I the original code below the bold is the static or the file that is always used. The italics output is set by prefand $file is the underlined portion and would be dependent on each .txt file in the directory.
Quote:
I also note that the exon.sh can't be the script that I supplied in post #11. That script didn't look at any of its operands; it only used the presence of one or more operands as a flag to enable debugging printouts. I will assume that you removed the debugging printf statements and the d variable and are using the two operands you are passing to exon.sh as the two filenames processed by that script.
Since one of the operands will never change and the other is set by the for loop are you saying (sorry for my confusion).I added comments as well. Thank you .
Code:
#!/bin/sh
awk -v d=$# ' (the d=$# is removed because the files are dependent on the for loop)
BEGIN { FS = "[\t_]"
OFS = "\t"
}
FNR == NR {
m[$1, $4, ++c[$1, $4]] = $2 + 0
M[$1, $4, c[$1, $4]] = $3 + 0
if(d) printf("m[%s,%s,%d]=%s,M[%s,%s,%d]=%s\n",
$1, $4, c[$1, $4], m[$1, $4, c[$1, $4]],
$1, $4, c[$1, $4], M[$1, $4, c[$1, $4]])
next
}
{ #if(d) printf("FNR=%d:\"%s\"\n",FNR,$0) (remove this line as it assumes d is typed in)
for(i = 1; i <= c[$1, $4]; i++) {
if(d) printf("m[%d]=%d,M[%d]=%d,$2=%d\n",
i, m[$1, $4, i],
i, M[$1, $4, i],
$2)
if(m[$1, $4, i] <= $2 && $2 <= M[$1, $4, i]) {
$5 = "exon"
break
} else {if(m[$1, $4, i] > $2 + 0) {
if(m[$1, $4, i] - 10 <= $2 + 0) {
$5 = "splicing"
break
} else {$5 = "intron"
break
}
}
}
}
if(i > c[$1, $4])
$5 = "intron"
}
1' all_cdsV200-0000low > 00-0000_filter
Last edited by cmccabe; 12-10-2018 at 04:05 PM..
Reason: corrected typo
I have a line like this:
I want to move HTTP/1.1 200 OK to the next line and put a blank line between the two lines i.e.
How can i get it using awk?
Thanks in advance (2 Replies)
Hi All,
I was wondering if anyone knew how to dynamically change the FS in awk to accept vairiable containing a field separator. the current code is as below and does not work when i introduce the dynamic FS change :-(
validate_source_file()
{
source_file=$1
... (2 Replies)
Hi, all
I need to get fields in a line that are separated by commas, some of the fields are enclosed with double quotes, and they are supposed to be treated as a single field even if there are commas inside the quotes.
sample input:
for this line, 5 fields are supposed to be extracted, they... (8 Replies)
First, thanks for the help in previous posts... couldn't have gotten where I am now without it!
So here is what I have, I use AWK to match $1 and $2 as 1 string in file1 to $1 and $2 as 1 string in file2. Now I'm wondering if I can extend this AWK command to incorporate the following:
If $1... (4 Replies)
Hi. I'd appreciate if I can get some direction in this issue to get me going.
Datafile1:
-About 4000 records, I have to update field#4 in selected records based on a match in the key field (Field#1).
-Field #1 is the key field (servername) . # of Fields may vary
# comment
server1 bbb ccc... (2 Replies)
Hi !
input:
111|222|333|aaa|bbb|ccc
999|888|777|nnn|kkk
444|666|555|eee|ttt|ooo|ppp
With awk, I am trying to change the FS "|" to "; " only from the 4th field until the end (the number of fields vary between records).
In order to get:
111|222|333|aaa; bbb; ccc
999|888|777|nnn; kkk... (1 Reply)
Hi Experts,
i need to change delimiter from tab to ","
sample test file
cat test
A0000368 A29938511 072569352 5 Any 2 for £1.00 BUTCHERS|CAT FOOD|400G Sep 12 2012 12:00AM Jan 5 2014 11:59PM Sep 7 2012 12:00AM M 2.000 group 5
... (2 Replies)
In the below awk in the first step I default Classification NF-1 to VUS. Next, I am trying to change the value of Classification (NF) to whatever CLINSIG (NF-1) is. If there is only one condition everything works great, but if there are two conditions it does not work. Is the syntax used... (4 Replies)
In the awk below I am trying to copy the entire contents of $6 there may be multiple values seperated by a ;, to $8, if $8 is . (lines 1 and 3 are examples). If that condition $8 is not . (line2 is an example) then that line is skipped and printed as is. The awk does execute but prints the output... (3 Replies)
Discussion started by: cmccabe
3 Replies
LEARN ABOUT V7
join
JOIN(1) General Commands Manual JOIN(1)NAME
join - relational database operator
SYNOPSIS
join [ options ] file1 file2
DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard
input is used.
File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in
each line.
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.
Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis-
carded.
These options are recognized:
-an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2.
-e s Replace empty output fields by string s.
-jn m Join on the mth field of file n. If n is missing, use the mth field in each file.
-o list
Each output line comprises the fields specifed in list, each element of which has the form n.m, where n is a file number and m is a
field number.
-tc Use character c as a separator (tab character). Every appearance of c in a line is significant.
SEE ALSO sort(1), comm(1), awk(1)BUGS
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 join, sort, comm, uniq, look and awk(1) are wildly incongruous.
JOIN(1)
12-10-2018
.