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Top Forums Shell Programming and Scripting Script to search and extract the gene sub-location from gff file. Post 302534410 by reena2305 on Tuesday 28th of June 2011 12:24:15 AM
Old 06-28-2011
@panyam

sorry this was my first post, so I didn't have much idea.

Regarding problem:

Code:
gene            39389788..39395643

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:

Code:
mRNA            join(39389788..39389839,39390696
 CDS             join(39390729..39390861,39391681..39..

etc..until the information of next gene comes..
like: (say gene2)
Code:
gene            39391466..39391614

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:

Code:
Gene_input_file: f3 
 sno_input_file: chr3  
 319 found_in_gene  52698648..52707224 at 52704105 and_count: 5457
 68 found_in_gene  52698648..52707224 at 52705463 and_count: 6815 
82 found_in_gene  52698648..52707224 at 52701967 and_count: 3319
 124 found_in_gene  39793218..40244467 at 40222682 and_count: 429464
 202 found_in_gene  9443305..10558922 at 10110734 and_count: 667429
 228 found_in_gene  46262602..46896241 at 46629723 and_count: 367121 ..and so on.

I have to read it line by line, extract gene position, then search it in the main gene info. (gff) file. like:

Code:
52698648..52707224 (of file2) match it in file1 and print its sub-location.

note: '..' denotes FROM postion 52698648 TO 52707224.

Last edited by reena2305; 06-28-2011 at 01:32 AM..
 

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PGASetIntegerInitRange(2)					      PGAPack						 PGASetIntegerInitRange(2)

NAME
PGASetIntegerInitRange - sets a flag to tell the initialization routines to set each integer-valued gene to a value chosen randomly from the interval given by an upper and lower bound. DESCRIPTION
No string initialization is done by this call. INPUT PARAMETERS
ctx - context variable min - array of lower bounds that define the interval the gene is initialized from max - array of upper bounds that define the interval the gene is initialized from OUTPUT PARAMETERS
none SYNOPSIS
#include "pgapack.h" void PGASetIntegerInitRange(ctx, min, max) PGAContext *ctx int *min int *max LOCATION
integer.c EXAMPLE
Set the initialization routines to select a value for gene i uniformly randomly from the interval [0,i]. Assumes all strings are of the same length. PGAContext *ctx; int *low, *high, stringlen, i; : stringlen = PGAGetStringLength(ctx); low = (int *) malloc(stringlen*sizeof(int)); high = (int *) malloc(stringlen*sizeof(int)); for(i=0;i<stringlen;i++) { low[i] = 0; high[i] = i } PGASetIntegerInitRange(ctx, low, high); 05/01/95 PGASetIntegerInitRange(2)
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