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manrysh/Blast_blastp shell command muiti2multi comparison

Last active October 10, 2018 13:18
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Blast_blastp shell command muiti2multi comparison
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Blast_blastp shell command muiti2multi comparison
#Blast_blastp shell command muiti2multi comparison
#formatdb
formatdb -i xx -p F
#blastp
for k in ./faa; do blastall -p blastp -i xx -d $k -e 1e-3 -o xx_${k##*/}.txt;done
#.faa.txt_rename
rename -v s/\.faa.txt/\.txt/ *
#zusammen
for k in ../faa_prokka/*.faa; do m=${k##*/}; for j in ../faa_prokka/*.faa; do n=${j##/};if ["$k"!="$j"]; then blastall -p blastp li $k -d $j -e 1e-5 -o ${m%.*}_${n%.*}.txt;fi;done;done;
#Blast+
#formatdb
makeblastdb -in xx.faa -dbtype prot -out xx.db -parse_seqids -hash_index
#blastp
blastp -query xx.faa -db xx.db -out xx.blast -outfmt NUMBER -evalue 1e-5 -num_threads NUMBER
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