The below awk verifies the count and order of each text file in the directory. The script does execute and produce output, however the order of the headers are not compared to key . The portion in bold is supposed to do that. If the order of the headers in each text file is the same as key , then the file is good else the out of order header is printed. I am not sure what I am doing wrong. Thank you :).
file.txt tab-delimited in /home/cmccabe/Desktop/validate/*.txt --- each text file ( usually 3) are the same format or should be ----
Index Chr Start End Ref Alt Inheritence Score Quality HGMD Classification
1 1 10 100 A - . 2 GOOD . VUS
2 1 100 1000 - C . 5 STRAND BIAS . Benign
3 5 50 500 AA T . 1 GOOD . Benign
key tab-delimited --- order of each header (always the same) ----
Index Chr Start End Ref Alt Inheritence Score Quality HGMD Classification
awk
logfile=/home/cmccabe/Desktop/validate/process.log # define log
for f in /home/cmccabe/Desktop/validate/*.txt ; do # start loop
echo "Start header validation creation: $(date) - File: $f" # start entry for file in log
bname=`basename $f` # strip off path from filename
awk ' # call awk
FNR==NR { # process lines in fields
for(n=1;n<=NF;n++) # iterate through headers from file
a[$n] # define array N
nextfile # next
}
NF==(n-1) { # check header count matches key file
print FILENAME " file has expected number of 11 fields" # good message
nextfile # next
}
{
for(i=1;i<=NF;i++) # iterate through headers from file
b[$i] # define array b
print FILENAME " is missing header for: " # bad message
for(i in a) # compare each header to array a
if(i in b==0) # if header not found
print i # print missing header
nextfile # next
}
{
for(n=1;n<=NF;n++) # iterate through headers from file
a[$n] # define array N
nextfile # next
}
NF==(/home/cmccabe/Desktop/validate/key) { # check order of headers in file to key
print FILENAME " has expected header order" # good message
nextfile # next
}
{
for(i=1;i<=NF;i++) # iterate through headers from file
b[$i] # define array b
print FILENAME " header is out of order for: " # bad message
for(i in a) # compare each header to array a
if(i in b==0) # if header out of order as compared to key
print i # print header
nextfile # next
}' /home/cmccabe/Desktop/validate/key $f # define compare file (key) and each text file ($f)
done << "$logfile" # store in log and close loop
current output
Start header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file1.txt
/home/cmccabe/Desktop/validate/file1.txt file has expected number of 11 fields
End header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file1.txt
Start header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file2.txt
/home/cmccabe/Desktop/validate/file2.txt file has expected number of 11 fields
End header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file2.txt
Start header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file3.txt
/home/cmccabe/Desktop/validate/file3.txt file has expected number of 11 fields
End header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file3.txt
desired output
Start header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file1.txt
/home/cmccabe/Desktop/validate/file1.txt file has expected number of 11 fields
/home/cmccabe/Desktop/validate/file1.txt file has expected header order
End header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file1.txt
Start header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file2.txt
/home/cmccabe/Desktop/validate/file2.txt file has expected number of 11 fields
/home/cmccabe/Desktop/validate/file2.txt file has expected header order
End header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file2.txt
Start header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file3.txt
/home/cmccabe/Desktop/validate/file3.txt file has expected number of 11 fields
/home/cmccabe/Desktop/validate/file3.txt file has expected header order
End header validation creation: Fri Apr 21 07:39:09 CDT 2017 - File: /home/cmccabe/Desktop/validate/file3.txt