# zagor # set of commands B) ########################### ### post R script chunk ### # if not: cd ../intermediate dos2unix singletons.tetra.seqID.txt dos2unix singletons.DM.seqID.txt xargs faidx -d ' ' ../input/5cv.aa.fasta < singletons.tetra.seqID.txt > stPanTr_aa_singletons.tetraploid.fasta 2> stPanTr_aa_singletons.tetraploid.error; xargs faidx -d ' ' ../input/5cv.aa.fasta < singletons.DM.seqID.txt > stPanTr_aa_singletons.DM.fasta 2> stPanTr_aa_singletons.DM.error; # replace * in polypeptide Sotub sequences with X sed 's/[*]/X/g' stPanTr_aa_singletons.DM.fasta | sponge stPanTr_aa_singletons.DM.fasta ################## ### cdhit-2d ### ################## cdhit-2d -i stPanTr_aa_singletons.DM.fasta \ -i2 stPanTr_aa_singletons.tetraploid.fasta \ -o stPanTr_aa_singletons_tetra_on_DM_aS.45_c.90 \ -G 0 -n 5 -g 1 -c 0.90 -aS 0.45 -p 1 -bak 1 -d 200 -b 45 -uS 0.55 \ -M 0 -T 28; # 43005 compared 429 clustered cdhit-2d -i stPanTr_aa_singletons.tetraploid.fasta \ -i2 stPanTr_aa_singletons.DM.fasta \ -o stPanTr_aa_singletons_DM_on_tetra_aS.45_c.90 \ -G 0 -n 5 -g 1 -c 0.90 -aS 0.45 -p 1 -bak 1 -d 200 -b 45 -uS 0.55 \ -M 0 -T 28; # 17439 compared 262 clustered # now run ## chunks: cdhit-2d 1 - cdhit-2d 8 and , merge 1 - , merge 5 rm ../input/5cv.aa.fasta rm ../input/5cv.cds.fasta