Thanks! I am chasing genes. I sequenced whole genomes and built large contigs (Example.txt). I am fishing out the contigs (sequences with > as identifiers) containing the genes of interest using conserved DNA stretches (Bait). Then, I am trimming the sequences using conserved flanking regions (Primers) to keep exclusively the nucleotide sequences coding for those genes (Gene). The sequences can be in the right direction (forward) or reversed (antisense), depending on the raw sequences generated by our MySeq sequencer. I am using a modified version of your perl one-liner script to determine if the sequence is forward or reverse (the script in this thread). If the sequence is in the right direction nothing is done; however, if the sequence is in the opposite direction, your script will reverse and complement it, outputting a forward sequence every time. Then I just proceed to name the sequence and files. Thus, this bash script outputs four different genes from the original fasta file.
My bash file is complete and working like a charm but I am interested in learning better ways to use awk and/or perl to improve my script
Thanks!
PS. My Example.txt file was trimmed to fit the size limit.
Hi All,
I have a file that I need to be able to find a pattern match on one line then parse data on the next or subsequent lines - I will know which line needs to be parsed beforehand.
This is what I currently have:
while (<COMMAND_OUT>) {
if ($_ =~ m/TEST/) {
... (4 Replies)
Hi All,
I have a file that I need to be able to find a pattern match on a line, search that line for a text pattern, and replace that text.
An example of 4 lines in my file is:
1. MatchText_randomNumberOfText moreData ReplaceMe moreData
2. MatchText_randomNumberOfText moreData moreData... (4 Replies)
Hi,
I have a line where i need to get certain part of it.. example..
text txt tt: 1909
thats how exactly it looks and all spaces are to be counted.. i need to retrieve 1909..
Thanks (11 Replies)
ok so what I am trying to do is search through 200k files that have ext .000 or .702. for *@yahoo.com.tw and if it finds that in the file. then remove the file. this is my code... what am i doing wrong. it seams it will only find asdflkajsdf@yahoo.com.tw as a string and not *@yahoo.com.tw so it... (5 Replies)
Hi All
I want to search a string from an array in Perl. If a match occurs, assign that string to a variable else assign 'No match'. I tried writing the script as follows but it's in vain. Please help me..
#!/usr/bin/perl
use strict;
my $NER;
my @text=("ORG","PER");
... (4 Replies)
Hello All,
Im a Hardware engineer, I have written this script to automate my job. I got stuck in the following location.
CODE:
..
..
...
foreach $key(keys %arr_hash) {
my ($loc,$ind,$add) = split /,/, $arr_hash{$key};
&create_verilog($key, $loc, $ind ,$add);
}
sub create_verilog{... (2 Replies)
Hi,
Need some help...
I want to execute sequence commands, like below
test1.sh
test2.sh
...etc
test1.sh file will generate log file, we need to search for 'complete' string on test1.sh file, once that condition success and then it should go to test2.sh file, each .sh scripts will take... (5 Replies)
Hello,
I want to search two strings in a file and print the same in the new file using perl script.
Can anyone suggest me how to do this...
The file looks like below:
<UML:ModelElement.requirement>
<UML:Dependency name="Row_MainColumn_FW_0009"> <UML:ModelElement.taggedValue>... (3 Replies)
Hello,
Opearting System Environment : HP Unix B.11.31 U
I look for script to
On specific folders list
On specific filelist
Search for given string
For Example :
r48_buildlib.txt contains
wpr480.0_20161027
wpr480.0_20161114
wpr481.0_20161208
wpr482.0_20161222... (4 Replies)
Discussion started by: Siva SQL
4 Replies
LEARN ABOUT DEBIAN
ace::sequence::transcript
Ace::Sequence::Transcript(3pm) User Contributed Perl Documentation Ace::Sequence::Transcript(3pm)NAME
Ace::Sequence::Transcript - Simple "Gene" Object
SYNOPSIS
# open database connection and get an Ace::Object sequence
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 transcripts
@genes = $seq->transcripts;
# get the exons from the first one
@exons = $genes[0]->exons;
# get the introns
@introns = $genes[0]->introns
# get the CDSs (NOT IMPLEMENTED YET!)
@cds = $genes[0]->cds;
DESCRIPTION
Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It inherits all the methods of Ace::Sequence::Feature, but adds the ability
to retrieve the annotated introns and exons of the gene.
OBJECT CREATION
You will not ordinarily create an Ace::Sequence::Gene object directly. Instead, objects will be created in response to a transcripts()
call to an Ace::Sequence object.
OBJECT METHODS
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
exons()
@exons = $gene->exons;
Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.
introns()
@introns = $gene->introns;
Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.
cds()
@cds = $gene->cds;
Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED.
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 168:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-05-22 Ace::Sequence::Transcript(3pm)