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Shell Programming and Scripting

Match string from two files and print line

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Top Forums Shell Programming and Scripting Match string from two files and print line
# 8  
Old 05-10-2017
Quote:
Originally Posted by zward
Apologies, this is my first post. I thought it would be easier to explain with an ammended file but I've learnt this confuses things. My file 2 looks like this.

Code:
1       StringTie       exon    18887   19382   .       +       .       transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "1";
1       StringTie       exon    189836  191490  .       +       .       transcript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "2";
1       StringTie       exon    18887   19382   .       +       .       transcript_id "MSTRG.49.4"; gene_id "MSTRG.5"; exon_number "1";
1       StringTie       exon    189836  191490  .       +       .       transcript_id "MSTRG.49.4"; gene_id "MSTRG.5"; exon_number "2";

If I
Code:
 awk '{print$10} file2

this prints out the "MSTRG###"; string that I want to match to (I don't want to match the string from "gene_id".
try - not tested (yet)
Code:
awk 'FNR==NR {f1[$1];next} $2 in f1' file1 FS='"' file2

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---------- Post updated at 10:41 PM ---------- Previous update was at 10:36 PM ----------

sorry - counted the fields wrong and don't have the matching file1, but:
Code:
awk 'FNR==NR {f1[$1];next} $4 in f1' file1 FS='"' file2

It should be either $2 or $4 depending on what MSTRG you want to match on......
# 9  
Old 05-10-2017
Can you explain the code ( the $4??)
My file 1 is like:
Code:
MSTRG.1.1       233     0       0       0
MSTRG.5.1       2151    300     0.7186  
MSTRG.13.1      1705    261     0.4076
MSTRG.49.1      1746    357     1.189
MSTRG.50.1      1809    273     1.0285
MSTRG.50.2      890     201     1.1133  
MSTRG.50.3      466     75      0.7497  
MSTRG.49.4      1743    246     1.0052
MSTRG.49.5      885     246     1.0052

# 10  
Old 05-10-2017
give file1 and file2 posted above, the code should be:
Code:
awk 'FNR==NR {f1[$1];next} $2 in f1' file1 FS='"' file2

The FieldSeparator (FS) for file2 is ". When file2 is processed ($2 in f1), given FS="'", $2 becomes the FIRST quoted string withOUT the quotes.
Not sure if my explanation is consumable tho Smilie
This User Gave Thanks to vgersh99 For This Post:
zward
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