Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Bash to create new directory by date followed by identifier and additional subdirectories

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Bash to create new directory by date followed by identifier and additional subdirectories
# 1  
Old 02-15-2016
Bash to create new directory by date followed by identifier and additional subdirectories
I have a bash that downloads a list and if that list has data in it then a new main directory is created (with the date) with several subdirectories (example1, example2, example3). My question is in that list there are portion of specific file types (.vcf.gz) - identifier towards the end that have an identifier in it that I would like to use a subdirectory. The identifier is also at the beginning of the .bam. The identifiers in this case are IonXpress_001, IonXpress_002, and IonXpress_003). The data in the list (identifiers) will be different each time and the order may also be different but the naming structure within the list file will always be consistent. Is this possible, I am not able to figure it out. That naming structure will always be the same (IonXpress_001 or IonXpress_010)... what will change is the text after the (3digits)_ for the .bam files. In the .vcf.gz files the only thing that will change are the (3digits) so that type may be easiest to use. For example, in the case of TSVC_variants_IonXpress_001.vcf.gz compared to TSVC_variants_IonXpress_002.vcf.gz, only the digits changed while the text remains the same. Thank you Smilie

bash that produces current structure
Code:
    wget -q --user=xxx --password=xxx --xxxx \
    xxxx://www.xxx.com/xxx/xxxxx/xxxx/list
    line_no=$(awk '{x++} END {print x}' /home/cmccabe/list) # count new files and store as variable
    if [[ -s /home/user/list ]]; then
    DATE=`date +%-m-%-d-%Y` 
    mkdir -p /home/user/Desktop/xxx/xxx/$DATE/{example1,example2,example3} # make new directory and subfolders

current structure
Code:
Date is the main directory with each of the examples being a sub-directory within Date. 
Date - example1, example2, example3

list
Code:
IonXpress_001_R_2016_02_11_11_51_07_user_Proton-34-160210_Lurie_MedExome_Hi-Q_Auto_user_Proton-34-160210_Lurie_MedExome_Hi-Q_84.bam
IonXpress_002_R_2016_02_11_11_51_07_user_Proton-34-160210_Lurie_MedExome_Hi-Q_Auto_user_Proton-34-160210_Lurie_MedExome_Hi-Q_84.bam
IonXpress_003_R_2016_02_11_11_51_07_user_Proton-34-160210_Lurie_MedExome_Hi-Q_Auto_user_Proton-34-160210_Lurie_MedExome_Hi-Q_84.bam
TSVC_variants_IonXpress_001.vcf.gz
TSVC_variants_IonXpress_002.vcf.gz
TSVC_variants_IonXpress_003.vcf.gz

desired output
Code:
Date is the main directory with the identifier as a subdirectory within Date and each of the example are subdirectories within the identifier.

`Date - Identifier - example1, example2, example3
 2-13-2015 (main directory) - IonXpress_001 (identifier as a sub-directory within 2-13-2015) - example1, example2, example3 (all sub-directories within the identifier).

Last edited by cmccabe; 02-15-2016 at 12:34 PM.. Reason: fixed format
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Create directory and sub-directory with awk and bash

In the below I am trying to create a parent directory using the R_2019 line from f1 if what above it is not empty. I then create sub-directories under each parent if there is a match between $2 of f1 and $2. Inside each sub-folder the matching paths in $3 and $4 in f2are printed. If there is no... (2 Replies)
Discussion started by: cmccabe
2 Replies

2. Shell Programming and Scripting

List files with date, create directory, move to the created directory

Hi all, i have a folder, with tons of files containing as following, on /my/folder/jobs/ some_name_2016-01-17-22-38-58_some name_0_0.zip.done some_name_2016-01-17-22-40-30_some name_0_0.zip.done some_name_2016-01-17-22-48-50_some name_0_0.zip.done and these can be lots of similar files,... (6 Replies)
Discussion started by: charli1
6 Replies

3. Shell Programming and Scripting

Bash script monitor directory and subdirectories for new pdfs

I need bash script that monitor folders for new pdf files and create xml file for rss feed with newest files on the list. I have some script, but it reports errors. #!/bin/bash SYSDIR="/var/www/html/Intranet" HTTPLINK="http://TYPE.IP.ADDRESS.HERE/pdfs" FEEDTITLE="Najnoviji dokumenti na... (20 Replies)
Discussion started by: markus1981
20 Replies

4. Shell Programming and Scripting

Create a directory with previous date

Hi All, can any body tell me how to create a new directory with previous time stamp in HP-UX?. e.g i am creating a file liketouch -t 07022013 kkk -rw-r----- 1 feeds sys 0 Jul 2 20:13 kkksame how can i create a directory? please help me. Thanks & Regards, Krupa (4 Replies)
Discussion started by: krupasindhu18
4 Replies

5. Shell Programming and Scripting

Create a directory named as the current date

I am preparing a shell script to backup a few config files on a daily basis, with a retention of 30 days. Need some help with syntax/examples: The shell script (running as cron) would require the following: 1. create a sub-directory within a specified (backup) directory, in the format... (3 Replies)
Discussion started by: FeNiCrC_Neil
3 Replies

6. UNIX for Dummies Questions & Answers

Create a directory using current date

Hi, I have a question, is there any way I can, when i create a directory, put the current date on it so that the directory name will be "name-current date"? just curious (3 Replies)
Discussion started by: aric87
3 Replies

7. Shell Programming and Scripting

Bash: Gzip files in Directory and itīs Subdirectories

Hello dear Community, I have a task to wrtie a script which will gzip not zipped files in a directory and itīs subdirectories. I succeeded in gzippung the directory but not the subdirectories: #/bin/bash #go to the directory where to zip cd $1 #Zip unzipped files for i in `ls | xargs... (2 Replies)
Discussion started by: JamesCarter
2 Replies

8. Shell Programming and Scripting

want to create directory with the previous date

I need some help to complet the below script: DATE1=`date "+%d"` #DATE2=`expr $DATE1 - 1` #DATE3=$DATE2`date "+%m%y"` DATE4=`date "+%a"` if ; then DATE2=`expr $DATE1 - 3` else DATE2=`expr $DATE1 - 1` fi (7 Replies)
Discussion started by: sridhusha
7 Replies

9. UNIX for Dummies Questions & Answers

Directory create date

Hi, How do you find the create date of a directory? I can see the modification date using ls -l but I'm looking for the create date. Many thanks Helen (2 Replies)
Discussion started by: Bab00shka
2 Replies

10. UNIX for Dummies Questions & Answers

create directory named current date

Since this site solved my problems before, I am back for more (solutions) I down load via a script every day a file that has the same name as the file of the day before. I want to move that file to its own directory like: /archive/jul30 How do I capture the systems date in a script an... (2 Replies)
Discussion started by: flowrats
2 Replies
Login or Register to Ask a Question