Answers.Body: <p>Using awk, this can be done in the following way:</p>
  
  <pre><code>awk 'NR==FNR{a[<span class="math-container">$1]=$</span>2; next}<span class="math-container">$1 in a{print $1, $2, a[$</span>1]}' file1.txt file2.txt &gt; same.txt
  </code></pre>
  
  <p>Explanation:</p>
  
  <pre><code>NR==FNR (along with the next command) 
  </code></pre>
  
  <p>Will go through the first file only and create an associative array of of the geneIDs corresponding with the geneNames. </p>
  
  <p>Then if the 1st column in the 2nd file is present in the array, a, it will print both columns from the file plus the geneName.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-27T18:04:57.560Z
Answers.LastActivityDate: 2019-06-27T18:21:10.383Z
Answers.LastEditDate: 2019-06-27T18:21:10.383Z
Answers.UserDisplayName: h3ab74
Answers.Body: <p>I like to use the <code>join</code> command for this. For your example above, you can simply use the following:</p>
  
  <pre><code>$ join file2 file1
  ENST00000000412 0.779142 M6PR
  ENST00000001008 0.738143 FKBP4
  ENST00000002501 0.715315 DBNDD1
  ENST00000002596 0.713664 HS3ST1
  </code></pre>
  
  <p>This assumes your files are sorted. If they aren't sorted, you can use input redirection if your shell supports it (bash and other modern shells do):</p>
  
  <pre><code>join &lt;(sort -k 1b,1 file2) &lt;(sort -k 1b,1 file1)
  </code></pre>
  
  <p>If your shell doesn't support <code>&lt;()</code>, sort the files first:</p>
  
  <pre><code>sort file1 &gt; file1.sorted; sort file2 &gt; file2.sorted
  join &lt;(sort -k 1b,1 file2.sorted) &lt;(sort -k 1b,1 file1.sorted)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-26T23:21:32.700Z
Answers.Text: But the number of lines in file 2 and file 1 are not same. In an output file, I need a 1st and 2nd column of file 2 and 3rd column values to be extracted from file1
Answers.UserDisplayName: Megha
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-26T23:31:02.680Z
Answers.Text: The result matches your desired output - can you clarify what you want?
Answers.UserDisplayName: Scot
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-26T23:58:17.743Z
Answers.Text: Note that the `join` command does not simply `paste` files together, it matches two files based on a common column (by default column 1), and then tacks on the additional columns from the files in the specified order. I think it is exactly what you want, given what you've written. One caveat is that the files must be sorted by the matching column, though in your example above, they already are.
Answers.UserDisplayName: Scot
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-27T05:05:29.510Z
Answers.Text: If they're not sorted, this might work: ``join <(sort -k 1b,1 file1.txt) <(sort -k 1b,1 file2.txt)``
Answers.UserDisplayName: gringer
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-27T09:01:46.967Z
Answers.Text: @Scot Thank you for the answer, I figured out my file (completed one) was not sorted that's why it didn't work initially
Answers.UserDisplayName: Megha
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-26T22:54:06.377Z
Answers.LastActivityDate: 2019-06-27T15:48:46.800Z
Answers.LastEditDate: 2019-06-27T15:48:46.800Z
Answers.UserDisplayName: Scot
Body: <p>File1:</p>
  
  <pre><code>ENST00000000233 ARF5
  ENST00000000412 M6PR
  ENST00000001008 FKBP4
  ENST00000001146 CYP26B1
  ENST00000002501 DBNDD1
  ENST00000002596 HS3ST1
  </code></pre>
  
  <p>File 2:</p>
  
  <pre><code>ENST00000000412 0.779142
  ENST00000001008 0.738143
  ENST00000002501 0.715315
  ENST00000002596 0.713664
  </code></pre>
  
  <p>Desired Output</p>
  
  <pre><code>ENST00000000412 0.779142    M6PR
  ENST00000001008 0.738143    FKBP4
  ENST00000002501 0.715315    DBNDD1
  ENST00000002596 0.713664    HS3ST1
  </code></pre>
  
Tags: <bash><awk>
Title: How to extract values from second file on the basis common first column?
ThreadText: # How to extract values from second file on the basis common first column?
  
  (Asked by: username_0 on 2019-06-26)
  
  File1:
  
  ```
  ENST00000000233 ARF5
  ENST00000000412 M6PR
  ENST00000001008 FKBP4
  ENST00000001146 CYP26B1
  ENST00000002501 DBNDD1
  ENST00000002596 HS3ST1
  
  ```
  
  File 2:
  
  ```
  ENST00000000412 0.779142
  ENST00000001008 0.738143
  ENST00000002501 0.715315
  ENST00000002596 0.713664
  
  ```
  
  Desired Output
  
  ```
  ENST00000000412 0.779142    M6PR
  ENST00000001008 0.738143    FKBP4
  ENST00000002501 0.715315    DBNDD1
  ENST00000002596 0.713664    HS3ST1
  
  ```
  
  **Tags:** bash, awk
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2019-06-26. Score: 6 | Accepted answer
  
  I like to use the `join` command for this. For your example above, you can simply use the following:
  
  ```
  $ join file2 file1
  ENST00000000412 0.779142 M6PR
  ENST00000001008 0.738143 FKBP4
  ENST00000002501 0.715315 DBNDD1
  ENST00000002596 0.713664 HS3ST1
  
  ```
  
  This assumes your files are sorted. If they aren't sorted, you can use input redirection if your shell supports it (bash and other modern shells do):
  
  ```
  join <(sort -k 1b,1 file2) <(sort -k 1b,1 file1)
  
  ```
  
  If your shell doesn't support `<()`, sort the files first:
  
  ```
  sort file1 > file1.sorted; sort file2 > file2.sorted
  join <(sort -k 1b,1 file2.sorted) <(sort -k 1b,1 file1.sorted)
  
  ```
  
  > **Comments:**
  > **username_0**: But the number of lines in file 2 and file 1 are not same. In an output file, I need a 1st and 2nd column of file 2 and 3rd column values to be extracted from file1  
  > **username_2**: The result matches your desired output - can you clarify what you want?  
  > **username_2**: Note that the `join` command does not simply `paste` files together, it matches two files based on a common column (by default column 1), and then tacks on the additional columns from the files in the specified order. I think it is exactly what you want, given what you've written. One caveat is that the files must be sorted by the matching column, though in your example above, they already are.  
  > **username_3**: If they're not sorted, this might work: ``join <(sort -k 1b,1 file1.txt) <(sort -k 1b,1 file2.txt)``  
  > **username_0**: @username_2 Thank you for the answer, I figured out my file (completed one) was not sorted that's why it didn't work initially  
  
  ---
  
  ### Answer by username_1 on 2019-06-27. Score: 1
  
  Using awk, this can be done in the following way:
  
  ```
  awk 'NR==FNR{a[$1]=$2; next}$1 in a{print $1, $2, a[$1]}' file1.txt file2.txt > same.txt
  
  ```
  
  Explanation:
  
  ```
  NR==FNR (along with the next command) 
  
  ```
  
  Will go through the first file only and create an associative array of of the geneIDs corresponding with the geneNames.
  
  Then if the 1st column in the 2nd file is present in the array, a, it will print both columns from the file plus the geneName.
  
  
  ---
  
  