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comparison make_pan_library.sh @ 0:f1a157358d4d draft default tip

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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
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-1:000000000000 0:f1a157358d4d
1 #!/usr/bin/env bash
2
3 known_te=($1)
4
5 echo 'get classification info and convert #unknown to #DNA/Helitron'
6 for j in *mod.EDTA.TElib.novel.fa; do
7 for i in `cat $j.real`; do
8 grep $i $j;
9 done| \
10 perl -nle 's/#unknown/#DNA\/Helitron/; print $_' > $j.real.ori &
11 done
12
13 wait
14
15 echo 'aggregate novel TE libraries'
16 i=0
17 for j in *real.ori; do
18 i=$(($i+5000));
19 perl /EDTA/util/rename_TE.pl $j $i;
20 done > NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw
21 perl /EDTA/util/rename_TE.pl NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw > NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw2
22 mv NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw2 NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw
23
24 # wait
25
26 # echo 'remove redundant'
27 # nohup perl /EDTA/util/cleanup_nested.pl \
28 # -in NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw \
29 # -cov 0.95 \
30 # -minlen 80 \
31 # -miniden 80\
32 # -blast /opt/conda/lib/python3.6/site-packages/Bio/Blast &
33
34 # ls
35 # wait
36
37 # echo 'remove a number of false TEs and rename IDs'
38 # 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
39 # perl /EDTA/util/output_by_list.pl 1 NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw.cln 1 \
40 # <(awk '{print $5}' NAM.EDTA1.8.0.EDTA.TElib.novel.fa.raw.cln.out|grep TE) -ex -FA | \
41 # perl /EDTA/util/rename_TE.pl - > NAM.EDTA1.8.0.EDTA.TElib.novel.fa
42
43 # echo 'make comprehensive TE library'
44 # cat $known_te NAM.EDTA1.8.0.EDTA.TElib.novel.fa > NAM.EDTA1.8.0.TE11122019.TElib.fa
45
46 # echo 'finished make_pan_library'
47