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Kindly check it: Camparison of files only column1 of 2 files

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Top Forums Shell Programming and Scripting Kindly check it: Camparison of files only column1 of 2 files
# 1  
Old 07-27-2012
Kindly check it: Camparison of files only column1 of 2 files
Hi all,

I have 2 files in which i have to find commom entries in column 1 an dif soemthing is common write other data of both files in front of it mentioned.

Gene symbol and disease name

Code:
column 1    column2
ARFGEF2 CAD
DDEF2 CAD
PSCD3 CAD
PSCD4 CAD
CAMK1 CAD,HT,HT,HT,HT,HT,HT,HT,HT,HT,HT,HT,HT
HSP90AA1 CAD,CAD,CAD,T2D,T2D
KDR CAD,CD,CD
VEGF CAD,CAD,CAD,CAD,T2D,T2D,T2D
CTNNA3 CAD,HT,T2D
PTPRM CAD,T2D
RAC2 CAD,CAD,T1D,T1D
SMAD3 CAD,T2D,T2D,T2D,T2D,T2D,T2D,T2D
SORBS1 CAD,CAD,CAD
CD36 CAD
IRS1 CAD,CAD,CAD
IRS2 CAD,CAD,CAD,CAD
MTFMT CAD,CAD,CAD,T1D,T1D,T1D
SARS CAD
GNPDA2 CAD
NANS CAD
SRD5A1 CAD

Second file with 3 colu

second file is like this


Gene symbol drug drug
Code:
F2        Lepirudin    Refludan
FCGR2A,FCGR2B,FCGR2C,EGFR,FCGR3B,C1R,C1QA,C1QB,C1QC,FCGR3A,C1S,FCGR1A        Cetuximab    Erbitux
Not Available        Dornase Alfa    Pulmozyme
IL2RA,IL2RB,IL2RG        Denileukin diftitox    Ontak
C1S,C1R,C1QA,C1QB,C1QC,TNF,TNFRSF1B,FCGR1A,FCGR3A,FCGR2A,FCGR2B,FCGR2C,LTA,FCGR3B        Etanercept    Enbrel
F2        Bivalirudin    Angiomax
GNRHR        Leuprolide    Eligard
IFNAR2,IFNAR1        Peginterferon alfa-2a    Pegasys
PLG,FGA,PLAUR,SERPINE1        Alteplase    Activase (Genentech Inc

The expected out put contain
Code:
common entries of first column                        disease from first file                         drug from second file                drug from second file

Last edited by Scott; 07-27-2012 at 03:04 AM.. Reason: Code tags
# 2  
Old 07-27-2012
I didnt get u properly.. can u explain a bit..
# 3  
Old 07-27-2012
hi

thanks for ur reply.

I have to compare entries in coumn 1 o ffirst file with entries in column 1 of secoond file both are gene names in capitalised letters.

And, if there is a gene naem for exaple IFNAR1 is common in first column of both files then I have to write the entries of second file and and first file in front of it. so that I will get 4 columns in out put file

first column: common gene entry
secoond column: disease name in front of common entry in first file(CAD,HT)
third column drug in second filein front of common entry
fourth column drug in second file in front of common entry

Please let me know if u need any other information.

Mani
# 4  
Old 07-27-2012
join
Hi,

Try this,
Code:
join -11 -21 file1 file2

Cheers,
Ranga:-)
# 5  
Old 07-27-2012
Request to check
Hi

thanksf orr reply.
The output is completely blank!

Code:
bash-3.2$ join -11 -21 SARAIN_FILE drugbankin_file >sara-drugbankout
bash-3.2$ join -11 -21 SARAIN_FILE drugbankin_file
bash-3.2$ join -11 -21 SARAIN_FILE drugbankin_file
bash-3.2$ join -11 -21 SARAIN_FILE drugbankin_file
bash-3.2$ join -11 -21 SARAIN_FILE drugbankin_file
bash-3.2$

Last edited by Scott; 07-27-2012 at 03:05 AM.. Reason: Code tags
# 6  
Old 07-27-2012
Sorry i didnt get you. can you exaplain with some examples. I didnt get the examples which you specified above..
# 7  
Old 07-27-2012
Alright for example

1 file contains data in 3 columns
Code:
column1         col2     col3     
1,2,3                c          d 
4                     g          h 
6,7                  k           c

second file contain 2 columns

Code:
1  x
2  u
3  s
4  l

output shuld be check common entreis in column 1 of both files and write the data before it like this as mentione din file 1 and file 2

Code:
1  x    c  d 
2  u   c  d 
3  s   c   d 
4  l    g h

Last edited by manigrover; 07-27-2012 at 07:16 AM.. Reason: Code tags
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