Hi
I am looping through the contents of a file as follows
cat file |while read inrec
do
echo $inrec >> $TMP
done
(obviously this isn't all i am doing as it would be pointless but for the sake of the problem this is the important bit)
The file has fields which are separated by... (1 Reply)
HI,
Supose I have the folowing strings: "unix" and "linux". I want to concatenate the two strings, inserting between them a variable number of spaces.
ex1: unix linux
ex2: unix linux
Can you help me in this simple problem?
Regards,
Elio (2 Replies)
Greetings all,
I'm in need of some help in coming up with this command which requires me to append 5 strings together:
1. echo "Status from system:"
2. `cat logs.txt` (i need the output of this command)
3. echo "Error output: "
4. `cat errors.txt`(i need the output of this command)
5.... (3 Replies)
I would like to append the numbers 1, 2, 3, 4 and so on to the lines of the file:
Adam Wilkins | Colorado | 36
John Butler | Los Angeles | 47
Cassey Johnson | Minneapolis | 25
Albert Aniston | Miami | 19
....
Tony Legler | Sacramento | 55
Matt Simmons | New York | 38
Output would look... (4 Replies)
Hi
Following is an example line.
echo "192.22.22.22 \"33dffwef\" 200 300 dsdsd" | sed "s:\(\ *\ \):\1:"
I want it's output to be
200
However this is not the case. Can you tell me how to do it? I don't want to use AWK for this. Secondly, how can i fetch just 300? Should I use "\2"... (3 Replies)
I have a 13 number string, some whitespace, and then /mp3.
I need to join them. Everyline that I need this for begins with "cd" (without the quotes).
What it looks like now:
cd media/Audio/WAVE/9781933976334 /mp3 What I want my output to be:
cd media/Audio/WAVE/9781933976334/mp3 The 13... (7 Replies)
The question is not as simple as the title... I have a file, it looks like this
<string name="string1">RZ-LED</string>
<string name="string2">2.0</string>
<string name="string2">Version 2.0</string>
<string name="string3">BP</string>
I would like to check for duplicate entries of... (11 Replies)
hi gurus,
I'm executing some commands and I want to append both the command and output to a text file. Example:
echo "strings -a wicmex.o|grep '$Header'" >> tmp.txt
strings -a wicmex.o|grep '$Header' >> tmp.txt
echo "strings -a libwip.a|grep '$Header'" >> tmp.txt
strings -a libwip.a|grep... (1 Reply)
Hi ,
I am writing a shell script to check pvsizes in linux box.
# for i in `cat vgs1`
> do
> echo "########### $i ###########"
> pvs|grep -i $i|awk '{print $2,$1,$5}'>pvs_$i
> pvs|grep -i $i|awk '{print $1}'|while read a
> do
> fdisk -l $a|head -2|tail -1|awk '{print $2,$3}'>pvs_$i1
>... (3 Replies)
Hello Everyone ,
Iam a newbie to shell programming and iam reaching out if anyone can help in this :-
I have two files
1) Insert.txt
2) partition_list.txt
insert.txt looks like this :-
insert into emp1 partition (partition_name)
(a1,
b2,
c4,
s6,
d8)
select
a1,
b2,
c4, (2 Replies)
Discussion started by: nubie2linux
2 Replies
LEARN ABOUT DEBIAN
bio::tools::run::alignment::sim4
Bio::Tools::Run::Alignment::Sim4(3pm) User Contributed Perl Documentation Bio::Tools::Run::Alignment::Sim4(3pm)NAME
Bio::Tools::Run::Alignment::Sim4 - Wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
SYNOPSIS
use Bio::Tools::Run::Alignment::Sim4;
my @params = (W=>15,K=>17,D=>10,N=>10,cdna_seq=>"mouse_cdna.fa",genomic_seq=>"mouse_genomic.fa");
my $sim4 = Bio::Tools::Run::Alignment::Sim4->new(@params);
my @exon_sets = $sim4->align;
foreach my $set(@exon_sets){
foreach my $exon($set->sub_SeqFeature){
print $exon->start." ".$exon->end." ".$exon->strand."
";
print " Matched ".$exon->est_hit->seq_id." ".$exon->est_hit->start." ".$exon->est_hit->end."
";
}
}
One can also provide a est database
$sio = Bio::SeqIO->new(-file=>"est.fa",-format=>"fasta");
@est_seq=();
while(my $seq = $sio->next_seq){
push @est_seq,$seq;
}
my @exon_sets = $factory->align(@est_seq,$genomic);
DESCRIPTION
Sim4 program is developed by Florea et al. for aligning cdna/est sequence to genomic sequences
Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome
Res 1998 Sep;8(9):967-74
The program is available for download here: http://globin.cse.psu.edu/
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 - Shawn Hoon
Email shawnh@fugu-sg.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 : not supported
Function: Cannot determine from program
Example :
Returns : float or undef
Args : none
align
Title : align
Usage :
$cdna = 't/data/cdna.fa';
$genomic = 't/data/cdna.fa';
@exon_set = $factory->align($cdna,$genomic);
or
#@seq_array is array of Seq objs
$cdna = @seq_array;
@exon_set = $factory->align($cdna,$genomic);
of
@exon_set = $factory->align($cdna->[0],$genomic)
Function: Perform a Sim4 alignment
Returns : An array of Bio::SeqFeature::Generic objects which has
exons as sub seqfeatures.
Args : Name of two files containing fasta sequences,
or 2 Bio::SeqI objects
or a combination of both
first is assumed to be cdna
second is assumed to be genomic
More than one cdna may be provided. If an object,
assume that its an array ref.
_run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to Sim4 program
Example :
Returns : nothing; Sim4 output is written to a temp file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to Sim4
_setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for Sim4 program
Example :
Returns : name of file containing Sim4 data input
Args : Seq or Align object reference or input file name
_setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for Sim4 program
Example :
Returns : parameter string to be passed to Sim4
during align or profile_align
Args : name of calling object
perl v5.12.3 2011-06-18 Bio::Tools::Run::Alignment::Sim4(3pm)