Looks like the last file in the directory is getting renamed with both matching not the unique. Is another loop needed or all the values on one line instead of separate? Thank you .
11-1111-yy-yy-yyy_test.bam ---- this is IonCode_0402_xxx.xxx_xxx ---
11-1111-yy-yy-yyy_test.bam.bai ---- this is IonCode_0402_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam ---- this is IonCode_0404_xxx.xxx_xxx ---
00-0000-xxx-xxx-xxx_test.bam.bai ---- this is IonCode_0404_xxx.xxx_xxx ---
Last edited by cmccabe; 10-24-2019 at 01:52 PM..
Reason: fixed format
Hi,
I am having file which contains around 15 columns, i need to fetch column 3,12,14 based on the condition that column 3 starts with 40464
this is the sample data
how to achieve that (3 Replies)
I’m trying to modify someone perl script to fix a bug. The piece of code checks that the zone name you want to add is unique. However, when the code runs, it finds a partial match using grep, and decides it already exists, so the “create” command exits.
$cstatus = `${ZADM} list -vic | grep... (3 Replies)
Hi, I was trying to figure this out but failed so I hope someone here can help me, thank you in advance.
I have two files.
file1: aa M
bb N
cc O
dd P
ee Q file2: aa A_87_P254063
cc A_87_P016532
bb A_87_P104793
dd A_87_P055331
ee A_87_P059706
aa A_87_P071636
ee A_87_P028302... (2 Replies)
Hi I have a question and hope I can get answer here. Thank you in advance.
I have two files:
file1:
aa X
bb Y
cc Z
file2:
cc A
bb B
dd C
aa D
bb E
If the 1st column match in both file1 and file2, the 2nd column in file2 will be replaced by the 2nd column in file1. If there is no... (2 Replies)
I posted the incorrect files yesterday and apologize. I also modified the awk script but with no luck. There are two text files in the zip (name.txt and output.txt). I am trying to match $2 in name.txt with $1 in output.txt and if they match then $1 of name.txt is copied to $7 of output.txt. ... (7 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)
Hi All,
I have 100 folders with the first delimiter has a unique name i.e (123_hello and 575_hello) and each folder have atlist 1000 plus files with naming convention i.e (575_hello_1.iso ... 575_hello_1000.iso).
575_hello/575_hello_1.iso
575_hello/575_hello_2.iso
575_hello/575_hello_3.iso... (8 Replies)
Hi, I have a tab delimited text file like this one. I need to do a partial match of a particular cell and then replace matches with an empty cell. So here is a sample:
Smith FordMustang ChevroletCamaro
Miller FordFiesta
Jones KiaSorrento
Davis ChevroletCamaro
Johnson ToyotaHighlander
I... (4 Replies)
I am trying to create a cronjob that will run on startup that will look at a list.txt file to see if there is a later version of a database using database.txt as the source. The matching lines are written to output.
$1 in database.txt will be in list.txt as a partial match. $2 of database.txt... (2 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 SUSE
guards
GUARDS(1) User Contributed Perl Documentation GUARDS(1)NAME
guards - select from a list of files guarded by conditions
SYNOPSIS
guards [--prefix=dir] [--path=dir2:dir2:...] [--default=0|1] [-v|--invert-match] [--list|--check] [--config=file] symbol ...
DESCRIPTION
The script reads a configuration file that may contain so-called guards, file names, and comments, and writes those file names that satisfy
all guards to standard output. The script takes a list of symbols as its arguments. Each line in the configuration file is processed
separately. Lines may start with a number of guards. The following guards are defined:
+xxx Include the file(s) on this line if the symbol xxx is defined.
-xxx Exclude the file(s) on this line if the symbol xxx is defined.
+!xxx Include the file(s) on this line if the symbol xxx is not defined.
-!xxx Exclude the file(s) on this line if the symbol xxx is not defined.
- Exclude this file. Used to avoid spurious --check messages.
The guards are processed left to right. The last guard that matches determines if the file is included. If no guard is specified, the
--default setting determines if the file is included.
If no configuration file is specified, the script reads from standard input.
The --check option is used to compare the specification file against the file system. If files are referenced in the specification that do
not exist, or if files are not enlisted in the specification file warnings are printed. The --path option can be used to specify which
directory or directories to scan. Multiple directories are eparated by a colon (":") character. The --prefix option specifies the location
of the files.
AUTHOR
Andreas Gruenbacher <agruen@suse.de> (SuSE Linux AG)
perl v5.12.1 2010-07-05 GUARDS(1)
10-24-2019
.