Mercurial > repos > bgruening > edta
diff make_pan_library.sh @ 0:f1a157358d4d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta commit 24cb0421330e54b144b3e6f1be4ae35ac0e48c1c
| author | bgruening |
|---|---|
| date | Sun, 16 Oct 2022 12:41:19 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_pan_library.sh Sun Oct 16 12:41:19 2022 +0000 @@ -0,0 +1,47 @@ +#!/usr/bin/env bash + +known_te=($1) + +echo 'get classification info and convert #unknown to #DNA/Helitron' +for j in *mod.EDTA.TElib.novel.fa; do + for i in `cat $j.real`; do + grep $i $j; + done| \ + perl -nle 's/#unknown/#DNA\/Helitron/; print $_' > $j.real.ori & +done + +wait + +echo 'aggregate novel TE libraries' +i=0 +for j in *real.ori; do + i=$(($i+5000)); + perl /EDTA/util/rename_TE.pl $j $i; +done > NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw +perl /EDTA/util/rename_TE.pl NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw > NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw2 +mv NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw2 NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw + +# wait + +# echo 'remove redundant' +# nohup perl /EDTA/util/cleanup_nested.pl \ +# -in NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw \ +# -cov 0.95 \ +# -minlen 80 \ +# -miniden 80\ +# -blast /opt/conda/lib/python3.6/site-packages/Bio/Blast & + +# ls +# wait + +# echo 'remove a number of false TEs and rename IDs' +# RepeatMasker -pa 36 -q -no_is -norna -nolow -div 40 -lib rm.fa -cutoff 225 NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw.cln +# perl /EDTA/util/output_by_list.pl 1 NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw.cln 1 \ +# <(awk '{print $5}' NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw.cln.out|grep TE) -ex -FA | \ +# perl /EDTA/util/rename_TE.pl - > NAM.EDTA1.8.0.EDTA.TElib.novel.fa + +# echo 'make comprehensive TE library' +# cat $known_te NAM.EDTA1.8.0.EDTA.TElib.novel.fa > NAM.EDTA1.8.0.TE11122019.TElib.fa + +# echo 'finished make_pan_library' +