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Top Forums Shell Programming and Scripting Joining multiple files based on one column with different and similar values (shell or perl) Post 302517621 by seqbiologist on Wednesday 27th of April 2011 09:52:00 AM
Old 04-27-2011
Joining multiple files based on one column with different and similar values (shell or perl)

Hi,

I have nine files looking similar to file1 & file2 below.

Code:
File1:
  1 ABCA1
   1 ABCC8
   1 ABR:N
   1 ACACB
   1 ACAP2
   1 ACOT1
   1 ACSBG
   1 ACTR1
   1 ACTRT
   1 ADAMT
   1 AEN:N
   1 AKAP1

Code:
File2:
   1 A4GAL
   1 ACTBL
   1 ACTL7
   1 ACTR1
   2 ADAMT
   1 AGPAT
   1 AHNAK
   1 AKAP1
   1 AKR1B
   1 AMT:N
   1 AOX1:
   1 APAF1

I would like to obtain a file like this (with either shell or perl?)

Code:
gene    file1    file2    file3 etc 
A4GAL    0    1    ?
ABCA1    1    0    ?
ABCC8    1    0
ABR:N    1    0
ACACB    1    0
ACAP2    1    0
ACOT1    1    0
ACSBG    1    0
ACTL7    0    1
ACTR1    1    1
etc

Unfortunately, I don't have an idea myself so any help is appreciated!

Best wishes, seqbiologist
 

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COMBINE(1)																COMBINE(1)

NAME
combine - combine sets of lines from two files using boolean operations SYNOPSIS
combine file1 and file2 combine file1 not file2 combine file1 or file2 combine file1 xor file2 _ file1 and file2 _ _ file1 not file2 _ _ file1 or file2 _ _ file1 xor file2 _ DESCRIPTION
combine combines the lines in two files. Depending on the boolean operation specified, the contents will be combined in different ways: and Outputs lines that are in file1 if they are also present in file2. not Outputs lines that are in file1 but not in file2. or Outputs lines that are in file1 or file2. xor Outputs lines that are in either file1 or file2, but not in both files. "-" can be specified for either file to read stdin for that file. The input files need not be sorted, and the lines are output in the order they occur in file1 (followed by the order they occur in file2 for the two "or" operations). Bear in mind that this means that the operations are not commutative; "a and b" will not necessarily be the same as "b and a". To obtain commutative behavior sort and uniq the result. Note that this program can be installed as "_" to allow for the syntactic sugar shown in the latter half of the synopsis (similar to the test/[ command). It is not currently installed as "_" by default, but you can alias it to that if you like. SEE ALSO
join(1) AUTHOR
Copyright 2006 by Joey Hess <joey@kitenet.net> Licensed under the GNU GPL. moreutils 2012-04-09 COMBINE(1)
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