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Full Discussion: Determining number of overlaps between two files using Hashes?
Top Forums Shell Programming and Scripting Determining number of overlaps between two files using Hashes? Post 302236095 by labrazil on Sunday 14th of September 2008 08:03:43 PM
Old 09-14-2008
Determining number of overlaps between two files using Hashes?
Hi there,

I have a doubt about how to set this up. This is the situation.

I have two files, one that is ~31,000 in length and has the following information (7 fields):
file1
Code:
1    +       100208127       100261594       6       100208127,100231680,100237404,100245177,100249508,100260529,    100208306,100231885,100237559,100245300,100249677,100261594,
1    +       100217082       100217185       1       100217082,      100217185,
1    +       100276376       100321515       12      100276376,100288052,100296809,100298021,100299978,100306120,100306616,100307757,100315308,100316594,100318639,100320146,        100276460,100288148,100296872,100298149,100300093,100306339,100306730,100307829,100315421,100316692,100318803,100321515,

the 5th field is important and it explains the number of segments represented in fields 6 and 7. So for example, the first line shows 6, so if you took the first number of field 6 this would represent the start of the first segment and the first number of field 7 would represent the end of the first segment, and so on till you have the total 6 segments. The second line for example shows only 1 in field 5 and hence there's only one segment starting at 100217082 and ending at 100217185.

the second file I have is variable in length and can be from 3,000,000 to 10,000,000 lines. The format contains 4 fields:
file2
Code:
1    100208130       100208166       +
1    100208310       100208346       +
1    100217090       100217126       +
1    100231689       100231725       +

As you can see, field 2 and 3 is just a difference of 36 numbers and I want to know how many times each line in file2 is contained within file1 specifically when looking at the segments (remember each line in file1 has different numbers of segments above, e.g. 6, 1, and 12 as represented in field 5).

So if I use these two files to generate my output, my output would tell me:

There are 3 lines from file2 that matches or overlaps segments in file1 and 1 line from file2 that DOESNOT match or overlap segments in file1.

Code:
YES 1    100208130       100208166       +
NO 1    100208310       100208346       +
YES 1    100217090       100217126       +
YES 1    100231689       100231725       +

To get this kind of computation, do you think it's important to use hashes for the first file or second file and if so, how would I set this up? Can someone assist here? Thanks!
 

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LEARN ABOUT CENTOS

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.

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

       --rtl  Do rtl layout.

       --paper ps
	      Choose paper size. Known paper sizes are legal, letter, a4. Default is A4.

       --bottom-margin=bm
	      Set bottom margin in postscript points (1/72 inch). Default is 36.

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

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

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

       --help Show summary of options.

       --header
	      Draw page header for each page.

       --markup
	      Interpret the text as pango markup.

       --encoding=ENCODING
	      Assume the documentation encoding is ENCODING.

       --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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