How to join 2 .txt files based on a common column?

Login or Register to Ask a Question and Join Our Community

How to join 2 .txt files based on a common column?

Tags

Top Forums UNIX for Dummies Questions & Answers How to join 2 .txt files based on a common column?

05-17-2013

Registered User

11, 0

Join Date: May 2013

Last Activity: 22 May 2014, 10:57 PM EDT

Posts: 11

Thanks Given: 0

Thanked 0 Times in 0 Posts

How to join 2 .txt files based on a common column?

Hi all,

I'm trying to join two .txt file tab delimitated based on a common column.

File 1

Code:

transcript_id   gene_id length  effective_length        expected_count  TPM     FPKM    IsoPct
comp1000201_c0_seq1     comp1000201_c0  337     183.51  0.00    0.00    0.00    0.00
comp1000297_c0_seq1     comp1000297_c0  612     458.50  0.00    0.00    0.00    0.00
comp100036_c0_seq1      comp100036_c0   333     179.51  1.00    6.72    6.17    100.00
comp10003_c1_seq1       comp10003_c1    328     174.51  0.00    0.00    0.00    0.00
comp100041_c0_seq1      comp100041_c0   338     184.51  0.00    0.00    0.00    0.00
comp100041_c0_seq2      comp100041_c0   302     148.52  0.00    0.00    0.00    0.00
comp100041_c0_seq3      comp100041_c0   339     185.51  0.00    0.00    0.00    0.00
comp100051_c0_seq1      comp100051_c0   323     169.51  0.00    0.00    0.00    0.00
comp1000890_c0_seq1     comp1000890_c0  460     306.51  2.00    7.87    7.23    100.00

File 2

Code:

transcript_id       Seq. Description        Seq. Length     #Hits   min. eValue mean Similarity #GOs    GOs     Enzyme Codes    InterProScan
comp1000201_c0_seq1     ---NA---        337     0                       0       -               
comp1000297_c0_seq1     ---NA---        612     0                       0       -               
comp100036_c0_seq1      ---NA---        333     0                       0       -               
comp10003_c1_seq1       ---NA---        328     0                       0       -               
comp100041_c0_seq1      ---NA---        338     0                       0       -               
comp100041_c0_seq2      ---NA---        302     0                       0       -               
comp100041_c0_seq3      ---NA---        339     0                       0       -               
comp100051_c0_seq1      pogo transposable element with krab domain-like 323     5       8.05925533998611E-10    55.8%   0       -       
        
comp1000890_c0_seq1     ---NA---        460     0                       0       -               
comp1000928_c0_seq1     40s ribosomal protein s7        317     5       1.02118911037712E-20    66.6%   4       F:GO:0003735; P:GO:0006412; C:GO:0005840; C:GO:0005622

Both files have 307154 lines and the common column is the first one, transcript_id

I've been trying:

Code:

$join <file 1> <file 2> > <output file>

and two things are happening:

- I'm losing the tab delimitation in the output file
- My output file is 307049 lines, so i'm losing lines...

I've looking for some answer in previous threats without success.
Any help will be great!

Thanks!

alisrpp

View Public Profile for alisrpp

Find all posts by alisrpp

05-18-2013

Registered User

440, 71

Join Date: Oct 2009

Last Activity: 26 June 2018, 6:52 PM EDT

Location: spaceBAR Central

Posts: 440

Thanks Given: 0

Thanked 71 Times in 70 Posts

You have to specify the tab via "ctrl-v <tab>":

Code:

join -t'      ' f1 f2 > f3

Check out this info:Unix Join with tabs

spacebar

View Public Profile for spacebar

Find all posts by spacebar

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Join columns across multiple lines in a Text based on common column using BASH

Hello, I have a file with 2 columns ( tableName , ColumnName) delimited by a Pipe like below . File is sorted by ColumnName. Table1|Column1 Table2|Column1 Table5|Column1 Table3|Column2 Table2|Column2 Table4|Column3 Table2|Column3 Table2|Column4 Table5|Column4 Table2|Column5 From...

2. Shell Programming and Scripting

Paste columns based on common column: multiple files

Hi all, I've multiple files. In this case 5. Space separated columns. Each file has 12 columns. Each file has 300-400K lines. I want to get the output such that if a value in column 2 is present in all the files then get all the columns of that value and print it side by side. Desired output...

3. UNIX for Dummies Questions & Answers

Join 2 files based on certain column

I have file input1.txt 11103|11|OTTAWA|City|AA|CAR|0|0|1|-1|0|8526|2014-09-07 23:00:14 11103|11|OTTAWA|City|BB|TRAIN|0|0|2|-2|6|6359|2014-09-07 23:00:14 11104|11|CANADA|City|CC|CAR|0|0|2|-2|0|5947|2014-09-07 23:00:14 11104|11|CANADA|City|DD|TRAIN|0|0|2|-2|1|4523|2014-09-07 23:00:14...

4. Shell Programming and Scripting

common entries between files based on 1st column

Hi, I am trying to get the common entries from 2 files based on 1st field.. However when I try to do in perl I am getting blank output.. How can I do this in awk? open(BUFF1, "my_genes"); open(BUFF3, "rawcounts"); #open(WRBUFF,">result_rawcounts"); while($line =<BUFF1>) { ...

5. UNIX for Dummies Questions & Answers

How to use the the join command to join multiple files by a common column

Hi, I have 20 tab delimited text files that have a common column (column 1). The files are named GSM1.txt through GSM20.txt. Each file has 3 columns (2 other columns in addition to the first common column). I want to write a script to join the files by the first common column so that in the...

6. Shell Programming and Scripting

join two files based on one column

Hi All, I am trying to join to files based on one common column. Cat File1 ID HID Ab_1 23 Cd 45 df 22 Vv 33 Cat File2 ID pval Ab_1 0.3 Cd 10 Vv 0.0444

7. Shell Programming and Scripting

join files based on a common field

Hi experts, Would you please help me with this? I have several files and I need to join the forth field of them based on the common first field. here's an example... first file: 280346 39.88 -75.08 547.8 280690 39.23 -74.83 538.7 280729 40.83 -75.08 499.2 280907 40.9 -74.4 507.8...

8. Shell Programming and Scripting

Join multiple files based on 1 common column

I have n files (for ex:64 files) with one similar column. Is it possible to combine them all based on that column ? file1 ax100 20 30 40 ax200 22 33 44 file2 ax100 10 20 40 ax200 12 13 44 file2 ax100 0 0 4 ax200 2 3 4

9. Shell Programming and Scripting

Merging 2 files based on a common column

Hi All, I do have 2 files file 1 has 4 tab delimited columns 234 a c dfgyu 294 b g fih 302 c h jzh 328 z c san 597 f g son File 2 has 2 tab delimted columns 234 23 302 24 597 24 I want to merge file 2 with file 1 based on the data common in both files which is the first column so...

10. Shell Programming and Scripting

"Join" or "Merge" more than 2 files into single output based on common key (column)

Hi All, I have working (Perl) code to combine 2 input files into a single output file using the join function that works to a point, but has the following limitations: 1. I am restrained to 2 input files only. 2. Only the "matched" fields are written out to the "matched" output file and...

Login or Register to Ask a Question