topic Re: how to import .obx file into SAS in New SAS User

how to import .obx file into SAS

Nehemiah — Fri, 01 Feb 2019 04:47:05 GMT

Here is the example format of hl7 message

MSH|^~\&||||1171400021|201811151034||ORU^R01|002186496759697690|P|2.3
PID||LLQBK010450|E1404514631^^^Y^EPI||98818^999 AAA||20000505|M|||^^^^^||||||||999999999|
PV1|1||||||^^^^^^^||||||||U||||||||||||||||||||||||
ORC|RE||||P
OBR|1|LLQBK0484340||LAB1725^CBC WITH DIFFERENTIAL^^|||201811141725||||||SCR|201811150930||^QPS^Bio-Kinetic^||||||201811151033|||F|||||||||||||||
NTE|1||CLINICAL INFO: SCR
OBX|1||1202450^WBC^^|| 6.2|K/uL|4.5-12.5||||F||||11|||
OBX|2||1202305^RBC^^|| 4.09|M/uL|4.60-6.20|L|||F||||11|||
OBX|3||1202108^HEMOGLOBIN^^|| 12.6|g/dL|14.0-18.0|L|||F||||11|||
OBX|4||1202105^HEMATOCRIT^^|| 37.8|%|41.0-53.0|L|||F||||11|||
OBX|5||1202197^MCV^^|| 92.4|fL|84.0-103.0||||F||||11|||
OBX|6||1202195^MCH^^|| 30.8|pg|27.0-34.0||||F||||11|||
OBX|7||1202196^MCHC^^|| 33.3|g/dL|30.0-35.0||||F||||11|||
OBX|8||1202306^RDW^^|| 12.6|%|11.0-14.5||||F||||11|||
OBX|9||1204184^RDW-STDEV^^|| 42.4|fL|37.0-54.0||||F||||11|||
OBX|10||1202276^PLATELETS^^|| 195|K/uL|140-440||||F||||11|||
OBX|11||1202550^MPV^^|| 12.1|fL|8.9-12.8||||F||||11|||
OBX|12||1202615^NEUTROPHILS^^|| 52|%|42-75||||F||||11|||
OBX|13||1202616^LYMPHOCYTES^^|| 36|%|24-44||||F||||11|||
OBX|14||1202617^MONOCYTES^^|| 10|%|2-10||||F||||11|||
OBX|15||1202618^EOSINOPHILS^^|| 1|%|0-7||||F||||11|||
OBX|16||1202619^BASOPHILS^^|| 1|%|0-1||||F||||11|||
OBX|17||1205095^IMMATURE GRANULOCYTES^^|| 0|%|0-2||||F||||11|||
OBX|18||1202578^NEUTROPHIL ABSOLUTE^^|| 3.22|K/uL|2.00-8.00||||F||||11|||
OBX|19||1202579^LYMPHOCYTE ABSOLUTE^^|| 2.20|K/uL|1.20-4.00||||F||||11|||
OBX|20||1202580^MONOCYTE ABSOLUTE^^|| 0.61|K/uL|0.10-0.60|H|||F||||11|||
OBX|21||1202581^EOSINOPHIL ABSOLUTE^^|| 0.06|K/uL|0.00-0.70||||F||||11|||
OBX|22||1202582^BASOPHILS ABSOLUTE^^|| 0.04|K/uL|0.00-0.20||||F||||11|||
OBX|23||1205096^IMMATURE GRANULOCYTES ABSOLUTE^^|| 0.02|K/uL|0.00-0.10||||F||||11|||
NTE|1||CLINICAL INFO: SCR
FTS|1|End Of File

If there any procedure to import hl7/.obx file in SAS

Please help me out!!!!

Thanks in advance!!!

Nehemiah.

Re: how to import .obx file into SAS

ScottBass — Fri, 01 Feb 2019 06:43:11 GMT

Please help us out!!!!

What is your desired output?

This may get you started. I don't see anything in your file that tells me the column names, but you could rename them in a post-processing step.

