Rename specific file extension in directory with match to another file in bash
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 $2 in name to rename the downloaded files. To make things a more involved the date of the folder is unique and in the header of name the date of the match exists and is where the match in name is located. I am not sure how to do this or if it is possible. I have tried a sed command with no luck, maybe that isn't the best way. Thank you .
contents of folder /home/cmccabe/Desktop/NGS/API/2-15-2016
for f in /home/cmccabe/Desktop/NGS/API/2-12-2016/*.bam ; do
bname=$(basename $f)
cmd=$(sed -n "/$f/,/[0-9]{1,2}-[0-9]{1,2}-20[0-9]{2}/{s/\(.*\.bam\) \(.*\)/mv \1 \2/p}" /home/cmccabe/Desktop/NGS/panels/name.txt)
echo "$cmd"
done
sed: -e expression #1, char 4: extra characters after command
Last edited by cmccabe; 03-04-2016 at 06:38 PM..
Reason: fixed format
I am trying for loop to rename file extension from .txt to .html :
as below :
for i in *.txt; do mv "$i" `basename $i`.html; done
-------------------------------------------
But this renames a file file1.txt as file1.txt.html
anyone know how get avoid .html added after .txt ?
it... (4 Replies)
Hi guys,
i had many files like filename.20110520_20110519_050030
i have to rename the file by removint the last numerics ..
i.e filename.dat
i tried with cut command and removed the numerics but i'm not able to add .dat to the files.
is there any command insted of cut command to... (1 Reply)
Hi,
I am trying to make all file in the directory uppercase but not their extension (ex: image.jpg becoming IMAGE.jpg)
here is code i am trying.
$ ls | while read file
do
name=${file%%.*}
newfilename=$(echo $name | tr 'a-z' 'A-Z')
mv $file $newfilename
done
any suggestions of... (4 Replies)
I have a list file that contains names of many files. I am reading one file name at a time using for loop
Then I like to create one more list file but with the file extension changed to "ctl".
Note: The file name can have any number of dots ".". But the extension after the last dot should be... (4 Replies)
Hello,
I have multiple files named rscclog_2013-03-25.txt;3 in a directory, where 2013-03-25 is the previous day's date and the number after extension .txt preceded by a ';' is any number which i do not know beforehand.
Now, i have to rename all such files as rscclog_2013-03-25.txt
thus,... (2 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 am trying to rename all text files in a directory that match a pattern. The current command below seems to be using the directory path in the name and since it already exists, will not do the rename. I am not sure what I am missing? Thank you :).
Files to rename in... (3 Replies)
In the bash below I am trying to create sub-directories inside a directory from files with specific .bam extensions. There may be more then one $RDIR ing the directory and the .bam file(s) are trimmed (removing the extension and IonCode_0000_) and the result is the folder name that is saved in... (2 Replies)
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... (4 Replies)
In the portion of bash below I am using rename to match the $id variable to $file and when a match (there will alwsys be one) is found then the $id is removed from each bam and bam.bai in $file and _test is added to thee file name before the extension. Each of the variables is set correctly but... (3 Replies)
Discussion started by: cmccabe
3 Replies
LEARN ABOUT DEBIAN
dbs-edit-patch
DBS-EDIT-PATCH(1) Debian Build System DBS-EDIT-PATCH(1)NAME
dbs-edit-patch - Edit a DBS patch
SYNOPSIS
dbs-edit-patch [options] patch
dbs-edit-patch -h|--help
DESCRIPTION
dbs-edit-patch is script to generate or modify patches for Debian source-packages in DBS format.
WARNING
dbs is deprecated, please switch to the `3.0 (quilt)' Debian source package format instead. See http://wiki.debian.org/Projects/Deb-
Src3.0#FAQ for a short guide how to do it.
OPTIONS -h, --help
Show summary of options.
-t dir, --tmpdir=dir
Directory for the temporary files, default is /tmp or if set $TMP.
-s dir, --sourcedir=dir
Top level directory of the debian-package source-tree, default is the present working directory.
-P dir, --sourcepatchdir=dir
Directory containing upstream patches.
-T dir, --sourcetardir=dir
Directory containing the upstream tarball.
-p level, --strip=level
Striplevel -p of patch (Option -p of diff(1)), accepted values are 0 and 1, default is 0.
ENVIRONMENT VARIABLES
TMP Sets the directory for the temporary files, can be overridden with -t dir.
debian/vars
dbs-edit-patch will automatically use variables defined in the optional debian/vars file.
When a file debian/vars.in exists and debian/vars either does not exist or is older than any of the following files: debian/vars.in,
debian/changelog, debian/rules or debian/control, then dbs-edit-patch will try updating the vars file by running the following command
make -f debian/rules -W debian/vars.in debian/vars
EXAMPLES
Edit the 021_debian patch of Heimdal:
~/heimdal-0.3d> dbs-edit-patch -t/tmp 021_debian
Extracting source heimdal-0.3d.tar.gz ... successful.
Applying patch 001_replay ... successful.
etc.
Copying heimdal-0.3d to heimdal-0.3d-old ... successful.
Applying patch 021_debian ... successful.
Edit files under /tmp/021_debian/heimdal-0.3d as required, then put a short description into /tmp/021_debian/patch-description if desired,
and finally execute /tmp/021_debian/dbs-update-patch to save the results.
Technical note: dbs-edit-patch extracts all patches before 021_debian into /tmp/021_debian/heimdal-0.3d, copies the result to
/tmp/021_debian/heimdal-0.3d-old, and applies the last patch 021_debian (if it exists). Also, it creates a shell script which will create
the diff between the old and new directories:
~/heimdal-0.3d> ls -la /tmp/021_debian
total 12
-rwxr-xr-x 1 bam users 112 Jan 31 13:31 dbs-update-patch*
-rw-r--r-- 1 bam users 0 Jan 31 13:31 patch-description
drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d/
drwxr-xr-x 14 bam users 4096 Jan 31 13:31 heimdal-0.3d-old/
drwxr-xr-x 5 bam users 4096 Jan 31 13:31 .stampdir/
~/heimdal-0.3d> cat /tmp/021_debian/dbs-update-patch
#!/bin/sh -e
cd "/tmp/021_debian"
HOOK_DIR="/usr/src/heimdal/debian/dbs-hooks"
test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-prediff
find -name "*.bak" -print0 | xargs -0 --no-run-if-empty rm
find -name "*~" -print0 | xargs -0 --no-run-if-empty rm
: > new_patch
test ! -e patch-description || cp patch-description new_patch
diff -ruN heimdal-0.3d-old heimdal-0.3d >> new_patch || test $? -eq 1
mv new_patch /usr/src/heimdal/debian/patches/021_debian
test -d "$HOOK_DIR" && run-parts "$HOOK_DIR" --arg update-patch-postdiff
SEE ALSO diff(1), dbs(7), /usr/share/doc/dbs/
AUTHOR
DBS was written by Adam Heath, modified by Ben Collins, modified and packaged for Debian by Brian May. This manpage was generated by
Andreas Metzler and modified by Robert Luberda.
Debian February 15th, 2011 DBS-EDIT-PATCH(1)
03-04-2016
.