i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is:
I have file1 is this
file2 is this :
and i want result like this:
when i run this command :
i got no output or output file. why so?
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---------- Post updated at 01:28 AM ---------- Previous update was at 01:21 AM ----------
i am using Ubuntu OS
Last edited by Scrutinizer; 08-05-2015 at 04:07 AM..
Reason: Add CODE tags, remove extraneous closing COLOR tag. Removed spurious space and a newline from first sample file
I have this tar file which has files of (.ksh, .ini &.sql) and their hard and soft links.
Later when the original files and their directories are deleted (or rather lost as in a system crash), I have this tar file as the only source to restore all of them.
In such a case when I do,
tar... (4 Replies)
Hi all,
I have a data file from which i would like to extract only certain fields, which are not adjacent to each other. Following is the format of data file (data.txt) that i have, which has about 6 fields delimited by "|"
HARRIS|23|IT|PROGRAMMER|CHICAGO|EMP
JOHN|35|IT|JAVA|NY|CON... (2 Replies)
I need to extract the character before the last "|" in the following lines, which are 'N' and 'U'. The last "|" shouldn't be extracted. Also the no.s of "|" may vary in a line, but I need only the character before the last one.
... (5 Replies)
Hello,
I need your help to extract text from following:
./sherg_fyd_rur:blkabl="R23.21_BL2008_0122_1"
./serge_a75:rlwual="/main/r23.21=26-Mar-2008.05:00:20UTC@R11.31_BL2008_0325"
./serge_a75:blkabl="R23.21_BL2008_0325"
./sherg_proto_npiv:bkguals="R23.21_BL2008_0302 I80_11.31_LR"
I... (11 Replies)
Hi,
Can you help me on this two problems?
how can i get :
from input: /ect/exp/hom/bin ==> output: exp
and
from input: aex1234 =====>output: ex
thanks, (1 Reply)
Hi everyone,
I have a large text file containing DNA sequences in fasta format as follows:
>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450... (4 Replies)
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
I am trying to extract a time from the below string in perl but not able to get the time properly
I just want to extract the time from the above line I am using the below syntax
x=~ /(.*) (\d+)\:(\d+)\:(\d+),(.*)\.com/
$time = $2 . ':' . $3 . ':' . $4;
print $time
Can... (1 Reply)
Hello, here I am posting my query again with modified data input files.
see my query is :
i have two input files file1 and file2.
file1 is smalldata.fasta
>gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
Discussion started by: harpreetmanku04
20 Replies
LEARN ABOUT DEBIAN
bio::seqfeature::sirna::oligo
Bio::SeqFeature::SiRNA::Oligo(3pm) User Contributed Perl Documentation Bio::SeqFeature::SiRNA::Oligo(3pm)NAME
Bio::SeqFeature::SiRNA::Oligo - Perl object for small inhibitory RNAs.
SYNOPSIS
use Bio::SeqFeature::SiRNA::Oligo;
my $oligo = Bio::SeqFeature::SiRNA::Oligo->
new( -seq => 'AUGCCGAUUGCAAGUCAGATT',
-start => 10,
-end => 31,
-strand => -1,
-primary => 'SiRNA::Oligo',
-source_tag => 'Bio::Tools::SiRNA',
-tag => { note => 'A note' }, );
# normally two complementary Oligos are combined in an SiRNA::Pair
# object
$pair->antisense($oligo);
DESCRIPTION
Object methods for single SiRNA oligos - inherits Bio::SeqFeature::Generic. Does not include methods for designing SiRNAs - see
Bio::Tools::SiRNA for that.
SEE ALSO
Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA::Pair.
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR
Donald Jackson (donald.jackson@bms.com)
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $sirna_oligo = Bio::SeqFeature::SiRNA::Oligo->new();
Function : Create a new SiRNA::Oligo object
Returns : Bio::Tools::SiRNA object
Args : -seq sequence of the RNAi oligo. Should be in RNA alphabet
except for the final TT overhang.
-start start position
-end end position
-strand strand
-primary primary tag - defaults to 'SiRNA::Oligo'
-source source tag
-score score value
-tag a reference to a tag/value hash
-seq_id the display name of the sequence
-annotation the AnnotationCollectionI object
-location the LocationI object
Currently passing arguments in gff_string or gff1_string is not supported. SiRNA::Oligo objects are typically created by a design
algorithm such as Bio::Tools::SiRNA
seq
Title : Seq
Usage : my $oligo_sequence = $sirna_oligo->seq();
Purpose : Get/set the sequence of the RNAi oligo
Returns : Sequence for the RNAi oligo
Args : Sequence of the RNAi oligo (optional)
Note : Overloads Bio::SeqFeature::Generic seq method - the oligo and
parent sequences are different.
Note that all but the last 2 nucleotides are RNA (per Tuschl and colleagues).
SiRNA::Pair objects are typically created by a design algorithm such as
Bio::Tools::SiRNA.
perl v5.14.2 2012-03-02 Bio::SeqFeature::SiRNA::Oligo(3pm)