UNIX for Beginners Questions & Answers

If you want to read 19 values from a file I have no idea why you don't read those values from the file instead of using unneeded intermediate variables:

Code:

#!/bin/bash
echo " I AM OUTSIDE THE LOOP"

infile="calls.txt"

while IFS=',' read -r my_file1 species1 chrom1 my_file2 species2 chrom2 binSize foo1 foo2 foo3 \
    foo4 variance bar1 bar2 java_jar bar3 bar4 unit bar5
do
        echo " I AM INSIDE THE LOOP"

        # program calls here

done < "$infile"

But, of course, neither the way you were doing it nor what I have shown above does anything that shows the values of any of the 19 variables read from line in calls.txt.

What makes you think your code or the code above is not working? Do you actually have any code in place of:

Code:

        # program calls here

that actually tries to print those values? The only thing you have shown us in this script that produces (or should produce) any output is the two echo statements (which shows us that despite you saying that calls.txt contains one line, it appears that your script is reading three lines from it).

the point is, I can't even echo variables.

I get

Code:

> bash HiCoPi.sh 
I AM OUTSIDE THE LOOP

It seems he never enters the while loop. this is why the stuff in the "program calls"
section never runs.

once again, please show the output of cat -vet ./calls.txt using code tags.

calls.txt:

Code:

/path/to/my/file.txt,string1,string2,/path/to/my/other/file.txt,string3,string4,int1,string5,string6,int2,int3,int4,/path/to/a/third/file.txt,path/to/a/fourth/file.txt,/path/to/a/java.jar,anotherString,anotherString,anotherString,aFloatNumber

If the output you showed us in post #11 was the output you get from the command:

Code:

cat -vet calls.txt

then the problem is that there is no <newline> character at the end of the file. The read command reads lines of input until it hits EOF, and without a <newline> character there is no line.

By definition, non-empty text files end with a <newline> character. By convention, a file with the .txt filename extension should be a text file.

If you are using an editor that creates files in DOS text file format (with <carriage-return><newline> two character line separators and no last line terminator), it is going to cause you headaches whenever you try to use those files on UNIX-like operating systems. Ffix your input file(s) so that they use UNIX <newline> single character line terminators. Then try our suggestions again.

NOTE that the text files containing the code we have suggested MUST also be UNIX format text files; not DOS format text files.

Don Cragun Sir, you deserve a medal! That's it! I had no end of line character!

I used sublime text, like I always do for coding. Maybe the editor has some formatting default with the .txt ending, I don't know.
My solution: I put the same line from the former calls.txt into a file just called "calls" (no ending), created with nano.
Now I have a "$" as line ending character, somehow not intuitive for me, I was expecting "\n" but it works anyway. My <#program calls here> section gets executed. Fantastic!