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::sim4::exon
Bio::Tools::Sim4::Exon(3pm) User Contributed Perl Documentation Bio::Tools::Sim4::Exon(3pm)NAME
Bio::Tools::Sim4::Exon - A single exon determined by an alignment
SYNOPSIS
# See Bio::Tools::Sim4::Results for a description of the context.
# an instance of this class is-a Bio::SeqFeature::SimilarityPair
# coordinates of the exon (recommended way):
print "exon from ", $exon->start(),
" to ", $exon->end(), "
";
# the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
print "exon from ", $exon->feature1()->start(),
" to ", $exon->feature1()->end(), "
";
# also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->query()->start(),
" to ", $exon->query()->end(), "
";
# coordinates on the matching EST (recommended way):
print "matches on EST from ", $exon->est_hit()->start(),
" to ", $exon->est_hit()->end(), "
";
# the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
print "matches on EST from ", $exon->feature2()->start(),
" to ", $exon->feature2()->end(), "
";
# also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->subject()->start(),
" to ", $exon->subject()->end(), "
";
DESCRIPTION
This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity, that is, by
aligning an EST sequence (using Sim4 in this case). Consequently, the notion of query and subject is always from the perspective of the
genomic sequence: query refers to the genomic seq, subject to the aligned EST hit. Because of this, $exon->start(), $exon->end() etc will
always return what you expect.
To get the coordinates on the matching EST, refer to the properties of the feature returned by est_hit().
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney, Hilmar Lapp
Ewan Birney <birney-at-sanger.ac.uk> Hilmar Lapp <hlapp-at-gmx.net> or <hilmar.lapp-at-pharma.novartis.com>.
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
percentage_id
Title : percentage_id
Usage : $obj->percentage_id($newval)
Function: This is a synonym for 100 * $obj->est_hit()->frac_identical().
Returns : value of percentage_id
Args : newvalue (optional)
est_hit
Title : est_hit
Usage : $est_feature = $obj->est_hit();
Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this
exon (i.e., genomic region). At present, merely a synonym for
$obj->feature2().
Returns : An Bio::SeqFeatureI implementing object.
Args :
perl v5.14.2 2012-03-02 Bio::Tools::Sim4::Exon(3pm)