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Full Discussion: Matrix to 3 col sorted
Top Forums Shell Programming and Scripting Matrix to 3 col sorted Post 303003840 by senhia83 on Thursday 21st of September 2017 11:32:58 AM
Old 09-21-2017
Matrix to 3 col sorted
Hello experts, I have matrices sorted by position, there are 400k rows, 3000 columns.

Code:
ID      CHR     POS     M1      M2      M3      M4      M5
ID1     1       1       4.6     2.6     2.1     3.5     4.2
ID2     1       100     3.6     2.9     3.2     2.6     2.5
ID3     1       1000    4.1     2.9     2.4     2.8     2.5
ID4     1       2000    4.2     2.4     2.8     3.7     2.8
ID5     1       3000    4.6     2.9     3.7     3.5     2.7
ID6     1       4000    5.2     3       3.2     4.2     3.7
ID7     1       5000    5.8     2.2     2.8     3.1     2.7

I`m looking for a sorted long-format output by position, grouped by markers (Ms)

Code:
M1 ID1__1__1 4.6
M1 ID2__1__100 3.6
M1 ID3__1__1000 4.1
M1 ID4__1__2000 4.2
M1 ID5__1__3000 4.6
M1 ID6__1__4000 5.2
M1 ID7__1__5000 5.8
M2 ID1__1__1 2.6
M2 ID2__1__100 2.9
M2 ID3__1__1000 2.9
M2 ID4__1__2000 2.4
M2 ID5__1__3000 2.9
M2 ID6__1__4000 3
M2 ID7__1__5000 2.2
M3 ID1__1__1 2.1
M3 ID2__1__100 3.2
M3 ID3__1__1000 2.4
M3 ID4__1__2000 2.8
M3 ID5__1__3000 3.7
M3 ID6__1__4000 3.2
M3 ID7__1__5000 2.8
M4 ID1__1__1 3.5
M4 ID2__1__100 2.6
M4 ID3__1__1000 2.8
M4 ID4__1__2000 3.7
M4 ID5__1__3000 3.5
M4 ID6__1__4000 4.2
M4 ID7__1__5000 3.1

I have two working methods

1. This step requires a final sorting which for 400000x3000 datapoints will be very row or run out of memory.


Code:
awk -F"\t" 'NR==1{split($0,lines);}NR>1{for(i=4;i<length(lines);i++) print lines[i],$1"__"$2"__"$3,$i}' tmp | sort -k1,1


2. This step is very very slow as it requires to take the entire matrix into memory before making splits.

Code:
awk -F"\t" '{a[NR]=$0}END{split(a[1],lines); for(i=4;i<=length(lines);i++) { for(j=2;j<=length(a);j++) { split(a[j],haps); print lines[i],haps[1]"__"haps[2]"__"haps[3],haps[i]}}}'  tmp


Is there a more efficient way to get the output I need? Thanks in advance.
 

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LEARN ABOUT DEBIAN

paps

PAPS(1) 						      General Commands Manual							   PAPS(1)

NAME

       paps - UTF-8 to PostScript converter using Pango

SYNOPSIS

       paps [options] files...

DESCRIPTION

       paps reads a UTF-8 encoded file and generates a PostScript language rendering of the file. The rendering is done by creating outline curves
       through the pango ft2 backend.

OPTIONS

       These programs follow the usual GNU command line syntax, with long options starting with  two  dashes  (`-').   A  summary  of  options	is
       included below.

       --landscape
	      Landscape output. Default is portrait.

       --columns=cl
	      Number of columns output. Default is 1.
	      Please notice this option isn't related to the terminal length as in a "80 culums terminal".

       --font=desc
	      Set the font description. Default is Monospace 12.

       --rtl  Do right to left (RTL) layout.

       --paper ps
	      Choose paper size. Known paper sizes are legal, letter and A4. Default is A4.

       Postscript points
	      Each postscript point equals to 1/72 of an inch. 36 points are 1/2 of an inch.

       --bottom-margin=bm
	      Set bottom margin. Default is 36 postscript points.

       --top-margin=tm
	      Set top margin. Default is 36 postscript points.

       --left-margin=lm
	      Set left margin. Default is 36 postscript points.

       --right-margin=rm
	      Set right margin. Default is 36 postscript points.

       --gutter-width=gw
	      Set gutter width. Default is 40 postscript points.

       --help Show summary of options.

       --header
	      Draw page header for each page.

       --markup
	      Interpret the text as pango markup.

       --lpi  Set the lines per inch. This determines the line spacing.

       --cpi  Set the characters per inch. This is an alternative method of specifying the font size.

       --stretch-chars
	      Indicates  that  characters  should be stretched in the y-direction to fill up their vertical space. This is similar to the texttops
	      behaviour.

AUTHOR

       paps was written by Dov Grobgeld <dov.grobgeld@gmail.com>.

       This manual page was written by Lior Kaplan <kaplan@debian.org>, for the Debian project (but may be used by others).

								  April  17, 2006							   PAPS(1)
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