/gen_scripts

genetics python scripts

Primary LanguagePython

data

All the required data for scripts to run.

  • /absense
    • Bitscore, distances, and lengths files
  • /blast
    • Self vs self blast for all species
  • /busco
    • Dmel vs busco and busco v dmel blast files
  • /fasta
    • Gene sequences in all species
  • drosophilaDatabase_neop
    • Gene database (singletons, duplicable, rate)
  • orthogroups.txt
    • Orthofinder orthogroups file
  • sequence_ids.txt
    • Orthofinder gene ids file
  • species_ids.txt
    • Orthofinder species ids file

out

All the script outputs.

  • /absense
    • Absense results
  • /gprofiler
    • Gprofiler results
  • /plots
    • Various plots from different scripts
  • busco_groups.txt
    • Busco vs dmel reciprocal best hits -> orthogroups containing those genes
  • absense_example.png - temp
  • paralogs.txt - temp

scripts

All the scripts.

  • busco
    • Find all BUSCO Orthogroups
  • gp
    • Runs GProfiler (fastevo, singleton, duplicable)
  • lengths
    • Length comparison (fastevo, singleton, duplicable)
  • paralogs
    • Paralog detection vs e-value cutoff (fastevo)
  • restriction
    • Lineage restriction (fastevo)

misc

  • NOTE: not all scripts from the old repo have been refactored yet! - in particular the absesnse stuff
  • TODO: ask about the boxplot stuff
  • TODO: ask about the database
  • TODO: list required libs somewhere (is there a python ver of package.json?)