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Scripts-for-RepeatExplorer2-parsing

./screenshot_repex.py - script used to copy the most infromative lightweight files from RepeatExplorer2 output

./KA16, ./KA27, ./KA25KK6(1to2) - examples of RepeatExplorer2 output, copied with screenshot_repex.py ./cypher.csv - an example of species annotation used for table creation ./README.txt - demo analysis

./ncbi_repeats_db - the local variant of NCBI Nucleotide we have used with notes on how to adapt it for your experiment ./ncbi_naming.csv - an example of NCBI seqs annotation ./solo_annotation - an output directory for the most scripts

./get_fastas.sh - used to create blastdbs for blast.py, stores them in ./local_db_solo and ./comparatives_db e.g.: bash ./get_fastas.sh

./blast.py - required for represenation.py

./represenation.py - produces tables for the RepeatExplorer2 output e.g.: python3 ./represenation.py "KA16" "local" python3 ./represenation.py "KA25KK6(1to2)" "comp"

./repeat_sums_by_group.py - used to create tables with percentages of mobile elements by type

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