06-18-2017
Sorry Neo, does the below help?
The
NM_ value of
$2 in
file1, after splitting on the
., will match a substring
NM_ in
$12 (the majority of the time), or
$9 (in some cases).
The substring that matches is extracted starting from the
NM_ until the
; or break (if it is the last value, like in case 1 in the example).
The text in
$7 of
file2 determines the field to use/ extract from.... that is if
$7=exonic, then use
$12, but if
$7 is not =exonic, then use
$9.
The extracted value is used to update
$14 from a
. to the extracted value. Thank you very much
.
Last edited by cmccabe; 06-18-2017 at 08:39 AM..
Reason: added details
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JOIN(1) BSD General Commands Manual JOIN(1)
NAME
join -- relational database operator
SYNOPSIS
join [-a file_number | -v file_number] [-e string] [-o list] [-t char] [-1 field] [-2 field] file1 file2
DESCRIPTION
The join utility performs an ``equality join'' on the specified files and writes the result to the standard output. The ``join field'' is
the field in each file by which the files are compared. The first field in each line is used by default. There is one line in the output
for each pair of lines in file1 and file2 which have identical join fields. Each output line consists of the join field, the remaining
fields from file1 and then the remaining fields from file2.
The default field separators are tab and space characters. In this case, multiple tabs and spaces count as a single field separator, and
leading tabs and spaces are ignored. The default output field separator is a single space character.
Many of the options use file and field numbers. Both file numbers and field numbers are 1 based, i.e., the first file on the command line is
file number 1 and the first field is field number 1. The following options are available:
-a file_number
In addition to the default output, produce a line for each unpairable line in file file_number.
-e string
Replace empty output fields with string.
-o list
The -o option specifies the fields that will be output from each file for each line with matching join fields. Each element of list
has either the form file_number.field, where file_number is a file number and field is a field number, or the form '0' (zero), repre-
senting the join field. The elements of list must be either comma (',') or whitespace separated. (The latter requires quoting to
protect it from the shell, or, a simpler approach is to use multiple -o options.)
-t char
Use character char as a field delimiter for both input and output. Every occurrence of char in a line is significant.
-v file_number
Do not display the default output, but display a line for each unpairable line in file file_number. The options -v 1 and -v 2 may be
specified at the same time.
-1 field
Join on the field'th field of file1.
-2 field
Join on the field'th field of file2.
When the default field delimiter characters are used, the files to be joined should be ordered in the collating sequence of sort(1), using
the -b option, on the fields on which they are to be joined, otherwise join may not report all field matches. When the field delimiter char-
acters are specified by the -t option, the collating sequence should be the same as sort(1) without the -b option.
If one of the arguments file1 or file2 is '-', the standard input is used.
EXIT STATUS
The join utility exits 0 on success, and >0 if an error occurs.
COMPATIBILITY
For compatibility with historic versions of join, the following options are available:
-a In addition to the default output, produce a line for each unpairable line in both file1 and file2.
-j1 field
Join on the field'th field of file1.
-j2 field
Join on the field'th field of file2.
-j field
Join on the field'th field of both file1 and file2.
-o list ...
Historical implementations of join permitted multiple arguments to the -o option. These arguments were of the form
file_number.field_number as described for the current -o option. This has obvious difficulties in the presence of files named 1.2.
These options are available only so historic shell scripts do not require modification and should not be used.
SEE ALSO
awk(1), comm(1), paste(1), sort(1), uniq(1)
STANDARDS
The join command conforms to IEEE Std 1003.1-2001 (``POSIX.1'').
BSD
July 5, 2004 BSD