Mercurial > repos > dereeper > pangenome_explorer
comparison COG/bac-genomics-scripts/rod_finder/blast_rod_finder_legacy.sh @ 3:e42d30da7a74 draft
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author | dereeper |
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date | Thu, 30 May 2024 11:52:25 +0000 |
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2:97e4e3e818b6 | 3:e42d30da7a74 |
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1 #!/bin/bash | |
2 echo "###Running legacy BLASTN with subject '$1' and query '$2'" | |
3 formatdb -p F -i $1 -n ROD | |
4 blastall -p blastn -d ROD -i $2 -o blastn.out -e 2e-11 -F F | |
5 echo "###Running blast_rod_finder.pl with query '$3' and minimum ROD size '$4'" | |
6 perl blast_rod_finder.pl -q $3 -r blastn.out -m $4 |