Hello, I currently try to create a shell script to run a blast and then to align the result of my blast Here is the beginning of my script :
$1 -query $2 -db $3 -outfmt 6 -remote | awk '$3>95' > $4
Im not sure about the begining. Furthermore, i really dont know how i can, from my blast result extract the sequences and put them in a fasta file to run the alignement. Samtools ? I'd like to run the alignement using MAFFT.
can you help me ? Thanks a lot , iam really bloqued for now...
there is very little info to work on here, eg. what does the
$1
$2
... stand for? I also noticed you have twice$3
but in different places that do not make sense to have the same input.for extracting sequences based on a blast result you better use
blastdbcmd
from the blast package, as input for it you will need the DB used and the IDs of the hit sequences.Thank you for your answer.
I will try that and tell you if it fits my pupose. Thanks again