Probably your sed version doesn't support the -i option. Use a temporary file, and if you don't have to search in underlying directories you can avoid the use if find:
hi,
i have a file having datas like that
./a.txt
12344
12345
12346
12347
.....
.....
...
i want to save this datas to another file like that
./b.txt
12344 12345 12346 12347 ... ... ...
i think awk can make this but how? :) waiting for ur help. (3 Replies)
im a new student in programming and im stuck on this question so please please HELP ME. thanks.
the question is this:
enter a command to delete all files that have filenames starting with labtest, except labtest itself (delete all files startign with 'labtest' followed by one or more... (2 Replies)
I wrote a script to delete files which are older than "x" days, if the size of the directory is greater than "y"
#!/bin/bash
du -hs $1
while read SIZE ENTRY
do
if ;
then
find $1 -mtime +$2 -exec rm -f {} \;
echo "Files older than $2 days deleted"
else
echo "free Space available"... (4 Replies)
Hi All,
I have working (Perl) code to combine 2 input files into a single output file using the join function that works to a point, but has the following limitations:
1. I am restrained to 2 input files only.
2. Only the "matched" fields are written out to the "matched" output file and... (1 Reply)
logs:
"/home/abc/public_html/index.php"
"/home/abc/public_html/index.php"
"/home/xyz/public_html/index.php"
"/home/xyz/public_html/index.php"
"/home/xyz/public_html/index.php"
how to use "cut" or "awk" or "sed" to get the following result:
abc
abc
xyz
xyz
xyz (8 Replies)
I have a bunch of random character lines like ABCEDFG. I want to find all lines with "A" and then change any "E" to "X" in the same line. ALL lines with "A" will have an "X" somewhere in it. I have tried sed awk and vi editor. I get close, not quite there. I know someone has already solved this... (10 Replies)
Dear Ladies & Gents,
I have a requirement to delete all the log files in /var/log/test directory that are older than 10 days and their first line begin with "MSH" or "<?xml" or "FHS". I've put together the following BASH script, but it's erroring out:
for filename in $(find /var/log/test... (2 Replies)
Hello.
System : opensuse leap 42.3
I have a bash script that build a text file.
I would like the last command doing :
print_cmd -o page-left=43 -o page-right=22 -o page-top=28 -o page-bottom=43 -o font=LatinModernMono12:regular:9 some_file.txt
where :
print_cmd ::= some printing... (1 Reply)
Hi 2 all,
i have had AIX 7.2
:/# /usr/IBMAHS/bin/apachectl -v
Server version: Apache/2.4.12 (Unix)
Server built: May 25 2015 04:58:27
:/#:/# /usr/IBMAHS/bin/apachectl -M
Loaded Modules:
core_module (static)
so_module (static)
http_module (static)
mpm_worker_module (static)
... (3 Replies)
Discussion started by: penchev
3 Replies
LEARN ABOUT DEBIAN
bio::tools::run::erpin
Bio::Tools::Run::ERPIN(3pm) User Contributed Perl Documentation Bio::Tools::Run::ERPIN(3pm)NAME
Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of programs.
SYNOPSIS
#run
my @params = (
trset => 'BL.erpin',
region => [1, 10],
# Set up search strategy this way...
strategy => [ 'umask' => [1, 2],
'umask' => [1, 2, 3, 4],
'umask' => [1, 2, 3, 4, 5, 6],
'nomask',
'cutoff' => [0, 10, 15, 20]
]
# or use a simple string...
#strategy => '-umask 4 -add 5 -nomask -cutoff 0 10 15',
pcw => 100
);
my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',
@params);
# Pass the factory a Bio::Seq object or a file name
# Returns a Bio::SearchIO object
#my $search = $factory->run("B_sub.fas");
my $search = $factory->run($seq);
my @feat;
while (my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while (my $hsp = $hit->next_hsp){
print join(" ", ( $r->query_name,
$hit->name,
$hsp->hit->start,
$hsp->hit->end,
$hsp->meta,
$hsp->score,
)), "
";
}
}
}
DESCRIPTION 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 one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris Fields
Email: cjfields-at-uiuc-dot-edu
CONTRIBUTORS
cjfields-at-uiuc-dot-edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
Function: creates a new RNAMotif factory
Returns: Bio::Tools::Run::RNAMotif
Args : list of parameters
-tempfile => set tempfile flag (default 0)
-outfile_name => set file to send output to (default none)
program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
version
Title : version
Usage : $v = $prog->version();
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
run
Title : run
Usage : $obj->run($seqFile)
Function: Runs ERPIN programs and returns Bio::SearchIO
Returns :
Args : Must pass Bio::PrimarySeqI's or file names
tempfile
Title : tempfile
Usage : $obj->tempfile(1)
Function: Set tempfile flag. When set, writes output to a tempfile; this
is overridden by outfile_name() if set
Returns : Boolean setting (or undef if not set)
Args : [OPTIONAL] Boolean
_run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns :
Args :
_setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
_writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : writes passed Seq objects to tempfile, to be used as input
for program
Args :
perl v5.12.3 2011-06-18 Bio::Tools::Run::ERPIN(3pm)