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 FREEBSD
lam
LAM(1) BSD General Commands Manual LAM(1)NAME
lam -- laminate files
SYNOPSIS
lam [-f min.max] [-s sepstring] [-t c] file ...
lam [-p min.max] [-s sepstring] [-t c] file ...
DESCRIPTION
The lam utility copies the named files side by side onto the standard output. The n-th input lines from the input files are considered frag-
ments of the single long n-th output line into which they are assembled. The name `-' means the standard input, and may be repeated.
Normally, each option affects only the file after it. If the option letter is capitalized it affects all subsequent files until it appears
again uncapitalized. The options are described below:
-f min.max
Print line fragments according to the format string min.max, where min is the minimum field width and max the maximum field width.
If min begins with a zero, zeros will be added to make up the field width, and if it begins with a `-', the fragment will be left-
adjusted within the field.
-p min.max
Like -f, but pad this file's field when end-of-file is reached and other files are still active.
-s sepstring
Print sepstring before printing line fragments from the next file. This option may appear after the last file.
-t c The input line terminator is c instead of a newline. The newline normally appended to each output line is omitted.
To print files simultaneously for easy viewing use pr(1).
EXAMPLES
The command
lam file1 file2 file3 file4
joins 4 files together along each line. To merge the lines from four different files use
lam file1 -S "
" file2 file3 file4
Every 2 lines of a file may be joined on one line with
lam - - < file
and a form letter with substitutions keyed by `@' can be done with
lam -t @ letter changes
SEE ALSO join(1), paste(1), pr(1), printf(3)STANDARDS
Some of the functionality of lam is standardized as the paste(1) utility by IEEE Std 1003.2 (``POSIX.2'').
HISTORY
The lam utility first appeared in 4.2BSD.
BUGS
The lam utility does not recognize multibyte characters.
BSD August 12, 2004 BSD
12-11-2018
.