How to copy particular files from a multiple directories and paste in a new directory?
Dear all
I have a multiple directories, say for example org1, org2, org3 ..... org100 and each directory having a file namely dnaG.fasta. I need to copy all the dnaG.fasta file from each directory and paste in another directory fastconcatg. Therefore, my script has to copy dnaG.fasta file from each directory, add prefix to the file name like 1_dnaG.fasta, 2_dnaG.fasta ..... 100_dnaG.fasta and paste into the fastconcatg.
I have tried the following script but the script is not serving my purpose, It copy and paste only one file and rest is not copied and renamed finally end up with error. Kindly help me to do the same.
Thank you in advance.
Last edited by dineshkumarsrk; 12-27-2019 at 09:23 AM..
I have a report file that is generated every day by a scheduled process.
Each day the file is written to a directory named .../blah_blah/Y07/MM-DD-YY/reportmmddyy.tab
I want to copy all of this reports to a separate directory without having to do it one by one.
However, if I try
cp... (3 Replies)
So I am not sure if this should go in the shell forum or in the beginners. It is my first time posting on these forums.
I have a directory, main_dir lets say, with multiple sub directories (one_dir through onehundred_dir for example) and in each sub directory there is a test.txt. How would one... (2 Replies)
Hi,
I want to put the following values into Variables R2=0.999863 , V2=118.870318 , D2=-178.887511 and so on. There are six values for each variable R2-R8, V2-V8 and D2-D8, total of 18 values for all the variables. Can any one help me to copy and paste all the values in their respective... (2 Replies)
Hello,
I have a small question and i hope someone can help me, if i have 200 domains directories in my server under this directory
something like
now how i can copy one folder i have to this directories?
Thank You (5 Replies)
I have several directories and all those directories have .dat files in them. I want to copy all those .dat files to one directory say "collected_directory"
The problem is I don't want to overwrite files. So, if two file names match, I don't want the old file to be overwritten with a new one.
... (1 Reply)
I am using below scripts to copy all the files from multiple folders. By executing individually command i am able to copy all the files but using scripts only getting first file. System is ignoring the second CD and mget command.
HOST=server.com
USER=loginid
PASSWD="abc"
echo "open $HOST... (6 Replies)
my directory structure is like below:
basedir\
p.txt
q.htm
r.java
b\
abc.htm
xyz.java
c\
p.htm
q.java
rst.txt
my requirement is i want to copy all the files and directories... (0 Replies)
Hi,
Friends, i have a requirement where i need to rename my files residing in multiple sub directories and move them to one different directory along with some kind of directory indicator.
For eg:
test--is my parent directory and it has many files such as
a1.txt
a2.txt
a3.txt
... (5 Replies)
I have data of an excel files as given below,
file1
org1_1 1 1 2.5 100
org1_2 1 2 5.5 98
org1_3 1 3 7.2 88
file2
org2_1 1 1 2.5 100
org2_2 1 2 5.5 56
org2_3 1 3 7.2 70
I have multiple excel files as above shown.
I have to copy column 1, column 4 and paste into a new excel file as... (26 Replies)
Hey
im working on script that can compare 2 directory and check difference, then copy difference files in third diretory.
here is the story:
in folder one we have 12 subfolder and in each of them near 500 images hosted.
01 02 03 04 05 06 07 08 09 10 11 12
in folder 2 we have same subfolder... (2 Replies)
Discussion started by: nimafire
2 Replies
LEARN ABOUT DEBIAN
bp_index
BP_INDEX(1p) User Contributed Perl Documentation BP_INDEX(1p)NAME
bp_index.pl - indexes files for use by bp_fetch.pl
SYNOPSIS
bp_index.pl index_name file1 file2 etc.
DESCRIPTION
bp_index.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example
bp_index.pl nrdb /data/nrdb/nrdb.fasta
would build an index called 'nrdb' as the index name for the file nrdb.fasta, and
bp_index.pl -fmt EMBL swiss /data/swiss/*.dat
would build an index called swiss for all the files in /data/swiss which end in .dat which are in EMBL format.
The indexes are built using the Bio/Index/* modules, in particular, Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which
uses these modules can use the index. A good example script is bp_fetch which fetches sequences and pipes them to STDOUT, for example
bp_fetch swiss:ROA1_HUMAN
gets the ROA1_HUMAN sequence from the swiss index and writes it as fasta format on STDOUT.
OPTIONS -fmt <format> - Fasta (default), swiss or EMBL
-dir <dir> - directory where the index files are found
(overrides BIOPERL_INDEX environment variable)
Options for expert use
-type <db_type> - DBM_file type.
(overrides BIOPERL_INDEX_TYPE environment variable)
-v - report every index addition (debugging)
ENVIRONMENT
bp_index and bp_fetch coordinate where the databases lie using the enviroment variable BIOPERL_INDEX. This can be overridden using the -dir
option. There is no default value, so you must use the -dir option or set BIOPERL_INDEX.
The DB type is coordinated with BIOPERL_INDEX_TYPE which if it is not there, defaults to whatever the bioperl modules have installed, which
itself defaults to SDBM_File.
USING IT YOURSELF
bp_index.pl is a script that drives the Index modules. If you want to use this script heavily in your work, if it is Perl based, it is
almost certainly better to look at the code in this script and copy it across (probably you will be more likely to want to use the bp_fetch
code).
EXTENDING IT
bp_index is just a wrapper around James Gilbert's excellent Index modules found in bioperl
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney
Ewan Birney <birney@ebi.ac.uk>
perl v5.14.2 2012-03-02 BP_INDEX(1p)