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Grep solutions tab-delimited file

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# 1  
Old 04-26-2018
Grep solutions tab-delimited file
Hello, I am trying to find a solution to problem that's proving to be beyond my newbie skills. The below files comes from a genetics study. File 1 describes a position on the genome and file 2 does the same but is formatted differently and has more information. I am trying to match all lines in file 1 with the right line in file 2, and then print the full line from file 2. The first column in file 1 corresponds to the first and third column in file 2. File 1 has a colon as separator whereas file 2 has tab.

I tried to come up with a grep solution that would not require reformatting of files. I tried to come up with some easy manipulation of File 1 or file 2 to make the matching easier. Both failed. Any suggestions would be more than welcome.

Edit: Sorry if I made the first example look confusing. There are matches. Please consider the below example instead:

File 1
Code:
chr1:17373
chr1:17375
chr1:17398
chr1:17407

~100,000 rows


File 2
Code:
chr1    17372    17373    rs750111615
chr1    17374    17375    rs755771866
chr1    17378    17379    rs754322362
chr1    17384    17385    rs201535981
chr1    17395    17398    rs200784459
chr1    17405    17406    rs772228657
chr1    17405    17407    rs372841554

~15 M rows

The result I need is

Code:
chr1:17373 rs750111615
chr1:17375    rs755771866
chr1:17398    rs200784459
chr1:17407    rs372841554

Again, help would be much appreciated.
Last edited by andmal; 04-29-2018 at 04:27 PM..
# 2  
Old 04-26-2018
hmmm..... this is a bit confusing:
Code:
The first column in file 1 corresponds to the first and third column in file 2

.
I don't see the correlation in your sample files...
I don't follow - can you elaborate?
And maybe provide a desired result based on the samples provided.
This User Gave Thanks to vgersh99 For This Post:
RudiC
# 3  
Old 04-27-2018
Is there any match in your samples?
# 4  
Old 04-28-2018
Sorry if I made it look confusing. There are matches. PLease consider the below example instead:

File 1
Code:
chr1:17373
chr1:17375
chr1:17398
chr1:17407

~100,000 rows


File 2
Code:
chr1    17372    17373    rs750111615
chr1    17374    17375    rs755771866
chr1    17378    17379    rs754322362
chr1    17384    17385    rs201535981
chr1    17395    17398    rs200784459
chr1    17405    17406    rs772228657
chr1    17405    17407    rs372841554

~15 M rows

The result I need is

Code:
chr1:17373 rs750111615
chr1:17375    rs755771866
chr1:17398    rs200784459
chr1:17407    rs372841554

Again, help would be much appreciated.


Moderator's Comments:
Mod Comment Please use CODE tags as required by forum rules!
Last edited by RudiC; 04-28-2018 at 07:23 PM.. Reason: Added CODE tags.
# 5  
Old 04-28-2018
Still not unambiguous. Try
Code:
awk '
NR == FNR       {T[$2] = $0
                 next
                }
($2 in T)        {print T[$2], $NF
                }
($3 in T)        {print T[$3], $NF
                }
' FS=: file1 FS="\t" file2
chr1:17373 rs750111615
chr1:17375 rs755771866
chr1:17398 rs200784459
chr1:17407 rs372841554

If you want the range $2 - $3 checked, it would become more complex and time consuming for that large files.
This User Gave Thanks to RudiC For This Post:
andmal
# 6  
Old 04-29-2018
Thanks -this produces exactly what I was looking for. Next, I'll try and understand the code and customize to other similar data -you've given me a great starting point.
Example output below:

Code:
1:40370176:G_GT    g    gt    -0.0103    0.0222    0.6434    ???????+??+- rs564192510
19:4197562:A_AGAAT    a    agaat    0.1321    0.0121    1.019e-27    ?++++??+++-+ rs79305507
19:4210401:C_CA    ca    c    0.2934    0.0137    3.00e-101    ?++++??+++++ rs6683453
19:4259184:T_TTC    t    ttc    0.5397    0.0186    3.27e-185    ++++????++?? rs12092368
19:4268341:A_G    a    g    -0.6392    0.0106    1.95e-798    ----?------- rs12090408
4:38765867:A_G    a    g    -0.0641    0.0116    3.516e-08    ------------ rs1778050

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