Analysis of host-bacteria protein interactions reveals conserved domains and motifs that mediate fundamental infection pathways
These scripts allow for the preprocessing steps of the PHISTO database and the generation and enrichment of domain-domain and motif-domain combinations.
It is important to decompress the .tar.xz files so the scripts can read the input files!
clean_phisto.py: Cleans the PHISTO database and generate the FASTA files required to run InterProScan. Generates all the domain combinations given the InterProScan output. Three functions are defined in this script:
- clean_phisto() takes as an input the PHISTO database (phi_data.csv) and outputs the UniProt IDs of all the host/pathogen proteins.
- sequences_and_fasta() generates the FASTA files required for InterProScan to predict the domains. The uniprot_host.xlsl and uniprot_pathogen.xlsl files are required to execute this function.
- domain_combinations() generates all the domain-domain combinations (host and pathogen proteins).
interpro_to_pfam.sh: Extracts only the PFAM records from the Interproscan output. Usage: bash interpro_to_pfam.sh [INPUT_FOLDER_CONTAINING_INTERPROSCAN_OUTPUTS] [OUTPUT_FOLDER]'. The host_fasta and pathogen_fasta folders are used as input and contain the outputs from InterProScan (.fasta.tsv files). InterProScan v5.56 was used (bash interproscan.sh -i fasta_file -f tsv).
host_motifs.py: Computes the IDR regions of the human proteins and find the ELM motifs in these regions. Generates the MD and DD combinations. Three functions are defined in this script:
- host_IDR() defines the IDRs given the accessibility scores retrieved from https://github.com/normandavey/ProcessedAlphafold. This function requires as an input a folder containing the accessibility scores for each human protein (host_windowed_scores).
- search_motifs() fetches the ELM motifs found in the IDRs. The ELM database is required (ELM_motifs.tsv).
- motif_domain_combinations() generates the motif-domain combinations.
select_enriched.py: Selects the enriched domain-domain and motif-domain combinations.
LICENSE
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