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join two files

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# 8  
Old 10-22-2012
this works! wonderful!
# 9  
Old 10-22-2012
Quote:
Originally Posted by johnkim0806
what does -e "NA" -o mean?
Lookup the man page of join...
Code:
-e s        Replace empty output fields by string s.

-o list     Each output line comprises the fields specified in list,
            each element of which has the form n.m, where n is a file
            number and m is a field number.  The common field is not
            printed unless specifically requested.

# 10  
Old 10-22-2012
if i had more than 2 files, 6 files in my case
I used
Code:
join -a1 -a2 -e "NA" -o 2.1 1.2 2.2 ${metabo}/p.adjust_${i}_toast1 ${metabo}/p.adjust_${i}_toast2 \
  | join -a1 -a2 -e "NA" -o 2.1 1.2 2.2 - ${metabo}/p.adjust_${i}_toast3 \
  | join -a1 -a2 -e "NA" -o 2.1 1.2 2.2 - ${metabo}/p.adjust_${i}_toast4 \
  | join -a1 -a2 -e "NA" -o 2.1 1.2 2.2 - ${metabo}/p.adjust_${i}_ICH \
  | join -a1 -a2 -e "NA" -o 2.1 1.2 2.2 - ${metabo}/p.adjust_${i}_ICH_SV > ${metabo}/BH_${i}

and it doesnt work.
ignore ${i
Last edited by Scott; 10-22-2012 at 06:21 PM.. Reason: Code tags
# 11  
Old 10-23-2012
Quote:
Originally Posted by rdrtx1
Code:
awk 'NR==FNR{a[$1]=$2;next;}{a[$1]=(a[$1]==""?"NA":a[$1]) " " $2;}END{for (i in a) print i,a[i]}' file1 file2

this command will miss NA output if the record is in file1, but not in file2.
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