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
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Discussion started by: cmccabe
2 Replies
LEARN ABOUT CENTOS
install-info
INSTALL-INFO(1) User Commands INSTALL-INFO(1)NAME
install-info - update info/dir entries
SYNOPSIS
install-info [OPTION]... [INFO-FILE [DIR-FILE]]
DESCRIPTION
Add or remove entries in INFO-FILE from the Info directory DIR-FILE. INFO-FILE and DIR-FILE are required unless the --info-file or
--dir-file (or --info-dir) options are given, respectively.
OPTIONS --add-once
add only to first matching section, not all.
--align=COL
start description of new entries at column COL.
--calign=COL
format second and subsequent description lines to start at column COL.
--debug
report what is being done.
--delete
delete existing entries for INFO-FILE from DIR-FILE; don't insert any new entries.
--description=TEXT
the description of the entry is TEXT; used with the --name option to become synonymous with the --entry option.
--dir-file=NAME
specify file name of Info directory file; equivalent to using the DIR-FILE argument.
--dry-run
same as --test.
--entry=TEXT
insert TEXT as an Info directory entry, overriding any corresponding entry from DIR-FILE. TEXT is written as an Info menu item line
followed
by zero or more extra lines starting with whitespace.
If you specify more than one entry, all are added. If you don't specify any entries, they are determined
from information in the Info file itself.
--help display this help and exit.
--info-dir=DIR
same as --dir-file=DIR/dir.
--info-file=FILE
specify Info file to install in the directory; equivalent to using the INFO-FILE argument.
--item=TEXT
same as --entry=TEXT.
--keep-old
do not replace entries, or remove empty sections.
--maxwidth, --max-width=COL
wrap description at column COL.
--menuentry=TEXT
same as --name=TEXT.
--name=TEXT
the name of the entry is TEXT; used with --description to become synonymous with the --entry option.
--no-indent
do not format new entries in the DIR file.
--quiet
suppress warnings.
--regex=R
put this file's entries in all sections that match the regular expression R (ignoring case).
--remove
same as --delete.
--remove-exactly
only remove if the info file name matches exactly; suffixes such as .info and .gz are not ignored.
--section=SEC
put entries in section SEC of the directory. If you specify more than one section, all the entries
are added in each of the sections.
If you don't specify any sections, they are determined
from information in the Info file itself.
--section R SEC
equivalent to --regex=R --section=SEC --add-once.
--silent
suppress warnings.
--test suppress updating of DIR-FILE.
--version
display version information and exit.
REPORTING BUGS
Email bug reports to bug-texinfo@gnu.org, general questions and discussion to help-texinfo@gnu.org.
Texinfo home page: http://www.gnu.org/software/texinfo/
COPYRIGHT
Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.
SEE ALSO
The full documentation for install-info is maintained as a Texinfo manual. If the info and install-info programs are properly installed at
your site, the command
info install-info
should give you access to the complete manual.
install-info 5.1 June 2014 INSTALL-INFO(1)
04-09-2019
.