Bash to move specific files to directory based on match to file
I am trying to mv each of the .vcf files in the variants folder to the folder in /home/cmccabe/f2 that the .vcf id is found in file. $2 in file will always have the id of a .vcf in the variants folder. The line in blue staring with R_2019 in file up to the -v5.6 will always be an exact match to a folder in /home/cmccabe/f2. There may be multiple folders in /home/cmccabe/f2 but will only have one match in file. There also may be mulitple id's but always only one .vcf in /home/cmccabe/f1/variants.
When a match is found between the folder in /home/cmccabe/f2 and the R_ in file, then the id(s) in $2 will be found in /home/cmccabe/f1/variants as a .vcf. Each .vcf is then moved to the matching folder in /home/cmccabe/f2 in a the sub-folder variants. This is the last step of a procedure that I am stuck on. I have included an attempt in bash and included comments, but im sure there is a better way. Thank you .
for file in /home/cmccabe/f1/variants/*.vcf ; do
bname=$(basename $file) # strip of path
VCF="$(echo $bname|cut -d. -f1)" # remove .vcf extension
f=$(printf '%s' /home/cmccabe/f1/file/${VCF}) ## # Find matching id
FILE2=$(awk '{print $2}' $f') # set VCF lookup to column
for RDIR in "$DIR"/R_2019* ; do FOLDER=${RDIR%%-v5.6*}; done ## trim folder match in RDIR from -v5.6 and store in FOLDER
if [[ $VCF = $FILE2 ]] # only execute file on match
then
mkdir -p /home/cmccabe/f2/$FOLDER/variants ## create variants sub-folder
mv /home/cmccabe/f1/file/$VCF /home/cmccabe/f2/$FOLDER/$VCF/variants ## move vcf to folder/id/variants
fi ## end if
done ## close loop
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)
03-26-2019
.