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Below is the contents of the file I am trying to process.
The Field separator is an asterisk....

Do I have to convert the incoming file from ASCII to EBIDIC or is there some what to force it to use ASCII encoding within the Qshell processing?

ISA*00* *00* *ZZ*10301 *ZZ*TN001988 *151204*1217*^*00501*000000001*0*P*:~
GS*FA*10301*TN001988*20151204*121752*1*X*005010X231A1~
ST*999*0001*005010X231A1~
AK1*HC*11723001*005010X223A2~
AK2*837*011723001*005010X223A2~
IK5*A~
AK9*A*1*1*1~
SE*6*0001~
GE*1*1~
IEA*1*000000001~

-----Original Message-----
From: MIDRANGE-L [mailto:midrange-l-bounces@xxxxxxxxxxxx] On Behalf Of Buck Calabro
Sent: Wednesday, July 20, 2016 12:19 PM
To: midrange-l@xxxxxxxxxxxx
Subject: Re: Awk script running in QShell

On 7/20/2016 12:44 PM, Fuchs, James M wrote:
But if I put in print statements to print the records, the record number, and number of fields prior to the first pattern match and set the Field separator (hard coded ) within the variable/constants definitions the script will print all of individual records in the file along with accurate record numbers and field counts.

Well then we're back to character encoding / pattern matching. In particular, look at the ISA record. Column 4 should be the field separator for the rest of the records. To wildly generalise, CCSID 1252 is Windows. 819 is *nix.

Also tried with just printing the first field (print $1) as well as a
substring of the first 4 characters, that, for the most part worked
correctly also

That's a good diagnostic. What is the separator character on the ISA record? The names of the fields in the TA1 record are a bit generic, but the GS record looks easy to understand. Pretending that the vertical bar is the separator:

GS|fld2|PayerID|fld4|date YYYYMMDD|time HHMMSS|GroupCtl

Do you see something like this?
Is there a separator at the end of the line?
What characters are the field separators? (DSPF F10 to view in hex) What characters are the line endings?

--
--buck

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