Yingying-Buynak Submission#5
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Problem 2
lyy005
reviewed
Dec 11, 2017
| outfile1.close() | ||
| outfile2.close() | ||
| outfile3.close() | ||
| vcffile.close() No newline at end of file |
lyy005
reviewed
Dec 11, 2017
| cat transporter.hits | grep -v "#" | wc -l | ||
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| ./hmmsearch --tblout sporecoat.hits sporecoat.hmm Verrucomicrobia.fasta | ||
| cat sporecoat.hits | grep -v "#" | wc -l |
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The goal of this exercise is to practice for loop. It would be good to use a loop in Linux command:
Also, make sure you only print out the proteome, e-value of the alignment
-0.1 pts
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 $outSpore sporecoat.hmm $file
hmmsearch --tblout $outTrans 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
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