I truely appreciate the helpful troubleshooting tips and explanations. I will use them to debug and post back. I did learn as a reseacher and am always trying to refine and improve my technique. I don't know if I will get there, but i will always try and practice. Biology and programming are essential and interesting. Thank you again 😀.
--- Post updated 12-08-18 at 07:39 AM ---
The variables are all being populated correctly but using set -xv, thank you... the script never gets past or to the done (it stalls on the bold line.
Code:
for file in /home/cmccabe/folder/less/*.txt ; do
bname=$(basename "$file")
pref="${bname%%_*.txt}"
set -xv
/home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" \> /home/cmccabe/folder/less/${pref}_output.txt
done
set +xv
So since the first .txt file never completes the second one never starts processing. Why this is seems to be my issue no its a matter off figuring out the why. Thank you for the helpful "talk", I appreciate it .
I ran bash -x
Code:
for file in /home/cmccabe/folder/less/*.txt ; do
bname=$(basename "$file")
pref="${bname%%_*.txt}"
bash -x /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > /home/cmccabe/folder/less/${pref}_output.txt
done
and confirmed the .txt files are not being passed to the exon script as input.
Last edited by Don Cragun; 12-08-2018 at 10:22 AM..
Reason: Fix CODE tags.
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 OPENSOLARIS
rmf
RMF(1) [nmh-1.5] RMF(1)NAME
rmf - remove an nmh folder
SYNOPSIS
rmf [+folder] [-interactive | -nointeractive] [-version] [-help]
DESCRIPTION
Rmf removes all of the messages (files) within the specified (or default) folder, and then removes the folder (directory) itself.
If there are any files within the folder which are not a part of nmh, they will not be removed, and an error will be produced. If the
folder is given explicitly or the -nointeractive option is given, then the folder will be removed without confirmation. Otherwise, the
user will be asked for confirmation. If rmf can't find the current folder, for some reason, the folder to be removed defaults to `+inbox'
(unless overridden by user's profile entry "Inbox") with confirmation.
If the folder being removed is a subfolder, the parent folder will become the new current folder, and rmf will produce a message telling
the user this has happened. This provides an easy mechanism for selecting a set of messages, operating on the list, then removing the list
and returning to the current folder from which the list was extracted.
If rmf s used on a read-only folder, it will delete all the (private) sequences (i.e., "atr-seq-folder" entries) for this folder from your
context without affecting the folder itself.
Rmf irreversibly deletes messages that don't have other links, so use it with caution.
FILES
$HOME/.mh_profile The user profile
PROFILE COMPONENTS
Path: To determine the user's nmh directory
Current-Folder: To find the default current folder
Inbox: To find the default inbox
SEE ALSO rmm(1)DEFAULTS
`+folder' defaults to the current folder, usually with confirmation
`-interactive' if +folder' not given, `-nointeractive' otherwise
CONTEXT
Rmf will set the current folder to the parent folder if a subfolder is removed; or if the current folder is removed, it will make "inbox"
current. Otherwise, it doesn't change the current folder or message.
BUGS
Although intuitively one would suspect that rmf works recursively, it does not. Hence if you have a sub-folder within a folder, in order
to rmf the parent, you must first rmf each of the children.
MH.6.8 11 June 2012 RMF(1)
12-08-2018
.