I have been trying to understand your code and am just not understanding, but I am trying, I know it may seem like I am not but I assure yu that I am and will continue to do so. I added comments to each line and some questions. My understanding is not there completely but hopefully its a start. I apologize for the misleading output description, thousands of lines print, i only showed a few to keep the post short. Thank you .
Code:
#!/bin/sh
awk -v d=$# ' # does this define d as non-zero
BEGIN { FS = "[\t_]" # define FS as tab or underscore
OFS = "\t" # define output as tab delimited
}
FNR == NR { # process same line in file 2 as file1 and start processing file2 or /home/cmccabe/folder/less/all_cdsV2
m[$1, $4, ++c[$1, $4]] = $2 + 0 # split $4 and store $1 and $2in array m, what does the + 0 do?
M[$1, $4, c[$1, $4]] = $3 + 0 # split $4 and store $1 and $2in array M, what does the + 0 do?
if(d) printf("m[%s,%s,%d]=%s,M[%s,%s,%d]=%s\n", # debugging print
$1, $4, c[$1, $4], m[$1, $4, c[$1, $4]], # for m (m=min)?
$1, $4, c[$1, $4], M[$1, $4, c[$1, $4]]) # for M (M=max)?
next # process next line
}
{ if(d) printf("FNR=%d:\"%s\"\n",FNR,$0) # not sure what this doesI think it prints each line in $file?
for(i = 1; i <= c[$1, $4]; i++) { # start a loop using $4 and $1 value
#if(d) printf("m[%d]=%d,M[%d]=%d,$2=%d\n", # again not sure?
i, m[$1, $4, i], # loop through each m in /home/cmccabe/folder/less/all_cdsV2 for each $1 and $4 of $file
i, M[$1, $4, i], # loop through each M in /home/cmccabe/folder/less/all_cdsV2 for each $1 and $4 of $file
$2) # not sure what this does?
if(m[$1, $4, i] <= $2 && $2 <= M[$1, $4, i]) { # if the value of each matching m<=$2 and <=M then print
$5 = "exon" # exon in $5
break # break loop and move to next line
} else {if(m[$1, $4, i] > $2 + 0) { # if the value of each matching m>=$2 and >=M then print
if(m[$1, $4, i] - 10 <= $2 + 0) { # if the value of each matching -10and <=$2 then print
$5 = "splicing"
break # break loop and move to next line
} else {$5 = "intron" # print intron in $5
break # break loop and move to next line
}
}
}
}
if(i > c[$1, $4]) # what does this do hasn't intron already been printed?
$5 = "intron"
}
1' "$1" "$2" # parameters passed from for loop
Code:
(only a few lines of the thousands to show the desired output results from the grep)
grep -E 'splicing|intron|exon' /home/cmccabe/folder/less/00-0000_output.txt
chr7 30062272 30062492 FKBP14 splicing
chr7 30065867 30066087 FKBP14 intron
chr7 30065964 30066184 FKBP14 exon
chr7 94024268 94024488 COL1A2 intron
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 DEBIAN
igawk
IGAWK(1) Utility Commands IGAWK(1)NAME
igawk - gawk with include files
SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ...
igawk [ all gawk options ] [ -- ] program-text file ...
DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).
AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like
@include getopt.awk
in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.
OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports.
EXAMPLES
cat << EOF > test.awk
@include getopt.awk
BEGIN {
while (getopt(ARGC, ARGV, "am:q") != -1)
...
}
EOF
igawk -f test.awk
SEE ALSO gawk(1)
Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.
AUTHOR
Arnold Robbins (arnold@skeeve.com).
Free Software Foundation Nov 3 1999 IGAWK(1)
12-11-2018
.