Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: SBATCH trinity for multiple files and rename/move the output files
Top Forums Shell Programming and Scripting SBATCH trinity for multiple files and rename/move the output files Post 302980058 by @man on Tuesday 23rd of August 2016 10:39:10 AM
Old 08-23-2016
Code SBATCH trinity for multiple files and rename/move the output files
Hey guys,
I have wrote the following script to apply a module named "trinity" on my files. (it takes two input files and spit a trinity.fasta as output)
Code:
#!/bin/bash -l
#SBATCH -p node
#SBATCH -A <projectID>
#SBATCH -n 16
#SBATCH -t 7-00:00:00
#SBATCH --mem=128GB 
#SBATCH --mail-type=ALL
#SBATCH --mail-user=<email address>
#SBATCH -o /path/to/log/file
#SBATCH -e /path/to/error/file
#SBATCH -J trinity

module load bioinfo-tools trinity

Trinity --seqType fq --max_memory 120G --CPU 16 \
--left /path/to/first/input/input1.fq \
--right /path/to/second/input/input2.fq \
--normalize_reads --SS_lib_type RF --no_bowtie --output /path/to/output/directory/trinity_out_dir

Now I cannot figure out how to modify this to take multiple files (2 inputs in each iteration) and then rename the output file (which is "trinity.fasta") and move it to another folder so it won't be overwritten every time.
all my files are like this:
Code:
Sample1_1.fq
Sample1_2.fq

sample2_1.fq
Sample2_2.fq
...

and obviously the desired outputs:
Code:
Sample1.fasta, Sample2.fasta, ...

Thanks in advance!
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Move files and rename ??

1. If I have a file-yyyymmdd.dat in a directory DATA1, then how do I move this file to directory DATA2 and the file name change to file-yyyymmdd.dat.currenttime I can manual do this $mv fileA-yyyymmdd.dat ./DATA2/fileA-yyyymmdd.dat.`date +%Y%m%d%H%M%S` but how do I move all of the files in... (1 Reply)
Discussion started by: sabercats
1 Replies

2. Shell Programming and Scripting

Find, Append, Move & Rename Multiple Files

Using a bash script, I need to find all files in a folder "except" the newest file. Then I need to insert the contents of one text file into all the files found. This text needs to be placed at the beginning of each file and needs a blank line between it and the current contents of the file. Then I... (5 Replies)
Discussion started by: Trapper
5 Replies

3. UNIX for Dummies Questions & Answers

Using Rename to move files

I am connecting to a remote server (Unix) and doing a ftp dowmload of files. The script (VB script) works fine except for not being able to move the downloaded files on the remote server to another folder. I need to move all files with an .asc extesnion from folder "tovecellio_edi" to folder... (1 Reply)
Discussion started by: snufse
1 Replies

4. UNIX for Dummies Questions & Answers

rename multiple files from search output

Variations of multiple renames seems to come up a lot but i can't find the answer to this situation. Tidying up a directory where people rename files to .working, .bob, .attempt1 & so on. what i am trying to do is: list the file type, & rename from ".whatever" to .fixed. As the ".whatever" is... (5 Replies)
Discussion started by: woodstock
5 Replies

5. Shell Programming and Scripting

Rename/Move files and schedule the script

Hello, I'm new in the forum and in UNIX scripting, what I need is to write a simple batch script that renames or move the files back & forth from one directory to another, and then schedule the script to run on the server when the scheduled down time is, which is on Thursdays at 8pm and during... (5 Replies)
Discussion started by: dannyghost
5 Replies

6. Shell Programming and Scripting

Need to move and rename a list of files

Hi, I need to do something easy but I can't seem to figure out how to do this. Let's say I have 6 files in the directory below: /ebsbeta_f/flash/EBSUATQB/onlinelog o1_mf_6_55klt7nr_.log o1_mf_3_55klskj4_.log o1_mf_4_55klsrl1_.log o1_mf_5_55klt09p_.log o1_mf_2_55klv1ts_.log... (10 Replies)
Discussion started by: exm
10 Replies

7. UNIX for Dummies Questions & Answers

Rename files in a directory and move them

I have a directory e2e_ms_xfer/cent01 this contains the multiple files some of which will be named below with unique date time stamps e2e_ms_edd_nom_CCYYMMDD_HHMM.csv What I want to do is in a loop 1) Get the oldest file 2) Rename 3) Move it up one level from e2e_ms_xfer/cent01 to... (1 Reply)
Discussion started by: andymay
1 Replies

8. Shell Programming and Scripting

Script to unzip files and Rename the Output-files

Hi all, I have a many folders with zipped files in them. The zipped files are txt files from different folders. The txt files have the same names. If i try to find . -type f -name "*.zip" -exec cp -R {} /myhome/ZIP \; it fails since the ZIP files from different folders have the same names and... (2 Replies)
Discussion started by: pmkenya
2 Replies

9. Shell Programming and Scripting

How to rename (move) most recent files in directory?

I'm using cygwin32 on Windows. DN is an environment variable pointed at my download directory. This command works to move the single most recent file in my download directory to my current directory: mv "`perl -e '$p = $ARGV; opendir $h, $p or die "cannot opendir $p: $!"; @f = sort { -M $a... (2 Replies)
Discussion started by: siegfried
2 Replies

10. Shell Programming and Scripting

Rename (move) multiple files on remote server using sftp

I want to rename (move) multiple files on remote server. I tried the following command to move all TXT files from my_dir directory to /new_dir. But it does not work. Any help? #!/bin/ksh sftp -dev3 << ABC cd my_dir $(for i in TXT; do echo "ls *.$i" ; rename $x /new_dir/$x;... (1 Reply)
Discussion started by: Soham
1 Replies

LEARN ABOUT DEBIAN

prename

RENAME(1)						 Perl Programmers Reference Guide						 RENAME(1)

NAME

       rename - renames multiple files

SYNOPSIS

       rename [ -v ] [ -n ] [ -f ] perlexpr [ files ]

DESCRIPTION

       "rename" renames the filenames supplied according to the rule specified as the first argument.  The perlexpr argument is a Perl expression
       which is expected to modify the $_ string in Perl for at least some of the filenames specified.	If a given filename is not modified by the
       expression, it will not be renamed.  If no filenames are given on the command line, filenames will be read via standard input.

       For example, to rename all files matching "*.bak" to strip the extension, you might say

	       rename 's/.bak$//' *.bak

       To translate uppercase names to lower, you'd use

	       rename 'y/A-Z/a-z/' *

OPTIONS

       -v, --verbose
	       Verbose: print names of files successfully renamed.

       -n, --no-act
	       No Action: show what files would have been renamed.

       -f, --force
	       Force: overwrite existing files.

ENVIRONMENT

       No environment variables are used.

AUTHOR

       Larry Wall

SEE ALSO

       mv(1), perl(1)

DIAGNOSTICS

       If you give an invalid Perl expression you'll get a syntax error.

BUGS

       The original "rename" did not check for the existence of target filenames, so had to be used with care.	I hope I've fixed that (Robin
       Barker).

perl v5.14.2							    2014-09-26								 RENAME(1)
All times are GMT -4. The time now is 07:02 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy