Transposing a huge space delimited file


 
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# 8  
Old 02-02-2013
Quote:
Originally Posted by RudiC
I'm not sure any tool will handle lines at least 4 million chars long (one char cols assumed).
Many tools can do that including gawk and perl.
# 9  
Old 02-04-2013
Quote:
Originally Posted by elixir_sinari
Many tools can do that including gawk and perl.
Standard tool, then.

Even ordinary awk can handle this if you fiddle with the record and field separators so it reads one column at a time, what to do with it is the question. Millions of columns may verge on the point where awk's arrays start having index problems...

If this file has fixed size columns, an elegant solution may be possible. If not, I don't know if we can make anything faster.
This User Gave Thanks to Corona688 For This Post:
# 10  
Old 02-08-2013
I found this one-liner and it seems to do the trick:

Code:
awk '{for (i=1; i<=NF; i++) a[i]=a[i](NR!=1?FS:"")$i} END {for (i=1; i in a; i++) print a[i]}'

Thanks!
# 11  
Old 02-09-2013
I did this on a much smaller file:
Code:
$ cat file
GAATCCGGAAACAGCAACTTCAAANCA
GTNATTCGGGCCAAACTGTCGAA
$ mkfifo fifo1 fifo2
$ sed -n '2 {s:.:&\n:g;wfifo2
}
       ' file &
$ sed -n '1 {s:.:&\n:g;wfifo1
}
       ' file &
$ paste -d" " fifo1 fifo2
G G
A T
A N
.
.
.

Don't how it will deal with huuuge files...
 
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