Apologies, this is my first post. I thought it would be easier to explain with an ammended file but I've learnt this confuses things. My file 2 looks like this.
If I
this prints out the "MSTRG###"; string that I want to match to (I don't want to match the string from gene_id.
Last edited by Don Cragun; 05-10-2017 at 11:59 PM..
Reason: Add ICODE tags.
I am trying to match a pattern exactly in a shell script. I have tried two methods
awk '/\<mpath${CURR_MP}\>/{print $1 $2}' multipath
perl -ne '/\bmpath${CURR_MP}\b/ and print' /var/tmp/multipath
Both these methods require that I use the escape character. I am guessing that is why... (8 Replies)
Hi folks,
I have a text file that I need to parse, and I cant figure it out. The source is a report breaking down softwares from various companies with some basic info about them (see source snippet below). Ultimately what I want is an excel sheet with only Adobe and Microsoft software name and... (5 Replies)
Hi All,
Does anyone know how to print 1H1A....... in peal script
print line ^1H1A....... if next line equal 5R0RECEIPT....
Thank for help:D
Cat st.txt
1H1A-IN-11-5410-0009420|1010047766|dsds|1|N|IN|IN|000000|1||N|<<<line match
5R0RECEIPT|
5R0RECEIPT|... (2 Replies)
Hi all,
I'm trying to do some work on the authorized_keys file to do a check if there's any information after the hash key.. At the end of the hash key's in the file, there can be an = or ==
Is there a way to check if anything exists after these equals and if so print it out or else print... (2 Replies)
Hello,
I need an awk command to print only the lines that match regex on xth field from file.
For example if I use this command
awk -F"|" ' $22 == "20130117090000.*" 'It wont work, I think, because single quotes wont allow the usage of the metacharacter star * . On the other hand I dont know... (2 Replies)
Hi,
I have the logs :
cat logsx.txt
744906,{"reportingGroups":,"version":"2.0"}
678874,{"reportingGroups":,"version":"2.0"}
193571,{"reportingGroups":,"version":"2.0"}
811537,{"reportingGroups":,"version":"2.0"}
772024,{"reportingGroups":,"version":"2.0"}... (5 Replies)
I need to fetch particular string from log file based on grep condition match.
Actual requirement is need to print the next word from the same line based on grep string condtion match.
File :Java.lanag.xyz......File copied completed : abc.txt
Ouput :abc.txt
I have used below... (5 Replies)
Hello,
one step in a shell script i am writing, involves Grep command to search a regular expression in a line an only print the string after the match
an example line is below
/logs/GRAS/LGT/applogs/lgt-2016-08-24/2016-08-24.8.log.zip:2016-08-24 19:12:48,602 ERROR... (9 Replies)
Hi,
I have some data like below:
John 254
Chris 254
Matt 123
Abe 123
Raj 487
Moh 487
How can i print it using awk to have:
254 John,Chris
123 Matt,Abe
487 Raj,Moh
Thanks. (4 Replies)
Dear team,
Need support to built awk script for below requirement
Input file
LOTC cluster state:
-------------------
Node safNode=SC_2_1 joined cluster |
Node safNode=SC_2_2 joined cluster |
Node safNode=PL_2_3 fail cluster |
AMF cluster state:
------------------... (16 Replies)
Discussion started by: shanul karim
16 Replies
LEARN ABOUT DEBIAN
bio::seqfeature::gene::exon
Bio::SeqFeature::Gene::Exon(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::Exon(3pm)NAME
Bio::SeqFeature::Gene::Exon - a feature representing an exon
SYNOPSIS
# obtain an exon instance $exon somehow
print "exon from ", $exon->start(), " to ", $exon->end(),
" on seq ", $exon->seq_id(), ", strand ", $exon->strand(),
", encodes the peptide sequence ",
$exon->cds()->translate()->seq(), "
";
DESCRIPTION
This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. By default an Exon is
coding. Supply -is_coding => 0 to the constructor or call $exon->is_coding(0) otherwise.
Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
is_coding
Title : is_coding
Usage : if($exon->is_coding()) {
# do something
}
if($is_utr) {
$exon->is_coding(0);
}
Function: Get/set whether or not the exon codes for amino acid.
Returns : TRUE if the object represents a feature translated into protein,
and FALSE otherwise.
Args : A boolean value on set.
primary_tag
Title : primary_tag
Usage : $tag = $feat->primary_tag()
$feat->primary_tag('exon')
Function: Get/set the primary tag for the exon feature.
This method is overridden here in order to allow only for
tag values following a certain convention. For consistency reasons,
the tag value must either contain the string 'exon' or the string
'utr' (both case-insensitive). In the case of 'exon', a string
describing the type of exon may be appended or prefixed. Presently,
the following types are allowed: initial, internal, and terminal
(all case-insensitive).
If the supplied tag value matches 'utr' (case-insensitive),
is_coding() will automatically be set to FALSE, and to TRUE
otherwise.
Returns : A string.
Args : A string on set.
location
Title : location
Usage : my $location = $exon->location()
Function: Returns a location object suitable for identifying the location
of the exon on the sequence or parent feature.
This method is overridden here to restrict allowed location types
to non-compound locations.
Returns : Bio::LocationI object
Args : none
cds
Title : cds()
Usage : $cds = $exon->cds();
Function: Get the coding sequence of the exon as a sequence object.
The sequence of the returned object is prefixed by Ns (lower case)
if the frame of the exon is defined and different from zero. The
result is that the first base starts a codon (frame 0).
This implementation returns undef if the particular exon is
not translated to protein, i.e., is_coding() returns FALSE. Undef
will also be returned if no sequence is attached to this exon
feature.
Returns : A Bio::PrimarySeqI implementing object.
Args :
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::Exon(3pm)