08-05-2015
may be that entries would be at the bottom of the file actually sir, i just copied and posted very few entries from file1 and file2 may be matched would be skipped. i cant paste my whole data file here i have 4565005 sequence entries in my data.
and about negative value, please provide me the script for like 300 250 = 50
no problem if there is 250-300 =-50 i will correct it and will then apply script.
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
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)
Discussion started by: manthasirisha
4 Replies
2. Shell Programming and Scripting
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)
Discussion started by: harris2107
2 Replies
3. Shell Programming and Scripting
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)
Discussion started by: hidnana
5 Replies
4. Shell Programming and Scripting
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)
Discussion started by: abdurrouf
11 Replies
5. Programming
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)
Discussion started by: yeclota
1 Replies
6. Shell Programming and Scripting
I have following input
@xxxxxx@
I want to extract what's between @....@ that is : xxxx
using SED command (6 Replies)
Discussion started by: xerox
6 Replies
7. UNIX for Dummies Questions & Answers
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)
Discussion started by: Fahmida
4 Replies
8. Shell Programming and Scripting
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)
Discussion started by: manigrover
1 Replies
9. Shell Programming and Scripting
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)
Discussion started by: karan8810
1 Replies
10. Shell Programming and Scripting
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::homol
Ace::Sequence::Homol(3pm) User Contributed Perl Documentation Ace::Sequence::Homol(3pm)
NAME
Ace::Sequence::Homol - Temporary Sequence Homology Class
SYNOPSIS
# Get all similarity features from an Ace::Sequence
@homol = $seq->features('Similarity');
# sort by score
@sorted = sort { $a->score <=> $b->score } @homol;
# the last one has the highest score
$best = $sorted[$#sorted];
# fetch its associated Ace::Sequence::Homol
$homol = $best->target;
# print out the sequence name, DNA, start and end
print $homol->name,' ',$homol->start,'-',$homol->end,"
";
print $homol->asDNA;
DESCRIPTION
Ace::Sequence::Homol is a subclass of Ace::Object (not Ace::Sequence) which is specialized for returning information about a DNA or protein
homology. This is a temporary placeholder for a more sophisticated homology class which will include support for alignments.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Homol object directly. Instead, objects will be created in response to an info() or
group() method call on a similarity feature in an Ace::Sequence::Feature object. If you wish to create an Ace::Sequence::Homol object
directly, please consult the source code for the new() method.
OBJECT METHODS
Most methods are inherited from Ace::Object. The following methods are also supported:
start()
$start = $homol->start;
Returns the start of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are
relative to the target homology.
end()
$end = $homol->end;
Returns the end of the area that is similar to the Ace::Sequence::Feature from which his homology was derived. Coordinates are
relative to the target homology.
asString()
$label = $homol->asString;
Returns a human-readable identifier describing the nature of the feature. The format is:
$name/$start-$end
for example:
HUMGEN13/1-67
This method is also called automatically when the object is treated in a string context.
SEE ALSO
Ace, Ace::Object, Ace::Sequence,Ace::Sequence::FeatureList, Ace::Sequence::Feature, GFF
AUTHOR
Lincoln Stein <lstein@w3.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.
perl v5.14.2 2001-09-17 Ace::Sequence::Homol(3pm)