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Domain Analyzer

created 2023 by gaenssle written in Python 3.8

Process

  • The input is an ID, e.g. domain name (PFAM or UniProt ID)
  • Various databases are accessed via Genome.jp, e.g. KEGG or UnitProt
  • All available protein data associated with the input ID are downloaded
  • The downloaded data is extracted, accumulated and counted
  • Various output files are generated, including FASTA

Data

  • Downloaded sequence data:
    • Assigned description
    • Organism and taxonomy
    • Sequence
    • Domain architecture
    • Available IDs from other databases
  • Count:
  • Taxonomy (Phylum and organism)
  • Domain architecture
  • Save data in the following files:
    • Gene IDs
    • Gene details (organism, architecture, sequence, etc)
    • Summary domain architecture
    • Summary of taxonomic distribution
    • Fasta files (containing entire sequence)
    • Fasta files (only containing the target domain sequence)

Dependencies

  • The program used python 3.8 and the following modules:
    • pandas
    • argparse
    • multiprocessing (optional for Linux)

How to use

python3 Main.py name [-h] [-m] [-ask] 
               [-db DBLIST] [-a ACTION] [-st SEARCHTYPE]
               [-c CUTOFF] [-sam SAMPLESIZE] [-f FOLDER] [-cs CLUSTERSIZE]
               [-ft FILETYPE] [-sep SEPARATOR]


positional arguments:

  name                  name of the domain

optional arguments:
  -h, --help            show this help message and exit
  -m, --multiprocess    turn on mutltiprocessing (only for Linux)
  -ask, --askoverwrite  ask before overwriting files
  -db DBLIST, --dblist DBLIST
                        list databases to be searched, separated by ','
                        (default: UniProt;KEGG;PDB;swissprot)
  -a ACTION, --action ACTION
                        add actions to be conducted: a=all, i=entry IDs,
                        d=protein data, m=KEGG motif, e=extract (default: a)
  -st SEARCHTYPE, --searchtype SEARCHTYPE
                        type of the searched id (default: pf)
  -c CUTOFF, --cutoff CUTOFF
                        min E-Value of Pfam domains (default: 0.0001)
  -sam SAMPLESIZE, --samplesize SAMPLESIZE
                        max number of downloaded entries (default: 0)
  -f FOLDER, --folder FOLDER
                        name of the parent folder (default: same as 'name')
  -cs CLUSTERSIZE, --clustersize CLUSTERSIZE
                        entries/frament files (default: 100)
  -ft FILETYPE, --filetype FILETYPE
                        type of the generated files (default: .csv)
  -sep SEPARATOR, --separator SEPARATOR
                        separator between columns in the output files
                        (default: ;)