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 HPUX
merge
merge(1) General Commands Manual merge(1)NAME
merge - three-way file merge
SYNOPSIS
file1 file2 file3
DESCRIPTION
combines two files that are revisions of a single original file. The original file is file2, and the revised files are file1 and file3.
identifies all changes that lead from file2 to file3 and from file2 to file1, then deposits the merged text into file1. If the option is
used, the result goes to standard output instead of file1.
An overlap occurs if both file1 and file3 have changes in the same place. prints how many overlaps occurred, and includes both alterna-
tives in the result. The alternatives are delimited as follows:
lines in file1
lines in file3
If there are overlaps, edit the result in file1 and delete one of the alternatives.
This command is particularly useful for revision control, especially if file1 and file3 are the ends of two branches that have file2 as a
common ancestor.
EXAMPLES
A typical use for is as follows:
1. To merge an RCS branch into the trunk, first check out the three different versions from RCS (see co(1)) and rename them for
their revision numbers: 5.2, 5.11, and 5.2.3.3. File 5.2.3.3 is the end of an RCS branch that split off the trunk at file 5.2.
2. For this example, assume file 5.11 is the latest version on the trunk, and is also a revision of the "original" file, 5.2.
Merge the branch into the trunk with the command:
3. File 5.11 now contains all changes made on the branch and the trunk, and has markings in the file to show all overlapping
changes.
4. Edit file 5.11 to correct the overlaps, then use the command to check the file back in (see ci(1)).
WARNINGS
uses the ed(1) system editor. Therefore, the file size limits of ed(1) apply to
AUTHOR
was developed by Walter F. Tichy.
SEE ALSO diff3(1), diff(1), rcsmerge(1), co(1).
merge(1)
03-19-2017
.