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..
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Each day the file is written to a directory named .../blah_blah/Y07/MM-DD-YY/reportmmddyy.tab
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However, if I try
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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.
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something like
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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"
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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_mask_by_search
BP_MASK_BY_SEARCH(1p) User Contributed Perl Documentation BP_MASK_BY_SEARCH(1p)NAME
mask_by_search - mask sequence(s) based on its alignment results
SYNOPSIS
mask_by_search.pl -f blast genomefile blastfile.bls > maskedgenome.fa
DESCRIPTION
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which
you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit sequence assuming you've
provided the sequence file for the hit database. If you would like to do the reverse and mask the query sequence specify the -t/--type
query flag.
This is going to read in the whole sequence file into memory so for large genomes this may fall over. I'm using DB_File to prevent keeping
everything in memory, one solution is to split the genome into pieces (BEFORE you run the DB search though, you want to use the exact file
you BLASTed with as input to this program).
Below the double dash (--) options are of the form --format=fasta or --format fasta or you can just say -f fasta
By -f/--format I mean either are acceptable options. The =s or =n or =c specify these arguments expect a 'string'
Options:
-f/--format=s Search report format (fasta,blast,axt,hmmer,etc)
-sf/--sformat=s Sequence format (fasta,genbank,embl,swissprot)
--hardmask (booelean) Hard mask the sequence
with the maskchar [default is lowercase mask]
--maskchar=c Character to mask with [default is N], change
to 'X' for protein sequences
-e/--evalue=n Evalue cutoff for HSPs and Hits, only
mask sequence if alignment has specified evalue
or better
-o/--out/
--outfile=file Output file to save the masked sequence to.
-t/--type=s Alignment seq type you want to mask, the
'hit' or the 'query' sequence. [default is 'hit']
--minlen=n Minimum length of an HSP for it to be used
in masking [default 0]
-h/--help See this help information
AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
perl v5.14.2 2012-03-02 BP_MASK_BY_SEARCH(1p)