I made a typo in on of the file1 lines, BCRA1 should be BCRA2.
file1
Code:
BRCA2
BCR
SCN1A
fbn1
current output:
Code:
awk 'BEGIN{FS=OFS="\t"}
{$0=toupper($0)}
FNR==NR{
if(NR>1 && ($7 ~ "FULL GENE SEQUENC")) {
gsub(" ","",$5) #removing white space
n=split($5,v,"/")
d[v[1]] = $4 #from split, first element as key
}
next
}{print $1, ($1 in d?d[$1]:279)}' file2 file1
BRCA2 279
BCR 279
SCN1A 279
FBN1 85
FULL GENE SEQUENC could also be case in sensitive so I added a check in for that... why isn't FULL GENE SEQUENCE used, when I try that I get all the names with a value of 279.
Code:
awk 'BEGIN{FS=OFS="\t"}
{$0=toupper($0)} {$7=toupper($7)}
FNR==NR{
if(NR>1 && ($7 ~ "FULL GENE SEQUENC")) {
gsub(" ","",$5) #removing white space
n=split($5,v,"/")
d[v[1]] = $4 #from split, first element as key
}
next
}{print $1, ($1 in d?d[$1]:279)}' file2 file1
BRCA2 279
BCR 279
SCN1A 279
FBN1 85
desired output
Code:
BRCA2 81 - match in line 2 of $5 in file 2, BRCA 1, BRCA2
BCR 279 - match in line 2 of $5 in file but $7 is not full gene sequence
SCN1A 279
fbn1 85
Thank you .
Last edited by cmccabe; 03-19-2017 at 06:09 PM..
Reason: fixed format
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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)
03-19-2017
.