/selected_html_files DATA_RAW_ALIGNMENTS_AND_POSITIONS/Homo_sapiens.sorted.gff out/functional/cebi_lemu_byFGN.txt out/coordinates_cebi_lemu_genes005.tab DATA_RAW_ALIGNMENTS_AND_POSITIONS/proteiID_gene_equivalences.txt out/functional/genes_cebi_lemu005.tsv
I have downloaded Homo_sapiens.CDS.fa.gz made with the Ensemble 104 annotation version from
https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cds/
Info of this file on https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cds/README
python DATA_RAW_ALIGNMENTS_AND_POSITIONS/select_gene_files.py DATA_RAW_ALIGNMENTS_AND_POSITIONS/Complete_CDS_alignments.tar.gz DATA_RAW_ALIGNMENTS_AND_POSITIONS/FILTER_CODONS-001.tar.gz DATA_RAW_ALIGNMENTS_AND_POSITIONS/selected_html_files DATA_RAW_ALIGNMENTS_AND_POSITIONS/selected_cds_files out/functional/genes_cebi_lemu005.tsv
We run transvar script with:
bash DATA_RAW_ALIGNMENTS_AND_POSITIONS/run_obtain_protposition.sh