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


 
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# 1  
Old 05-17-2013
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!
# 2  
Old 05-18-2013
You have to specify the tab via "ctrl-v <tab>":
Code:
join -t'      ' f1 f2 > f3

Check out this info:Unix Join with tabs
 
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