Help with awk command

I have a file with 50 lines of sample names. I have use this awk one liner before, but today, it only prints out the 50th line of the file. I expect this command to print all sample names ("Sample1", "Sample2", "Sample3", "Sample4"), but it doesn't. Can anyone help me figure out why? File example and command below.

Command:

SHORT=`echo $FILE | awk -F "_" '{print $1}'`

Sample1_F.txt
Sample2_R.txt
Sample3_F.txt
Sample4_R.txt

When I print this command to a file I only get "Sample4".

awk print

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updated 6.8 years ago by GenoMax

• written 6.8 years ago by someler •

this can hardly be the complete command you try to execute. Can you also post the remainder? (eg. what is $FILE ?)

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written 6.8 years ago by lieven.sterck

It's not. I was trying to not have to make my entire script anonymous. This is the beginning of my script to add read groups:

FILELIST=`cat Samples.txt`

for FILE in $FILELIST

do

SHORT=`echo $FILE | awk -F "_" '{print $1}'`

java -jar $picard_path I=$FILE O="$SHORT".rg.bam RGID=$SHORT RGLB=library RGPL=platform RGPU=cohortname RGSM=$SHORT
done

It should be running this for all 50 samples, but only does it for the last one.

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updated 6.8 years ago by GenoMax

• written 6.8 years ago by someler •

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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written 6.8 years ago by GenoMax

Woops! Thank you, I will next time.

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written 6.8 years ago by someler •

Are you sure its the last line and not the first one? Maybe the newline is wrong. Think about what the awk actually does. (edit misread statement).

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written 6.8 years ago by Ido Tamir

100% positive it is only printing the last line.

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written 6.8 years ago by someler •

what does:

for file in `cat Samples.txt`; do echo $file; done

give as output?

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written 6.8 years ago by lieven.sterck

This echoes all my lines. This surprised me because when I do this command it prints the last line. When I run my fill script, it returns a bam file with read groups to the last sample from that file. Confused about where the disconnect is.

for file in `cat Samples.txt`; do echo $file; done > TestFile.txt

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written 6.8 years ago by someler •

that is strange indeed. With me it does print all entries to the output file. Your output looks more like what you would get with this command:

for file in `cat Samples.txt`; do echo $file > TestFile.txt ; done

If your script is a loop in loop kinda system, can you check you did not put the done in the wrong place?

which shell (version?) are you using btw?

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written 6.8 years ago by lieven.sterck

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