I have this shell script that I wrote to check an input file to see if it is empty or not, and then clean the file from any line that starts with the sign "<" (without quotation marks" and then spell the number of line of the file, and the empty lines, too. The script then will create two output files, DNA.out and RNA.out.
First I get an error message at that says:
Code:
./script.sh: line 3: [: dna_input.txt: integer expression expected
but it gives me the results I want.
Here is the code:
Code:
#!/bin/bash
#check to see if there is an input file:
if [ $1 -lt 1 ]
then
echo "Usage: $0 file ..."
exit 1
fi
#Check if the file is empty or not
file=$1
if [[ -s $1 ]]
then
echo ""
echo "**** $file has data."
echo "Number of non-empty lines:"
grep -cve '^\s*$' $file
echo "Mumber of empty lines:"
grep -ce '^\s*$' $file
#grep -cvP '^\s*$' $file -- above line originally was like this one
echo ""
cat $1 | sed 's/>/\n>/g' > temp1.txt
cat temp1.txt | sed '/^>/ d' > temp2.txt
#Remove duplicate empty lines:
awk '!NF{if(++n <=1) print; next}; {n=0; print}' < temp2.txt > DNA.out
echo ""
#convert to mRNA and remove temp1, temp2 to avoid confusion
tr ACGT UGCA < DNA.out > RNA.out
rm temp1.txt temp2.txt
else
echo "**** $1 has no data, or file does not exist."
echo "**** done!"
echo ""
fi;
After I get the two output files (DNA.out and RNA.out) I use another script to convert the contents of these two files into Amino Acids. The conversion script is:
Code:
#!/bin/sh
while read rna;do
aawork=$(echo "${rna}" |sed -n -e 's/\(...\)/\1 /gp' | sed -f rna.sed)
echo "$aawork" | sed 's/ //g'
echo "$aawork" | tr ' ' '\012' | sort | sed '/^$/d' | uniq -c | sed 's/[ ]*\([0-9]*\) \(.*\)/\2: \1/'
done
Can my scripts be combined together in just one script? My script gives the frequencies of each Amino Acid. Also, I ask to learn how to add a while loop in a script if it takes an input of its own.
I like my code to run in /tmp file when I am using a static files.
Code:
#!/bin/bash
for i in /home/*/Desktop/test.txt; do cp $i /tmp/test.txt && echo "Usage: $i file ... " || echo "File is not where you think it should be";
sleep 3
done
exit 0
Consider trapping ( think that is what it called. Do a google) the file. So after checking that's the file exists with code above, follow up with ...
Code:
cd /tmp
sudo ./test.txt
And then within test.txt. Have this line of code. Which also checks the file was placed in /tmp. Then runs your test.txt file.
This is called trapping and insure the program will stop running when it is completed. You can also run sub routines under the trap before running main code body.
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