I have been able to get a working solution that produces my desired results... using set -x and the below modifications
Code:
if [[ $VCF = ${STRING[*]} ]] # only execute file on match
then
RSTRING=$(awk '/R_2019/' "$DIR"/run) ## search for lines matching R_2019 pattern
VCFRUN=$(awk -F '\n' -v RS="" -v ref="$VCF" '$0 ~ ref {print $NF}' "$DIR"/file) ## search file for matching $VCF and return last column ($2)
RUN="$(echo $RSTRING|cut -d- -f1,2,3)" ## remove after third _ in line with R_2019
mv "$DIR"/variants/${VCF}.vcf "$DEST"/"$RUN"/"$VCF"/variants ## move vcf to folder in destination
This matched each .vcf and moved the match to the correct run file. Maybe this will help others as well.
Thank you very much for your help .
Last edited by cmccabe; 04-09-2019 at 10:22 PM..
Reason: added comments
My input:
File_1:
2000_t
g1110.b1
abb.1
2001_t
g1111.b1
abb.2
abb.2
g1112.b1
abb.3
2002_t
.
.
File_2:
2000_t Ali england 135
abb.1 Zoe british 150
2001_t Ali england 305
g1111.b1 Lucy russia 126 (6 Replies)
Hi all,
This is actually more for my lazyness then anything else, but I think others might find it useful to use as well. Basically this is what I am trying to achieve...
In my ubuntu home dir under Downloads is where firefox saves everything by default, now I know that you can manually... (3 Replies)
Move all files starting with a specific name to different directory.
This shell script program should have three parameters
File Name
Source Directory
Destination Directory
User should be able to enter ‘AB_CD*' in file name parameter. In this case all the files starting with AB_CD will... (1 Reply)
Hi Folks,
I have different type of file in my current directory. From my current directory i need to move the file which is start with csp_rules and if the file is having the string payg , then I need to move all this files to another directory /output/record. Please help me how to do this?
... (3 Replies)
Hi All,
Really stuck up with a requirement where I need to move a file (Lets say date_Employee.txt--the date will have different date values like 20120612/20120613 etc) from one directory to another based on creation/modification dates.
While visiting couple of posts, i could see we can... (3 Replies)
Hi all,
I'm new to this forum and bash scripting. I have the following problem, I need to copy some files (from one dir. to another) whose first 5 numbers (subjects' ID) match the directory names. Here a shortened version of what I'm trying to do:
names=(32983_f 35416_f 43579_f) # these are... (6 Replies)
I am using bash to prompt a user for a choice using: where a "y" response opens a menu with available panels that can be used.
while true; do
read -p "Do you want to get coverage of a specific panel?" yn
case $yn in
* ) menu; break;;
* ) exit;;
* ) echo... (6 Replies)
I have a specific set (all ending with .bam) of downloaded files in a directory /home/cmccabe/Desktop/NGS/API/2-15-2016. What I am trying to do is use a match to $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name... (1 Reply)
I have a directory /home/cmccabe/nfs/exportedReports that contains multiple folders in it. The find writes the name of each folder to out.txt. A new directory is then created in a new location /home/cmccabe/Desktop/NGS/API, named with the date. What I am trying to do, unsuccessfully at the moment,... (7 Replies)
In the below bash I am trying to rename eachof the 3 text files in /home/cmccabe/Desktop/percent by matching the numerical portion of each file to lines 3,4, or 5 in /home/cmccabe/Desktop/analysis.txt. There will always be a match between the files. When a match is found each text file in... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
notmuch-mutt
NOTMUCH-MUTT(1) User Contributed Perl Documentation NOTMUCH-MUTT(1)NAME
notmuch-mutt - notmuch (of a) helper for Mutt
SYNOPSIS
notmuch-mutt [OPTION]... search [SEARCH-TERM]...
notmuch-mutt [OPTION]... thread < MAIL
notmuch-mutt [OPTION]... tag [TAGS]... < MAIL
DESCRIPTION
notmuch-mutt is a frontend to the notmuch mail indexer capable of populating a maildir with search results.
OPTIONS -o DIR
--output-dir DIR
Store search results as (symlink) messages under maildir DIR. Beware: DIR will be overwritten. (Default:
~/.cache/notmuch/mutt/results/)
-p
--prompt
Instead of using command line search terms, prompt the user for them (only for "search").
-h
--help
Show usage information and exit.
INTEGRATION WITH MUTT
notmuch-mutt can be used to integrate notmuch with the Mutt mail user agent (unsurprisingly, given the name). To that end, you should
define macros like the following in your Mutt configuration (usually one of: ~/.muttrc, /etc/Muttrc, or a configuration snippet under
/etc/Muttrc.d/):
macro index <F8>
"<enter-command>unset wait_key<enter><shell-escape>notmuch-mutt --prompt search<enter><change-folder-readonly>~/.cache/notmuch/mutt/results<enter>"
"notmuch: search mail"
macro index <F9>
"<enter-command>unset wait_key<enter><pipe-message>notmuch-mutt thread<enter><change-folder-readonly>~/.cache/notmuch/mutt/results<enter><enter-command>set wait_key<enter>"
"notmuch: reconstruct thread"
macro index <F6>
"<enter-command>unset wait_key<enter><pipe-message>notmuch-mutt tag -inbox<enter>"
"notmuch: remove message from inbox"
The first macro (activated by <F8>) prompts the user for notmuch search terms and then jump to a temporary maildir showing search results.
The second macro (activated by <F9>) reconstructs the thread corresponding to the current mail and show it as search results. The third
macro (activated by <F6>) removes the tag "inbox" from the current message; by changing "-inbox" this macro may be customised to add or
remove tags appropriate to the users notmuch work-flow.
To keep notmuch index current you should then periodically run "notmuch new". Depending on your local mail setup, you might want to do that
via cron, as a hook triggered by mail retrieval, etc.
SEE ALSO mutt(1), notmuch(1)AUTHOR
Copyright: (C) 2011-2012 Stefano Zacchiroli <zack@upsilon.cc>
License: GNU General Public License (GPL), version 3 or higher
perl v5.14.2 2012-06-02 NOTMUCH-MUTT(1)
04-09-2019
.