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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 OPENSOLARIS

comm

comm(1) 							   User Commands							   comm(1)

NAME

       comm - select or reject lines common to two files

SYNOPSIS

       comm [-123] file1 file2

DESCRIPTION

       The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output:
       lines only in file1; lines only in file2; and lines in both files.

       If the input files were ordered according to the collating sequence of the current locale, the lines  written  will  be	in  the  collating
       sequence of the original lines. If not, the results are unspecified.

OPTIONS

       The following options are supported:

       -1    Suppresses the output column of lines unique to file1.

       -2    Suppresses the output column of lines unique to file2.

       -3    Suppresses the output column of lines duplicated in file1 and file2.

OPERANDS

       The following operands are supported:

       file1	A path name of the first file to be compared. If file1 is -, the standard input is used.

       file2	A path name of the second file to be compared. If file2 is -, the standard input is used.

USAGE

       See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes).

EXAMPLES

       Example 1 Printing a list of utilities specified by files

       If file1, file2, and file3 each contain a sorted list of utilities, the command

	 example% comm -23 file1 file2	| comm -23 - file3

       prints a list of utilities in file1 not specified by either of the other files. The entry:

	 example% comm -12 file1 file2 | comm -12 - file3

       prints a list of utilities specified by all three files. And the entry:

	 example% comm -12  file2 file3 | comm -23 -file1

       prints a list of utilities specified by both file2 and file3, but not specified in file1.

ENVIRONMENT VARIABLES

       See  environ(5)	for  descriptions  of  the  following  environment  variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE,
       LC_CTYPE, LC_MESSAGES, and NLSPATH.

EXIT STATUS

       The following exit values are returned:

       0     All input files were successfully output as specified.

       >0    An error occurred.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Availability		     |SUNWesu			   |
       +-----------------------------+-----------------------------+
       |CSI			     |enabled			   |
       +-----------------------------+-----------------------------+
       |Interface Stability	     |Standard			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5)

SunOS 5.11							    3 Mar 2004								   comm(1)
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