awk to compare each file in two directores by storing in variable
In the below bash I am trying to read each file from a specific directory into a variable REF or VAL. Then use those variables in an awk to compare each matching file from REF and VAL. The filenames in the REF are different then in the VAL, but have a common id up until the _ I know the awk portion works as I can run files through them manually. However, I am not sure if I am doing the variable part correctly. Thank you .
The two variables are:
REF comes from /home/cmccabe/Desktop/comparison/reference/10bp and is 3 files:
VAR comes from /home/cmccabe/Desktop/comparison/validation/files and is 3 files:
So, S1234_ref.txt would be REF and S1234_panel.vcf would be VAL, then those two files would be compared. I think I am close but not too sure about the variables.
Last edited by cmccabe; 09-30-2016 at 04:01 PM..
Reason: added details
Could you please try to keep those both variables values into a single Input_file like as follows.
Also to get the above Input_file you could use paste var_file ref_file > Input_file
Then you could try to read their values by a loop and try to put your awkinside it.
Could you please try it out and let us know how it goes then. If you have more requirements in here, kindly post with full details on same.
Thanks,
R. Singh
Last edited by RavinderSingh13; 09-30-2016 at 04:47 PM..
This User Gave Thanks to RavinderSingh13 For This Post:
Not sure if I follow completly, but here is what I did:
/home/cmccabe/Desktop/comparison/ref_val/out
out file used as input
Thank you .
Hello cmccabe,
As we have requested mutiple times, kindly do mention complete details about what's happening and what's not. Though you have used code as I suggested in post#2 but you haven't mention either that approach worked or not. Because you haven't showed us what are there in those Input_files(how Input_file looks with sample data) it is difficult to tell that you command will work or not, please let us know the complete details about your requirements with sample Input_file and ecpected output of your requirements with error messages(if any) you code by running any suggestions or your own codes, I hope this helps.
Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
I am not sure what you mean by create an input file, I created the input as the filenames of REF in $1 of and the filenames of VAL in $2. I then gave the full path to the location of each filename in $1 and the full path to each filename in $2. After giving the full paths to file1 file2 and input, I used the awk, it ran but nothing happened and no output was produced. I was trying to use your code but just misunderstood it. I hope this helps and thank you .
@RudiC and @RavinderSingh13, thank you both for all of your help.
it looks like the script reads all the vcf files from REF and puts them in a variable FN. How do the txt files from VAL get used by the awk. The awk looks at each REF file and compares it to each VAL file looking for what's common and what's different. If a difference is found it identifies which file the missing data came from. The awk portion works on individual files, but I have over 500to compare so a loop would help, however that is what I need help with .
REF there are 250 files all located at /home/cmccabe/Desktop/comparison/reference/10bp
Data structure in REF VAL there are 250 files all located at /home/cmccabe/Desktop/comparison/validation/files
Data structure in VAL
desired output (example not using these files that compares a REF file to a VAL file and finds what's in common, what's different, and where the difference comes from, it includes some additional data as well from another script)
I hope this helps and apologize for the long post but think these are all the details. Thank you .
Last edited by cmccabe; 10-01-2016 at 10:49 AM..
Reason: added details
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