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Top Forums Shell Programming and Scripting Read column and find differences... Post 302723323 by durden_tyler on Tuesday 30th of October 2012 12:22:10 AM
Old 10-30-2012
Code:
$
$
$ cat f13
427     A       C       A/C     12
436     G       C       G/C     12
445     C       T       C/T     12
447     A       G       A/G     9
451     T       C       T/C     5
456     A       G       A/G     12
493     G       A       G/A     12
$
$
$
$ perl -lane '$x{$F[0]} = [ @F ];
              END {
                foreach $k (sort keys %x) {
                  foreach $i ($k-10..$k+10) {
                    push (@y, $i) if defined $x{$i} and $i != $k;
                  }
                  printf ("%-7s %-7s %-7s %-7s %-7s %s\n",@{$x{$k}},join(",",@y));
                  @y=()
                }
              }' f13
427     A       C       A/C     12      436
436     G       C       G/C     12      427,445
445     C       T       C/T     12      436,447,451
447     A       G       A/G     9       445,451,456
451     T       C       T/C     5       445,447,456
456     A       G       A/G     12      447,451
493     G       A       G/A     12
$
$
$

tyler_durden
 

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join(1) 							   User Commands							   join(1)

NAME
join - relational database operator SYNOPSIS
join [-a filenumber | -v filenumber] [-1 fieldnumber] [-2 fieldnumber] [-o list] [-e string] [-t char] file1 file2 join [-a filenumber] [-j fieldnumber] [-j1 fieldnumber] [-j2 fieldnumber] [-o list] [-e string] [-t char] file1 file2 DESCRIPTION
The join command forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. This format can be changed by using the -o option (see below). The -a option can be used to add unmatched lines to the output. The -v option can be used to output only unmatched lines. The default input field separators are blank, tab, or new-line. In this case, multiple separators count as one field separator, and leading separators are ignored. The default output field separator is a blank. If the input files are not in the appropriate collating sequence, the results are unspecified. OPTIONS
Some of the options below use the argument filenumber. This argument should be a 1 or a 2 referring to either file1 or file2, respectively. -a filenumber In addition to the normal output, produce a line for each unpairable line in file filenumber, where filenumber is 1 or 2. If both -a 1 and -a 2 are specified, all unpairable lines will be output. -e string Replace empty output fields in the list selected by option -o with the string string. -j fieldnumber Equivalent to -1fieldnumber -2fieldnumber. -j1 fieldnumber Equivalent to -1fieldnumber. -j2 fieldnumber Equivalent to -2fieldnumber. Fields are numbered starting with 1. -o list Each output line includes the fields specified in list. Fields selected by list that do not appear in the input will be treated as empty output fields. (See the -e option.) Each element of which has the either the form filenum- ber.fieldnumber, or 0, which represents the join field. The common field is not printed unless specifically requested. -t char Use character char as a separator. Every appearance of char in a line is significant. The character char is used as the field separator for both input and output. With this option specified, the collating term should be the same as sort without the -b option. -v filenumber Instead of the default output, produce a line only for each unpairable line in filenumber, where filenumber is 1 or 2. If both -v 1 and -v 2 are specified, all unpairable lines will be output. -1 fieldnumber Join on the fieldnumberth field of file 1. Fields are decimal integers starting with 1. -2fieldnumber Join on the fieldnumberth field of file 2. Fields are decimal integers starting with 1. OPERANDS
The following operands are supported: file1 file2 A path name of a file to be joined. If either of the file1 or file2 operands is -, the standard input is used in its place. file1 and file2 must be sorted in increasing collating sequence as determined by LC_COLLATE on the fields on which they are to be joined, normally the first in each line (see sort(1)). USAGE
See largefile(5) for the description of the behavior of join when encountering files greater than or equal to 2 Gbyte (2**31 bytes). EXAMPLES
Example 1: Joining the password file and group file The following command line will join the password file and the group file, matching on the numeric group ID, and outputting the login name, the group name and the login directory. It is assumed that the files have been sorted in ASCII collating sequence on the group ID fields. example% join -j1 4-j2 3 -o 1.1 2.1 1.6 -t:/etc/passwd /etc/group Example 2: Using the -o option The -o 0 field essentially selects the union of the join fields. For example, given file phone: !Name Phone Number Don +1 123-456-7890 Hal +1 234-567-8901 Yasushi +2 345-678-9012 and file fax: !Name Fax Number Don +1 123-456-7899 Keith +1 456-789-0122 Yasushi +2 345-678-9011 where the large expanses of white space are meant to each represent a single tab character), the command: example% join -t"tab" -a 1 -a 2 -e '(unknown)' -o 0,1.2,2.2 phone fax would produce !Name Phone Number Fax Number Don +1 123-456-7890 +1 123-456-7899 Hal +1 234-567-8901 (unknown Keith (unknown) +1 456-789-012 Yasushi +2 345-678-9012 +2 345-678-9011 ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of join: LANG, LC_ALL, LC_CTYPE, LC_MES- SAGES, LC_COLLATE, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were output successfully. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
awk(1), comm(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) NOTES
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of the join, sort, comm, uniq, and awk commands are wildly incongruous. SunOS 5.10 8 Feb 2000 join(1)
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