#TEdenovo using REPET v2 #==============================================================================
#TEdenovo.py from REPET v2 WORKS with phyton2:
#module load python/2.7.15
#You can run TEdenovo using the sequence provided as example "DmelChr4.fa", or replace with your fasta file (assembly) of interest.
#RENAME the project name in the configuration file TEdenovo.cfg #[project] #project_name: DmelChr4
#Edit TEdenovo.cfg and ./runTEdenovo in order to adapt it to your personal situation. More in https://urgi.versailles.inra.fr/Tools/REPET/TEdenovo-tuto
#The output is a MCL-filtered library of TEs located in {NAME}_Blaster_GrpRecPil_Struct_Map_TEclassif_Filtered_MCL
#==============================================================================
On the FASTA files you use: * There is a 15-character limit on the name of the file (and the project name) * Make sure there is a line break at least once every 60 bases * Make sure there are no illegal characters in the FASTA headers
##LINE BREAK (https://bioinf.shenwei.me/seqkit/) seqkit seq -w 60 Sp.fasta > Sp.fna
##RENAME fasta headers awk '/^>/{print ">Sp_ctg" ++i; next}{print}' < Sp.fna > Sp.fst
##ALL CAPITAL LETTERS awk 'BEGIN{FS=" "}{if(!/>/){print toupper($0)}else{print $1}}' Sp.fst > Sp.fa
#==============================================================================