Question

I am new to shell script, so this might be a dumb question. I haven’t found an answer online though. I am taking a coworkers script and changing it so that it works for my data. Right now I am running a test that only uses three of my data files. The code hits a spot in the script where it goes through a for loop and it is supposed to run through the loop once for each of the different files (three times).

listtumor=`cat /Users/TReiersen/Work-Folder/OV/DataProcessing/TestRun/MatchedTumorTest.txt`
for i in $listtumor
do
lst=`ls /Users/TReiersen/Work-Folder/OV/DataProcessing/TestRun/freshstart/${i}*.txt | awk -F'/' '{print $9}'`

MatchedTumorTest.txt just contains the three different file names that I am using for the test without ‘.txt’ As far as I can tell, this code should just run through the script three times, one for each file. Instead I am getting this error:

ls: /Users/TReiersen/Work-Folder/OV/DataProcessing/TestRun/freshstart/TCGA-04-1514-01A-01D-0500-02_S01_CGH_105_Dec08\rTCGA-04-1530-01A-02D-0500-02_S01_CGH_105_Dec08\rTCGA-04-1542-01A-01D-0500-02_S01_CGH_105_Dec08*.txt: No such file or directory

For some reason all of the file names are stacked on top of each other instead of the loop going to each one individually. Any ideas why this is happening?

Thanks,
T.J.

Answer 1

It looks like the lines in your text file may be separated by carriage returns instead of newlines. Since none of the file names in your example have spaces, the for loop should work just fine if you initialize your listtumor like this:

listtumor=`tr '\r' '\n' < /Users/TReiersen/Work-Folder/OV/DataProcessing/TestRun/MatchedTumorTest.txt`

The tr command will translate the carriage returns into newlines, which is what most text-processors (like the shell’s own for command) will expect), and write the result to standard output.