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1. UNIX for Beginners Questions & Answers
I have the following Snps data
CHROM POS ID
chr7 78599583 rs987435
chr15 33395779 rs987436
chr1 189807684 rs987437
chr20 33907909 rs987438
chr12 75664046 rs987439
and the following gene data
genename name chrom strand txstart txend... (8 Replies)
Discussion started by: marwah
8 Replies
2. Shell Programming and Scripting
I am trying to modify the awk below to include the gene name ($5) for each target and can not seem to do so. Also, I'm not sure the calculation is right (average of all targets that are the same is $4 using the values in $7)? Thank you :).
awk '{if((NR>1)&&($4!=last)){printf("%s\t%f\t%s\n",... (1 Reply)
Discussion started by: cmccabe
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3. Shell Programming and Scripting
Hi,
May i ask if someone share some command for extracting a string between 2 ref string in a txt file
My objective: i had a file with multiple lines and wants only to extract the string "watch?v=IbkAXOmEHpY" or "watch?v=<11 random character>", when i used "grep 'watch?=*' i got a results per... (4 Replies)
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4. UNIX for Dummies Questions & Answers
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
Discussion started by: Ann Mc Cartney
1 Replies
5. Shell Programming and Scripting
I had two files 1.txt 2.txt. I want a 3rd file(o/p) 3.txt like below based on the common elements from the first coulmns of 1.txt and 2.txt.
1.txt
11
12
13
14
15
16
17
18
19
20
21
2.txt (6 Replies)
Discussion started by: p_sai_ias
6 Replies
6. UNIX for Advanced & Expert Users
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)
Discussion started by: liklstar
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7. Shell Programming and Scripting
Hi, my problem is that I have two files. File no. 1 is a gff text file (say gi1) that has gene information like :
********************
gene 39389788..39395643
/gene="RPSA"
/note="Derived by automated computational analysis using
... (2 Replies)
Discussion started by: reena2305
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8. Shell Programming and Scripting
FILE1
abc:xxx:abc:123:wer:AAA:12
csf:xxx:123:aeg:sar:BBB:13
asq:yer:321:wsa:qqq:CCC:14
FILE2
AAA:12:SET1:R1
AAA:12:SSS1:RR1
AAA:11:SET4:R3
BBB:13:SET2:R2
OUTPUT
abc:xxx:abc:123:wer:AAA:12:SET1:R1:SSS1:RR1
csf:xxx:123:aeg:sar:BBB:13:SET2:R2::... (4 Replies)
Discussion started by: greycells
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9. Shell Programming and Scripting
I had two files 1.txt 2.txt. I want a 3rd file(o/p) 3.txt like below (using awk)
1.txt
11 a1
12 a2
13 a3
14 a4
15 a5
16 a6
17 a7
18 a8
19 a9
20 a10
2.txt
14 b1
15 b2
16 b3 (8 Replies)
Discussion started by: p_sai_ias
8 Replies
10. Shell Programming and Scripting
Hi!
1. I have a parameter file containing path to log files. For this example both paths are the same, one is stated directly and the second using env variables.
/oracle/admin/orcl/bdump/:atlas:trc:N
${ORACLE_BASE}/admin/${ORACLE_SID}/bdump/:${ORACLE_SID}:trc:N
2. I try to parse the path... (1 Reply)
Discussion started by: lojzev
1 Replies
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)
01-19-2017
