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 PHP
rename
RENAME(3) 1 RENAME(3)rename - Renames a file or directorySYNOPSIS
bool rename (string $oldname, string $newname, [resource $context])
DESCRIPTION
Attempts to rename $oldname to $newname, moving it between directories if necessary. If $newname exists, it will be overwritten.
PARAMETERS
o $oldname
-
Note
The old name. The wrapper used in $oldname must match the wrapper used in $newname.
o $newname
- The new name.
o $context
-
Note
Context support was added with PHP 5.0.0. For a description of contexts, refer to "Streams".
RETURN VALUES
Returns TRUE on success or FALSE on failure.
CHANGELOG
+--------+---------------------------------------------------+
|Version | |
| | |
| | Description |
| | |
+--------+---------------------------------------------------+
| 5.3.1 | |
| | |
| | rename(3) can now rename files across drives in |
| | Windows. |
| | |
| 5.0.0 | |
| | |
| | rename(3) can now also be used with some URL |
| | wrappers. Refer to "Supported Protocols and Wrap- |
| | pers" for a listing of which wrappers support |
| | rename(3). |
| | |
| 4.3.3 | |
| | |
| | rename(3) may now be able to rename files across |
| | partitions on *nix based systems, provided the |
| | appropriate permissions are held. Warnings may be |
| | generated if the destination filesystem doesn't |
| | permit chown() or chmod() system calls to be made |
| | on files -- for example, if the destination |
| | filesystem is a FAT filesystem. |
| | |
+--------+---------------------------------------------------+
EXAMPLES
Example #1
Example with rename(3)
<?php
rename("/tmp/tmp_file.txt", "/home/user/login/docs/my_file.txt");
?>
SEE ALSO copy(3), unlink(3), move_uploaded_file(3).
PHP Documentation Group RENAME(3)