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Full Discussion: Creating matrix from folders and subfolders
Top Forums Shell Programming and Scripting Creating matrix from folders and subfolders Post 302745699 by newbie83 on Monday 17th of December 2012 10:43:16 PM
Old 12-17-2012
Creating matrix from folders and subfolders
Hello,

Greetings!
please help me produce the following solution. I need
to produce one big matrix file from several files in different levels.
If it helps, the index folder provides information on chromosome index and
the data folder provides information on values for chromosomes.

there are 2 folders at the same level, index and data.
The index folder has multiple files named chr1, chr2 etc.
The data folder has many subfolders, Each subfolder has multiple files named chr1, chr2 etc. with the same names
as files in the index folder. A particular file and its namesake will have the same number of rows in it.
So if chr1 in index has 5 rows, chr1 in all subfolders within data will also have 5 rows.

The output should be a big matrix with a nested format, where the rownames(first col) starting row2 should be the file names
and the column names(first row) startng col3 should be the names of corresponding subfolders in data folder.

All files have 1 column and multiple rows with only integer numbers.

Code:
Index folder 

chr1

1
2
3
5
6

chr2

1
2
3
4
5
7

chr3

1
5
7


Data Folder 

Subfolder1

chr1

1
0
1
0
0

chr2

0
1
0
1
0
1

chr3

0
0
2

Subfolder2

chr1

1
1
2
2
3

chr2

1
3
4
6
0
0


chr3

1
0
0

Output

		Subfolder1	Subfolder2
chr1	1	1	1
chr1	2	0	1
chr1	3	1	2
chr1	5	0	2
chr1	6	0	3
chr2	1	0	1
chr2	2	1	3
chr2	3	0	4
chr2	4	1	6
chr2	5	0	0
chr2	7	1	0
chr3	1	0	1
chr3	5	0	0
chr3	7	2	0

Last edited by newbie83; 12-18-2012 at 12:01 AM..
 

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LEARN ABOUT V7

rmf

RMF(1)								     [nmh-1.5]								    RMF(1)

NAME

       rmf - remove an nmh folder

SYNOPSIS

       rmf [+folder] [-interactive | -nointeractive] [-version] [-help]

DESCRIPTION

       Rmf removes all of the messages (files) within the specified (or default) folder, and then removes the folder (directory) itself.

       If  there  are  any  files  within the folder which are not a part of nmh, they will not be removed, and an error will be produced.  If the
       folder is given explicitly or the -nointeractive option is given, then the folder will be removed  without  confirmation.   Otherwise,  the
       user  will be asked for confirmation.  If rmf can't find the current folder, for some reason, the folder to be removed defaults to `+inbox'
       (unless overridden by user's profile entry "Inbox") with confirmation.

       If the folder being removed is a subfolder, the parent folder will become the new current folder, and rmf will produce  a  message  telling
       the user this has happened.  This provides an easy mechanism for selecting a set of messages, operating on the list, then removing the list
       and returning to the current folder from which the list was extracted.

       If rmf s used on a read-only folder, it will delete all the (private) sequences (i.e., "atr-seq-folder" entries) for this folder from  your
       context without affecting the folder itself.

       Rmf irreversibly deletes messages that don't have other links, so use it with caution.

FILES

       $HOME/.mh_profile	  The user profile

PROFILE COMPONENTS

       Path:		    To determine the user's nmh directory
       Current-Folder:	    To find the default current folder
       Inbox:		    To find the default inbox

SEE ALSO

       rmm(1)

DEFAULTS

       `+folder' defaults to the current folder, usually with confirmation
       `-interactive' if +folder' not given, `-nointeractive' otherwise

CONTEXT

       Rmf  will  set the current folder to the parent folder if a subfolder is removed; or if the current folder is removed, it will make "inbox"
       current.  Otherwise, it doesn't change the current folder or message.

BUGS

       Although intuitively one would suspect that rmf works recursively, it does not.	Hence if you have a sub-folder within a folder,  in  order
       to rmf the parent, you must first rmf each of the children.

MH.6.8								   11 June 2012 							    RMF(1)
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