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Pipe 2 bash loops together

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# 1  
Old 10-09-2015
Pipe 2 bash loops together
What is the proper way to run two bash loops in the same command? The two below loops run separately, the problem is when I pipe them I get an error that the file used for the second loop does not exist. I am not sure how to wait for the first loop to complete and then start the second. Thank you Smilie.

Code:
for f in /home/cmccabe/Desktop/panels/*.txt ; do
     bname=`basename $f`
     pref=${bname%%.txt}
     awk '
     FNR==NR{d[$0]; next;}          
    {                              
        for(k in d){               
            pat="(^|;)"k":";       
            if($2 ~ pat){
                print;             
                break;
            }
        }
    }' $f /home/cmccabe/Desktop/NGS/pool_I_090215/IonXpress_008_150902_4column.bed > /home/cmccabe/Desktop/panels/${pref}_loop_genes_IonXpress_008_150902.bed
done |  
for f in /home/cmccabe/Desktop/panels/*.bed ; do
     bname=`basename $f`
     pref=${bname%%.bed}
     awk '{k=$1 OFS $2;
     s[k]+=$4; c[k]++}
     END{for(i in s)
     print i, s[i]/c[i], c[i] " bases" }' $f > /home/cmccabe/Desktop/panels/${pref}_loop_genes_average_IonXpress_008_150902.bed
done

Last edited by cmccabe; 10-09-2015 at 11:35 AM.. Reason: fixed format
# 2  
Old 10-09-2015
Why pipe? What exactly do you think you pipe to the second loop?
# 3  
Old 10-09-2015
I am trying to take the output file produced in the first bash loop as the input for the second bash loop. Instead of running the two loops as separate commands (run the first loop and have the output created), then run a new loop in terminal using that output as the input. Thank you Smilie.
# 4  
Old 10-09-2015
As far as I can see, the only output produced in loop 1 is from the awk script which is redirectred to that .bed file. Nothing to pipe...
And, in loop 2, nothing is read from stdin - no pipe used...
# 5  
Old 10-09-2015
You are correct, I guess I am just not sure if what I am trying to do is possible and if so, the best way to do so. Thank you Smilie.
# 6  
Old 10-09-2015
Try just dropping the pipe symbol.
This User Gave Thanks to RudiC For This Post:
cmccabe
# 7  
Old 10-09-2015
That worked... I guess I just am confused about how to use |. I will do more reading on it and thank you very much Smilie.
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