Note that I am not sure why bakunin suggested using \> in the exon.sh command. Doing that makes the redirection operator and the intended output file become operands to exon.sh instead of being a redirection.
Exactly this was the point. When i suggested debugging the command i suggested to use an echo command in front of it. This echo would have been redirected instead of displayed. This was why i suggested to escape the redirection to display - for debugging purposes - the commands which would be issued by the script.
Quote:
The last thing, if the variables do produce the correct values, is to test the command itself: instead of running it we just display it. Notice that we need to escape the redirection:
[...]
Of course the escaped redirection has to be reverted back to normal once the debugging is over.
I have a line like this:
I want to move HTTP/1.1 200 OK to the next line and put a blank line between the two lines i.e.
How can i get it using awk?
Thanks in advance (2 Replies)
Hi All,
I was wondering if anyone knew how to dynamically change the FS in awk to accept vairiable containing a field separator. the current code is as below and does not work when i introduce the dynamic FS change :-(
validate_source_file()
{
source_file=$1
... (2 Replies)
Hi, all
I need to get fields in a line that are separated by commas, some of the fields are enclosed with double quotes, and they are supposed to be treated as a single field even if there are commas inside the quotes.
sample input:
for this line, 5 fields are supposed to be extracted, they... (8 Replies)
First, thanks for the help in previous posts... couldn't have gotten where I am now without it!
So here is what I have, I use AWK to match $1 and $2 as 1 string in file1 to $1 and $2 as 1 string in file2. Now I'm wondering if I can extend this AWK command to incorporate the following:
If $1... (4 Replies)
Hi. I'd appreciate if I can get some direction in this issue to get me going.
Datafile1:
-About 4000 records, I have to update field#4 in selected records based on a match in the key field (Field#1).
-Field #1 is the key field (servername) . # of Fields may vary
# comment
server1 bbb ccc... (2 Replies)
Hi !
input:
111|222|333|aaa|bbb|ccc
999|888|777|nnn|kkk
444|666|555|eee|ttt|ooo|ppp
With awk, I am trying to change the FS "|" to "; " only from the 4th field until the end (the number of fields vary between records).
In order to get:
111|222|333|aaa; bbb; ccc
999|888|777|nnn; kkk... (1 Reply)
Hi Experts,
i need to change delimiter from tab to ","
sample test file
cat test
A0000368 A29938511 072569352 5 Any 2 for £1.00 BUTCHERS|CAT FOOD|400G Sep 12 2012 12:00AM Jan 5 2014 11:59PM Sep 7 2012 12:00AM M 2.000 group 5
... (2 Replies)
In the below awk in the first step I default Classification NF-1 to VUS. Next, I am trying to change the value of Classification (NF) to whatever CLINSIG (NF-1) is. If there is only one condition everything works great, but if there are two conditions it does not work. Is the syntax used... (4 Replies)
In the awk below I am trying to copy the entire contents of $6 there may be multiple values seperated by a ;, to $8, if $8 is . (lines 1 and 3 are examples). If that condition $8 is not . (line2 is an example) then that line is skipped and printed as is. The awk does execute but prints the output... (3 Replies)
Discussion started by: cmccabe
3 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)