sorry this was my first post, so I didn't have much idea.
Regarding problem:
It is a particular gene position in the whole genome, now this gene is madeup of CDS, mRNA, Introns etc..the information is right below it like:
etc..until the information of next gene comes..
like: (say gene2)
So I have file with these 'gene' location, now I need to extract its sub-location, like whether its in CDS, mRNA or Intron(in case no match found).
The location of gene(that we need to find) is in separate file:
I have to read it line by line, extract gene position, then search it in the main gene info. (gff) file. like:
note: '..' denotes FROM postion 52698648 TO 52707224.
Last edited by reena2305; 06-28-2011 at 01:32 AM..
Good evening All,
I have a perl script to pull out all occurrences of a files beginning with xx and ending in .p. I will then loop through all 1K files in a directory. I can grep for xx*.p files but it gives me the entire line. I wish to output to a single colum with only the hits found. ... (3 Replies)
Create a script that copies files from one specified directory to another specified directory, in the order they were created in the original directory between specified times. Copy the files at a specified interval. (2 Replies)
Hi,
I am logging to a linux server through a user "user1" in /home directory.
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When the script is added to crontab, on... (1 Reply)
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}' $i
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I have a file with
<suit:run date="Trump Tue 06/19/2012 11:41 AM EDT" machine="garg-ln" build="19921" level="beta" release="6.1.5" os="Linux">
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I have hundreds of files to process. In each file
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search for value(s) selected from point (2) in the same file at a specific position.
HEADER ELECTRON TRANSPORT 18-MAR-98 1A7V
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Hi
This is my third past and very impressed with previous post replies
Hoping the same for below query
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I have a log file which is the output from a xml script :
<?xml version="1.0" ?>
<!DOCTYPE svc_result SYSTEM "MLP_SVC_RESULT_320.DTD">
<svc_result ver="3.2.0">
<slia ver="3.0.0">
<pos>
<msid type="MSISDN" enc="ASC">8093078040</msid>
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Discussion started by: ANKIT ROY
7 Replies
LEARN ABOUT DEBIAN
swiss::gns
SWISS::GNs(3pm) User Contributed Perl Documentation SWISS::GNs(3pm)Name
SWISS::GNs.pm
Description
SWISS::GNs represents the GN lines within an SWISS-PROT + TrEMBL entry as specified in the user manual
http://www.expasy.org/sprot/userman.html . The GNs object is a container object which holds a list of SWISS::GeneGroup objects.
Inherits from
SWISS::ListBase.pm
Attributes
"list"
Each list element is a SWISS::GeneGroup object.
"and" (deprecated, for old format only)
Delimiter used between genes. Defaults to " AND ".
"or" (deprecated, for old format only)
Delimiter used between gene names. Defaults to " OR ".
Methods
Standard methods
new
fromText
toText
Reading/Writing methods
text [($newText)]
Sets the text of the GN line to the parameter if it is present, and returns the (unwrapped) text of the line. Also sets 'and' and 'or'
delimiters to the first occurrences of the words "OR" and "AND" in the line, conserving the case.
lowercase (deprecated, for old format only)
Sets the GNs::and and GNs::or delimiters to their lower case values.
uppercase (deprecated, for old format only)
Sets the GNs::and and GNs::or delimiters to their upper case values.
getFirst()
Returns first gene name in gene line
getTags($target)
Returns evidence tags associated with $target
$target is a string
isPresent($target)
Returns 1 if $target is present in the GN line
$target is a string
needsReCasing($target)
If $target is present in the GN line, but wrongly cased, method returns the matching name in its current case
$target is a string
replace($newName, $target, $evidenceTag)
Replaces the first GN object in the GN line whose text attribute is $target with a new GN object whose text attribute is set to
$newName and whose evidenceTags attribute is is set using values set by splitting $evidenceTag on /, / (as name is not being changed,
programs should keep old tag and add new tag). Does nothing if $target is not found.
delete($target)
Removes synonym/single-member gene group matching $target. Note that if a "Name" is deleted, the first "Synonym" will be promoted to
"Name"
addAsNewSynonym($newName, $target, $evidenceTag, $location)
Adds a new GN object (with text attribute set to new $newName, and evidenceTags attribute set to ($evidenceTag)), as a synonym to the
first gene group in which $target is a gene name. Does nothing if $target is not found. Will not add a duplicate gene name.
$location determines where in gene group new object is added: if $location == 1, 2, 3, ..., new object added in the 1st, 2nd, 3rd, ...
position; if $location == 0, new object added before $target; if $location == -1, new object added after $target (default); if
$location == -2, new object added at end of gene group. Note that if the new synonym is inserted in the first postion, it will become
the "Name" and the previous "Name" will be downgraded to first "Synonym"
addAsNewGeneGroup($newName, $target, $evidenceTag, $location)
Adds a new GeneGroup object, comprising 1 GN object (with text attribute set to new $newName, and evidenceTags attribute set to
($evidenceTag)). Will not add a duplicate gene name. $location and $target determine where in GNs line new group is added: if
$location == 1, 2, 3, ..., new object added in the 1st, 2nd, 3rd, ... position; if $location == 0, new object added before $target; if
$location == -1, new object added after $target (default); if $location == -2, new object added at end of GNs line. Does nothing if
$target is not found, and $location == 0 or -1; otherwise $target does not need to be set.
replaceGeneGroup($newGeneGroup, $target)
Replaces the first gene group containing $target with $newGeneGroup. Creating the $newGeneGroup correctly is the user's responsibility
getGeneGroup($target)
Returns the first gene group that contains $target
setToOr()
Retruns a new GNs object, but with all GNs objects in a single gene group. Needed when adding 'C' to 'A and B', when the relationship
of 'C' to 'A' and 'B' is unknown: the universal use of ' or ' is the default delimeter for TrEMBL entries
TRANSITION
The format of the GN line will change in 2004 from:
GN (CYSA1 OR CYSA OR RV3117 OR MT3199 OR MTCY164.27) AND (CYSA2 OR
GN RV0815C OR MT0837 OR MTV043.07C).
to:
GN Name=CysA1; Synonyms=CysA; OrderedLocusNames=Rv3117, MT3199;
GN ORFNames=MtCY164.27;
GN and
GN Name=CysA2; OrderedLocusNames=Rv0815c, MT0837; ORFNames=MTV043.07c;
This module supports both formats. To convert an entry from the old to the new format, do:
$entry->GNs->is_old_format(0);
perl v5.10.1 2006-01-26 SWISS::GNs(3pm)