* create a file (for testing/development) ;
filename obx temp;
data _null_;
   file obx;
   input;
   put _infile_;
   datalines4;
MSH|^~\&||||1171400021|201811151034||ORU^R01|002186496759697690|P|2.3
PID||LLQBK010450|E1404514631^^^Y^EPI||98818^999 AAA||20000505|M|||^^^^^||||||||999999999|
PV1|1||||||^^^^^^^||||||||U||||||||||||||||||||||||
ORC|RE||||P
OBR|1|LLQBK0484340||LAB1725^CBC WITH DIFFERENTIAL^^|||201811141725||||||SCR|201811150930||^QPS^Bio-Kinetic^||||||201811151033|||F|||||||||||||||
NTE|1||CLINICAL INFO: SCR
OBX|1||1202450^WBC^^|| 6.2|K/uL|4.5-12.5||||F||||11|||
OBX|2||1202305^RBC^^|| 4.09|M/uL|4.60-6.20|L|||F||||11|||
OBX|3||1202108^HEMOGLOBIN^^|| 12.6|g/dL|14.0-18.0|L|||F||||11|||
OBX|4||1202105^HEMATOCRIT^^|| 37.8|%|41.0-53.0|L|||F||||11|||
OBX|5||1202197^MCV^^|| 92.4|fL|84.0-103.0||||F||||11|||
OBX|6||1202195^MCH^^|| 30.8|pg|27.0-34.0||||F||||11|||
OBX|7||1202196^MCHC^^|| 33.3|g/dL|30.0-35.0||||F||||11|||
OBX|8||1202306^RDW^^|| 12.6|%|11.0-14.5||||F||||11|||
OBX|9||1204184^RDW-STDEV^^|| 42.4|fL|37.0-54.0||||F||||11|||
OBX|10||1202276^PLATELETS^^|| 195|K/uL|140-440||||F||||11|||
OBX|11||1202550^MPV^^|| 12.1|fL|8.9-12.8||||F||||11|||
OBX|12||1202615^NEUTROPHILS^^|| 52|%|42-75||||F||||11|||
OBX|13||1202616^LYMPHOCYTES^^|| 36|%|24-44||||F||||11|||
OBX|14||1202617^MONOCYTES^^|| 10|%|2-10||||F||||11|||
OBX|15||1202618^EOSINOPHILS^^|| 1|%|0-7||||F||||11|||
OBX|16||1202619^BASOPHILS^^|| 1|%|0-1||||F||||11|||
OBX|17||1205095^IMMATURE GRANULOCYTES^^|| 0|%|0-2||||F||||11|||
OBX|18||1202578^NEUTROPHIL ABSOLUTE^^|| 3.22|K/uL|2.00-8.00||||F||||11|||
OBX|19||1202579^LYMPHOCYTE ABSOLUTE^^|| 2.20|K/uL|1.20-4.00||||F||||11|||
OBX|20||1202580^MONOCYTE ABSOLUTE^^|| 0.61|K/uL|0.10-0.60|H|||F||||11|||
OBX|21||1202581^EOSINOPHIL ABSOLUTE^^|| 0.06|K/uL|0.00-0.70||||F||||11|||
OBX|22||1202582^BASOPHILS ABSOLUTE^^|| 0.04|K/uL|0.00-0.20||||F||||11|||
OBX|23||1205096^IMMATURE GRANULOCYTES ABSOLUTE^^|| 0.02|K/uL|0.00-0.10||||F||||11|||
NTE|1||CLINICAL INFO: SCR
FTS|1|End Of File
;;;;
run;

* get the max column count of non-missing columns;
data _null_;
   retain column_count;
   count=0;
   infile obx end=eof;
   input;
   if _infile_ =: "OBX" then
   do i=1 to countc(_infile_,"|^")+1;
      if not missing(scan(_infile_,i,"|^")) then count+1;
      column_count=max(column_count,count);
   end;
   if eof then call symputx("column_count",column_count);
run;
%put &=column_count;

data foo;
   infile obx lrecl=32767;
   length var1-var&column_count $100;
   array vars{*} var:;
   input;
   if _infile_ =: "OBX";
   do i=1 to dim(vars);
      vars{i}=scan(_infile_,i,"|^");
   end;
   drop i;
run;

Re: how to import .obx file into SAS

RW9 — Fri, 01 Feb 2019 08:04:18 GMT

Its a pipe delimited file, therefore use a datastep with infile and specify dlm="|". As for format then look at the HL7 website for information:

https://blog.interfaceware.com/understanding-hl7-messages/

https://en.m.wikipedia.org/wiki/Health_Level_7

Re: how to import .obx file into SAS

Nehemiah — Thu, 07 Feb 2019 04:30:48 GMT

Hi Scott

Thank you for your solution..the given program code is really helped us a lot.

Regards

B.Nehemiah