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I'm having an issue getting the variables $myname, $filename, and a method that counts all the records in another file, wc -l < hs_alt_HuRef_chr10.fa >> "$CuestaP.txt, to append to the text file CuestaP.txt. Code is below I don't see why they aren't appending.

myname="Pablo Andres Cuesta"    #creates variable containing my name

echo "Hello my name is:"    
echo "$myname"            #Display myname
echo
echo "This program is called:"    
filename=$(basename "$0")    #Display name of file without ./
echo "$filename"

echo

echo "$myname" >> "$CuestaP.txt" #Puts myname inside text file
echo "$filename" >> "$CuestaP.txt" # Puts file name inside text file

echo "The number of records inside the file 'hs_alt_HuRef_chr10' are:"
wc -l < hs_alt_HuRef_chr10.fa
wc -l < hs_alt_HuRef_chr10.fa >> "$CuestaP.txt" #Put amount of records inside file



echo "$USER" >> "$CuestaP.txt" #Add username to text file
echo "$PWD" >> "$CuestaP.txt" #Add file location to text file


if [ -s *.fa ]; then
    # read the age from the file.
    # if the file exists and is not empty, see flags above
    echo "my *.fa file exists and has data in it" >> 
"$CuestaP.txt" 

else
echo "THIS DID NOT WORK CORRECTLY" >> "$CuestaP.txt" 

fi

echo
cat CuestaP.txt

My output: Hello my name is: Pablo Andres Cuesta

This program is called:
CuestaPOGpgm3.sh   

The number of records inside the file 'hs_alt_HuRef_chr10' are:
1842651

#myname is missing
#filename is missing
#my *.fa file exists and has data in it is missing
pcuesta    #my username went through though?
/home/pcuesta    #my pwd went through though?
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  • Did you check whether the variable CuestaP contains the correct value? Perhaps the strings get appended to a different file than you expect. Do a set -x before appending the strings. Commented Mar 26, 2018 at 6:27

2 Answers 2

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The problem is the file name $CuestaP.txt. Either you want $ to be literally part of the file name then you need single quotes or a backslash: '$CuestaP.txt', \$CuestaP.txt. Or this is supposed to be a variable but then you both forgot to define it and mixed it with a literal.

Your data is in the file .txt

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  • I do not want $ to literally be part of the file name, this is suppose to be a variable, I thought to append things to a text file this was the correct syntax: echo "$myname" >> "$CuestaP.txt" How come this works for $USER and not the other variables I created? Commented Mar 25, 2018 at 20:34
  • @PabloCuesta You need something like logfile=CuestaP.txt and then you can use ... >>"$logfile". I seriously doubt that this works with $USER. You must be more precise anyway. Commented Mar 25, 2018 at 20:41
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[ -s *.fa ] will fail if there are multiple files that have filenames that end in .fa. You either test it with a single filename (hs_alt_HuRef_chr10.fa?) or you loop:

for name in *.fa; do
    if [ -s "$name" ]; then
        printf '"%s" has data in it\n' "$name"
    fi
done >>"$CuestaP.txt"

This, along with much of the rest of the output statements, assumes that CuestaP is a variable. $CuestaP.txt will expand to the contents of that variable, and .txt will be added to the end of the value.

As far as I can see, $CuestaP will expand to nothing, and most of your data will go to a file named .txt (a hidden file in the current directory).

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