Not sure quite how to do this, but I am trying to use $1 of LCH.txt (exact match) to look for a match in $1 of genes.txt. If a match is found then in a new file match.txt $1 $2 ($4-$3) are copied.
Example, the first record in LCH is PPT1 and that matches row 713, column 1 of genes.txt.
Match.txt (tab-deliminated)
Thank you .
Moderator's Comments:
Please use CODE tags for sample input and output as well as for sample code.
Hello Every one,
I am in need of all ur's help.
Let me straight explain the problem ..
I have a file "player" which contains three players with their NAME , RUN and ECONOMY rate.
----------
Name Run Economy
David 23 8
stuart 12 12
string 33 4
-----------
Now i want to find... (7 Replies)
I have two files that have the date field in common. I request your help with some script that divide each field value from file1 by the correspond field value of the file2 only when the field date is equal in both files. Thanks in advance !
This is a sample of the files
file 1
12/16/2010,... (2 Replies)
Hi,
I need help on appending certain field in my file1.txt based on matched patterns in file2.txt using awk or sed.
The blue color need to match with one of the data in field $2 in file2.txt. If match, BEGIN and FINISHED value in red will have a new value from field $3 and $4 accordingly.
... (1 Reply)
Howdy!
I have multiple files with tab-separated data:
File1_filtered.txt
gnl|Amel_4.0|Group3.29 1 G R 42 42 60 15 ,.AAA.aa,aa.A.. hh00/f//hD/h/hh
gnl|Amel_4.0|Group3.29 2 C Y 36 36 60 5 T.,T, LggJh
gnl|Amel_4.0|Group3.29 3 A R 27 27 60 9 Gg,,.gg., B6hcc22_c
File2_filtered.txt
... (3 Replies)
Hi everybody (first time posting here)
I have a file1 that looks like >
1,101,0.1,0.1
1,26,0.1,0.1
1,3,0.1,0.1
1,97,0.5,0.5
1,98,8.1,0.218919
1,99,6.2,0.248
2,101,0.1,0.1
2,24,3.1,0.147619
2,25,23.5,0.559524
2,26,34,0.723404with 762 lines..
I have another 'similar' file2 >
... (10 Replies)
For an Output like below
Input : <Subject A="I" B="1039502" C="2015-06-30" D="010101010101">
Output : <Subject D="010101010101" B="1039502" C="2015-06-30" A="I">
I have been using something like below but not getting the desired output :
awk -F ' ' '/Subject/ BEGIN{OFS=" ";}... (19 Replies)
Trying to combine the matching $5 values between file1 and file2. If a match is found then the last $6 value in the match and the sum of $7 are outputted to a new file. The awk below I hope is a good start. Thank you :).
file1
chr12 9221325 9221448 chr12:9221325-9221448 A2M 1... (5 Replies)
In the awk below I am trying to output those lines that Match between file1 and file2, those Missing in file1, and those missing in file2. Using each $1,$2,$4,$5 value as a key to match on, that is if those 4 fields are found in both files the match, but if those 4 fields are not found then missing... (0 Replies)
Hi, I have two TEST files t.xyz and a.xyz which have three columns each. a.xyz have more rows than t.xyz. I will like to output rows at which $1 and $2 of t.xyz match $1 and $2 of a.xyz. Total number of output rows should be equal to that of t.xyz.
It works fine, but when I apply it to large... (6 Replies)
I need to print field and the next one if field matches 'patternA' and also print 'patternB' fields.
echo "some output" | awk '{for(i=1;i<=NF;i++){if($i ~ /patternA/){print $i, $(i+1)}elif($i ~ /patternB/){print $i}}}'
This code returnes me 'syntax error'. Pls advise how to do properly. (2 Replies)
Discussion started by: urello
2 Replies
LEARN ABOUT DEBIAN
ace::sequence::gene
Ace::Sequence::Gene(3pm) User Contributed Perl Documentation Ace::Sequence::Gene(3pm)NAME
Ace::Sequence::Gene - 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 genes
@genes = $seq->genes;
# 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 genes() 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 148:
You forgot a '=back' before '=head1'
perl v5.14.2 2001-02-18 Ace::Sequence::Gene(3pm)