Exercise 11 Problem Set#5
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whatzittoyah wants to merge 2 commits into
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collaborators S. Davitt and K. Fick
araiho
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Dec 6, 2017
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Good job working through this. You are almost there with problem 2. 3.9/4
| ../../../Bioinformatics/hmmer-3.1b2-macosx-intel/binaries/hmmbuild sporecoat.HMM sporecoat.align | ||
| ../../../Bioinformatics/hmmer-3.1b2-macosx-intel/binaries/hmmbuild transporter.HMM transporter.align | ||
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| for file in *.fasta |
Owner
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This works. Could have also done something like:
for file in *.fasta
do
outSigma=$file.Sigma.hits
outSpore=$file.Spore.hits
outTrans=$file.Trans.hits
./hmmsearch --tblout $outSigma sigma.hmm $file
./hmmsearch --tblout $out sporecoat.hmm $file
./hmmsearch --tblout $out transporter.hmm $file
done
cat *.hits | grep -v "#" | awk '{print $1,$3,$5}' | sed -E 's/tr|[A-Z0-9]+|[A-Z0-9]+_9//g' > hmmOut.txt
| } | ||
| #for loop to search for motifs and sort | ||
| for(i in data[,1]){ | ||
| if(grepl("AKKPRVZE", data[i,1])){ |
| for(i in data[,1]){ | ||
| if(grepl("AKKPRVZE", data[i,1])){ | ||
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| write(data[i,1], file = "motif1", append = TRUE) |
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