What I need to check is for each gene if column 2 of file 2 is present in column 2 of file 1 and column 3 of file 2 is present in column 3 of file 1 . If so then these two are supposed to be placed in column 4 and 5 of file 1. I just explained one example here. I have 15000 entries with different genes(column5 of file 2). so a for loop should be there to iterate..
o/p
Thanks,
Last edited by Franklin52; 02-11-2012 at 08:59 AM..
Reason: Adding code tags
Hi All, Prepare a perl script for extracting data from xml file. The xml data look like as
AC StartTime="1227858839" ID="88" ETime="1227858837" DSTFlag="false" Type="2" Duration="303" />
<AS StartTime="1227858849" SigPairs="119 40 98 15 100 32 128 18 131 23 70 39 123 20 120 27 100 17 136 12... (3 Replies)
Hi,
I'm using AWK to try to extract data from multiple files (*.txt). The script should look for a flag that occurs at a specific position in each file and it should return the data to the right of that flag.
I should end up with one line for each file, each containing 3 columns:... (8 Replies)
Hi,
Could someone please assist on a quick way of How to extract data from indexed files (ISAM files) maintained in an UNIX(AIX) server.The file data needs to be extracted in flat text file or CSV or excel format .
Usually we have programs in microfocus COBOL to extract data, but would like... (2 Replies)
Hello everyone, I'm new to this forum and i am new as a shell scripter.
my problem is to have html files in a directory and I would like to extract from these some data that lies between two different lines
Here's my situation
<td align="default"> oxidizability (mg / l):
data_to_extract... (6 Replies)
Hi!
I have one file with data that looks like this:
1 data data data data
2 data data data data
3 data data data data
.
.
.
1 data data data data
2 data data data data
3 data data data data
.
.
.
I would like to have awk to write each block to a separate file, like this:
1... (3 Replies)
Hi,
I want to make a query about extracting data from two files that both have data ranges.
the data that i want to extract; when there is matching between file1 column 2 is equal to file2 column2 , and file1 column 3 and column 4 is within the range of file2 columns 3 and 4. I would like rows... (1 Reply)
I am trying to extract common list of Organisms from different files
For example I took 3 files and showed expected result. In real I have more than 1000 files. I am aware about the useful use of awk and grep but unaware in depth so need guidance regarding it.
I want to use awk/ grep/ cut/... (7 Replies)
Hi,
I have directory with multiple files from which i need to extract portion of specif lines and insert it in a new file, the new file will contain a separate columns for each file data.
Example:
I need to extract Value_1 & Value_3 from all files and insert in output file as below:
... (2 Replies)
Hello,
Using the information in file 1, I would like to extract from file2 all rows which matchs in column 3.
file 1
1233
1230
1231
1232
file2
65733.00 19775.00 1220
65733.00 19793.00 1220
65733.00 19801.00 1220
65733.00 19809.00 1231
65733.00 19817.00 ... (2 Replies)
Discussion started by: jiam912
2 Replies
LEARN ABOUT DEBIAN
bio::tools::sim4::exon
Bio::Tools::Sim4::Exon(3pm) User Contributed Perl Documentation Bio::Tools::Sim4::Exon(3pm)NAME
Bio::Tools::Sim4::Exon - A single exon determined by an alignment
SYNOPSIS
# See Bio::Tools::Sim4::Results for a description of the context.
# an instance of this class is-a Bio::SeqFeature::SimilarityPair
# coordinates of the exon (recommended way):
print "exon from ", $exon->start(),
" to ", $exon->end(), "
";
# the same (feature1() inherited from Bio::SeqFeature::FeaturePair)
print "exon from ", $exon->feature1()->start(),
" to ", $exon->feature1()->end(), "
";
# also the same (query() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->query()->start(),
" to ", $exon->query()->end(), "
";
# coordinates on the matching EST (recommended way):
print "matches on EST from ", $exon->est_hit()->start(),
" to ", $exon->est_hit()->end(), "
";
# the same (feature2() inherited from Bio::SeqFeature::FeaturePair)
print "matches on EST from ", $exon->feature2()->start(),
" to ", $exon->feature2()->end(), "
";
# also the same (subject() inherited from Bio::SeqFeature::SimilarityPair):
print "exon from ", $exon->subject()->start(),
" to ", $exon->subject()->end(), "
";
DESCRIPTION
This class inherits from Bio::SeqFeature::SimilarityPair and represents an exon on a genomic sequence determined by similarity, that is, by
aligning an EST sequence (using Sim4 in this case). Consequently, the notion of query and subject is always from the perspective of the
genomic sequence: query refers to the genomic seq, subject to the aligned EST hit. Because of this, $exon->start(), $exon->end() etc will
always return what you expect.
To get the coordinates on the matching EST, refer to the properties of the feature returned by est_hit().
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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney, Hilmar Lapp
Ewan Birney <birney-at-sanger.ac.uk> Hilmar Lapp <hlapp-at-gmx.net> or <hilmar.lapp-at-pharma.novartis.com>.
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
percentage_id
Title : percentage_id
Usage : $obj->percentage_id($newval)
Function: This is a synonym for 100 * $obj->est_hit()->frac_identical().
Returns : value of percentage_id
Args : newvalue (optional)
est_hit
Title : est_hit
Usage : $est_feature = $obj->est_hit();
Function: Returns the EST hit pointing to (i.e., aligned to by Sim4) this
exon (i.e., genomic region). At present, merely a synonym for
$obj->feature2().
Returns : An Bio::SeqFeatureI implementing object.
Args :
perl v5.14.2 2012-03-02 Bio::Tools::Sim4::Exon(3pm)