Shell Programming and Scripting

Trying to match $2 in original_targets with $2 of new_targets . If the two numbers match exactly then a match.txt file is outputted using the information in the new_targets in the beginning 4 fields $1, $2, $3, $4 and value of $4 in the original_targets . If there is "No Match" then a no match file is created using the information in the original_targets $1,$2,$3,$4 Thank you .

So for example,
the first $2 in original_targets is 34529 and that value does not match exactly $2 of new_targets, so that is copied to a "No Match file" as

Code:

chr1	34529	35031     DTE3504500000001

the 150 $2 in original_targets is 1114780 and that values matches row 251201 exactly so is copied to a match.txt as

Code:

chr1	1114780	1115142	PXL-A0000150

Code:

awk 'FNR==NR { E[$2]=$2 ; next } { $2=$2 in E?E[$2]:"No Match" } 1' OFS="\t" original_targets.txt new_targets.txt > match.txt

I'm very confused.

Your description says that, for matched lines, output consisting of fields 1-4 of new_targets.txt and field 4 from the matched original_targets.txt line. Your example says the matched line is written unchanged. The sample code changes one or more spaces between fields to a single tab and keeps all input fields no matter how many fields are present in the input.

Your description says that fields 1-4 from unmatched lines are written to a different file. You sample code changes field 2 to the string "No Match" and changes every other sequence of one or more spaces in an input line to a tab (keeping all input fields no matter how many are present) and writes them to the same output file as the matched lines.

Your example says that there are 150 matches for field 2 containing 1114780 in original_targets (without .txt), so line 215201 from one of the files (which file is not specified) is to be copied to match.txt without adding field #4 from any of the 150 matching lines from original_targets.txt.

Please rewrite your requirements clearly, provide (small) samples of the two input files, and a corresponding sample output file that should be produced from those sample input files.

I apologize for the confusion and think I have found a method to do what I need. There seems to be one issue I am having, but I am going to try and figure it out then re-post if I need assistance. Thank you again and I apologize for the confusion .

I was able to figure it out using your explanation from this post:

Match or no match