UNIX for Beginners Questions & Answers

Hi there, I‘m a newbie in linux (ubuntu) working with several files, some of them containing hundred thousands of lines. I started to extract information out of 2 files, combining them by 1 column: I need a Vlookup-like command that reads sampleID (column 2)(line 2,..line by line) in file 1, looks up this sampleID in file 2 and writes all corresponding readIDs (e.g. 250000) that could be found to this sampleID to a new file (each in a new line). (new file: „sampleID“_readIDs.file) Try to do this for all sampleIDs in summary file1. In the end I have a number of .files as lines of sampleIDs in file 1.
file 1:

Code:

name    sampleID    nr 
Sample1    123    250000 
Sample2    345    200000 
Sample3    456    180000

file 2:

Code:

 readID    read_value    sampleID
15sj10n3-9372-9d73-i3i2-64b40faa330b    6000    123
19pe26j3-9372-9g22-i3i2-81f59a56d939    5900    123
93os17k5-9372-6k63-i3i2-b8b765b1a729    6050    456
49kk23o2-9372-9d73-i3i2-b09f4b1f0557    6080    123
09iy02p8-9372-9d73-i3i2-0d479e6fb751    5990    345

123_readID.file (output in new file):

Code:

15sj10n3-9372-9d73-i3i2-64b40faa330b
19pe26j3-9372-9g22-i3i2-81f59a56d939
49kk23o2-9372-9d73-i3i2-b09f4b1f0557

I am thankful for any help or suggestions. Nika

Welcome to the forum.

It usually helps to post your OS and shell versions as well as e.g. preferred tools, and to show your own attempts on a solution.

Howsoever, how far would this get you:

Code:

awk 'NR==FNR {SID[$2]; next} $3 in SID {FN = $3 "_readIDs.file"; print $1 >> FN; close (FN)}' file1 file2