Using variables to copy files with increasing numerical names.
Hello, I have been learning Linux shell commands for about 4 months now. I am trying to write a simple shell script, but I have encountered an issue I do not understand the cause of.
When I run my script I get an error.
[user@x dir]$ ./myscript.sh
cp: cannot stat `path/to/file/{1..2}.dat': No such file or directory
[user@x dir]$
However when I run it without variables.
Running script without variables.
[user@x dir]$ ./myscript.sh
It copies the ten *.dat files from the path/to/files to the directory of myscript.sh. How can I get the script working with variables? Thanks in advance for any help given.
Hi all,
I have to copy a directory to another location. While doing so with the cp command I got some errors due to invalid filenames of some files.
For example, some files have a colon in their names, which is throwing error. These files are not copied to the destination.
How to copy... (1 Reply)
Hi I was hoping that maybe someone could help me with a small piece of C code. I have a number of files, which are all of similar layout ie. three lines of text and 5-6 columns of numerical data. I need to add each of the elements of the second column in one file to their counterparts in the second... (17 Replies)
Hi everyone,
I would love to have a script that does the following:
I have one file that looks like that:
ATOM 1 BB SER 1 1 -31.958 -25.125 -11.061 1.00 0.00
ATOM 3 BB GLY 1 2 -32.079 -26.085 -14.466 1.00 0.00
ATOM 4 BB VAL 1 3 ... (1 Reply)
dear all.
how can i copy a list of files with different names into others directory have the same name
like i have 3 files
10_10
10_10_11
10_10_11_12
and i have 3 directories
10_10
10_10_11
10_10_11_12
how can i make a loop to cp this files into the directory have the same name like... (0 Replies)
dear all.
how can i copy a list of files with different names into others directory have the same name
like i have 3 files
10_10
10_10_11
10_10_11_12
and i have 3 directories
10_10
10_10_11
10_10_11_12
how can i make a loop to cp this files into the directory have the same name like... (31 Replies)
Hi, I have a series of files (upwards of 500) the filename format is as follows
CC10-1234P1999.WGS84.p190
each of this files is in a directory named for the file but excluding the extension.
Now the last three numeric characters, in this case 999, can be anything from 001 to 999, I need to... (3 Replies)
Hi,
I have a large number of files which are named as follows.
VF_50, VF_100, VF_150, VF_250, VF_300, VF_350, VF_400, VF_450, VF_500.
When I do an 'ls' it arranges the files in the following way
VF_100, VF_150, VF_250, VF_300, VF_350, VF_400, VF_450, VF_50, VF_500.
Is there a way to... (2 Replies)
Hello
I have a directory with a list of files which have a particular numerical suffix.
E.g
filename_0
filename_1
filename_18500
filename_10000
I want to delete all files from this directory which have a filename which have a numerical suffix greater than 10540.
So any files... (5 Replies)
Hi all,
Iam writing a perl script to create many files with variables in their name.
i am able to do it, if iam using only one variable. But with two variables the file
names are NOT getting generated in the way i want.
plz help me out.
1. open(SHW,">divw_unsigned_50_50_$k.reset") or die... (4 Replies)
Discussion started by: twistedpair
4 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)