I have two questions which I would massively appreciate help with.
1.
I am trying to insert a field into a file similar to the vlookup function in excel. In column 2 is a gene id for which i would like to insert the full name in the adjacent column. I have a map file (map.file) which has two columns - in column 1 is the gene ID and column 2 is the full gene name
The second query I have is that i want to be able to filter the file so that the output only contains those fields where for example column 7 <0.5 and column 8 <0.3 and column 9 <0.2 (sometimes there is just a blank in the field which effectively equals 0)
Is there a way to do this so that the filtering is done based on the column header rather than the column number as I have different files which have a different arrangement of columns but with the same headers.
Write a quick shell snippet to find all of the IPV4 IP addresses
in any and all of the files under /var/lib/output/*, ignoring
whatever else may be in those files. Perform a reverse lookup on
each, and format the output neatly, like "IP=192.168.0.1,
... (0 Replies)
Hello Guys,
I want to write a script which will search for all the *.c,*.h,*.txt in the file.
The result will be again search in a .csv file.
If that .c file or .h or .txt is existing in the .csv,then put a * mark corresponding to the row in .csv file.
---------- Post updated at 05:19 AM... (2 Replies)
Hi all
I had a mail issue earlier today where I was not receiving any emails from the servers of one of our clients.
The mail queue just showed this:
-----Q-ID----- --Size-- -----Q-Time----- ------------Sender/Recipient-----------
o8S7eSpp020274* 5858 Tue Sep 28 10:42... (0 Replies)
Hi,
I've internally searched through forums for about 2+ hours. Unfortunately, with no luck. Although I've found some cases close to mine below, but didn't help so much.
Actually, I'm in short with time. So I had to post my case. Hoping that you can help.
I have 2 files,
FILE1
... (0 Replies)
Hi,
I've internally searched through forums for about 2+ hours. Unfortunately, with no luck. Although I've found some cases close to mine below, but didn't help so much.
Actually, I'm in short with time. So I had to post my case. Hoping that you can help.
I have 2 files,
FILE1
... (1 Reply)
Hi, all:
My writed network device driver works fine when the transmitted file is under several MegaBytes, but above this size, especially dozens of or hundreds of MegaBytes, the kernel panic ocurres! I check the kern.log and find this error :
522 Nov 14 19:35:32 liklstar-server kerneNov 14... (2 Replies)
I have the below 2 files:
1) Third field from file1.txt should be compared to the first field of lookup.txt.
2) If match found then third field, file1.txt should be substituted with the second field from lookup.txt.
3)Else just print the line from file1.txt.
File1.txt:... (4 Replies)
Hi All,
I don't know how to fast do this field replace that need lookup from another file to form the update result:confused:
I want to do it by general shell script
Can anyone help to solve it ? Thanks for your kindly reply in advance.
CK (0 Replies)
I have 2 fixed length files input#1 & input#2. I want to match the rows based on the value in position 37-50 in both files (pos 37-50 will have same value in both files).
If any matching record is found then cut the value against company code & Invoice number from input file #1 (position 99 until... (3 Replies)
The below awk uses $3 and $4 in search as the min and max, then takes each $2 value in lookup and compares it. If the value in lookupfalls within the range in searchthen it prints the entire line in lookup/ICODE]. What I can't seem to figure out is how to print the matching $5 from search on that... (4 Replies)
Discussion started by: cmccabe
4 Replies
LEARN ABOUT DEBIAN
bio::map::geneposition
Bio::Map::GenePosition(3pm) User Contributed Perl Documentation Bio::Map::GenePosition(3pm)NAME
Bio::Map::GenePosition - A typed position, suitable for modelling the various
regions of a gene.
SYNOPSIS
use Bio::Map::GenePosition;
use Bio::Map::GeneMap;
# say that the first transcript of a particular gene on a particular map
# (species) is 1000bp long
my $map = Bio::Map:GeneMap->get(-universal_name => 'BRCA2',
-species => 'human');
my $gene = $map->gene;
Bio::Map::GenePosition->new(-map => $map,
-element => $gene,
-start => 0,
-length => 1000,
-type => 'transcript');
# say that the coding region of the gene starts 30bp into the first
# transcript
Bio::Map::GenePosition->new(-map => $map,
-element => $gene,
-start => 30,
-length => 600,
-type => 'coding');
# A GenePosition isa PositionWithSequence, so can have sequence associated
# with it
my $exon = Bio::Map::GenePosition->new(-map => $map,
-element => $gene,
-start => 0,
-type => 'exon',
-seq => 'ATGGGGTGGG');
my $length = $exon->length; # $length is 10
DESCRIPTION
Define where various sub-regions (transcripts, exons, introns etc.) of a gene are. Do this so that you can then go onto to model other
mappable elements as having positions 20bp upstream of transcript 2, or 10bp into intron 3 etc., all without having to know the absolute
position of anything.
See Bio::Map::GeneRelative and t/Map/Map.t for more example usage.
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 the
Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Map::GenePosition->new();
Function: Builds a new Bio::Map::GenePosition object
Returns : Bio::Map::GenePosition
Args : -map => Bio::Map::GeneMap object
-element => Bio::Map::Gene object
-relative => Bio::Map::GeneRelative object
-type => 'transcript|coding|exon|intron', REQUIRED
-seq => string, length of this string will set the length
of this position's range
* If this position has no range, or if a single value can describe
the range *
-value => scalar : something that describes the single
point position or range of this
Position, most likely an int
* Or if this position has a range, at least two of *
-start => int : value of the start co-ordinate
-end => int : value of the end co-ordinate
-length => int : length of the range
map
Title : map
Usage : my $map = $position->map();
$position->map($map);
Function: Get/set the map the position is in.
Returns : L<Bio::Map::MapI>
Args : none to get
new L<Bio::Map::MapI> to set
element
Title : element
Usage : my $element = $position->element();
$position->element($element);
Function: Get/set the element the position is for.
Returns : L<Bio::Map::MappableI>
Args : none to get
new L<Bio::Map::MappableI> to set
type
Title : type
Usage : my $type = $position->type();
$position->type($type);
Function: Get/set the type of this position.
Returns : string
Args : none to get, OR
string transcript|coding|exon|intron to set
relative
Title : relative
Usage : my $relative = $position->relative();
$position->relative($relative);
Function: Get/set the thing this Position's coordinates (numerical(), start(),
end()) are relative to, as described by a RelativeI object.
Returns : Bio::Map::GeneRelative. The default GeneRelative returned has a
meaning that depends on the type() of GenePosition this is:
'transcript' : "relative to the start of the gene on the
Position's map"
'coding|exon|intron' : "relative to the start of the default
transcript of the gene on the Position's map"
Args : none to get, OR
Bio::Map::GeneRelative to set
seq
Title : seq
Usage : my $string = $position->seq();
Function: Get/set the sequence as a string of letters. If no sequence is
manually set by you, the position's map will be asked for the
sequence, and if available, that will be returned.
Returns : scalar
Args : Optionally on set the new value (a string). An optional second
argument presets the alphabet (otherwise it will be guessed).
perl v5.14.2 2012-03-02 Bio::Map::GenePosition(3pm)