Please explain your example; it is not at all clear to me.
You say you want the output:
which seems to have been selected by the line:
from the file result.ods which I thought meant that you wanted characters 52962 through 52984 from the data following a line starting with:
in the file 1.fasta. But, that string does not appear in 1.fasta and, even if it did, the data from characters 52962 through 52984 would be 23 characters long; not the 138 characters you have said you want to have output.
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
ace::sequence::gappedalignment
Ace::Sequence::GappedAlignment(3pm) User Contributed Perl Documentation Ace::Sequence::GappedAlignment(3pm)NAME
Ace::Sequence::GappedAlignment - Gapped alignment object
SYNOPSIS
# open database connection and get an Ace::Sequence object
use Ace::Sequence;
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);
# get all the gapped alignments
@alignments = $seq->alignments('EST_GENOME');
# get the aligned segments from the first one
@segs = $alignments[0]->segments;
# get the position of the first aligned segment on the
# source sequence:
($s_start,$s_end) = ($segs[0]->start,$segs[0]->end);
# get the target position for the first aligned segment
($t_start,$t_end) = ($segs[0]->target->start,$segs[0]->target->end);
DESCRIPTION
Ace::Sequence::GappedAlignment is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds
the ability to retrieve the positions of the aligned segments. Each segment is an Ace::Sequence::Feature, from which you can retrieve the
source and target coordinates.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::GappedAlignment object directly. Instead, objects will be created in response to a
alignments() call to an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
segments()
@segments = $gene->segments;
Return a list of Ace::Sequence::Feature objects corresponding to similar segments.
relative()
$relative = $gene->relative;
$gene->relative(1);
This turns on and off relative coordinates. By default, the exons and intron features will be returned in the coordinate system used
by the gene. If relative() is set to a true value, then coordinates will be expressed as relative to the start of the gene. The first
exon will (usually) be 1.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF
AUTHOR
Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>
Copyright (c) 1999, Lincoln D. Stein
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 166:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-11-10 Ace::Sequence::GappedAlignment(3pm)