Skip to main content

JAVA pattern match pattern search split example


import java.util.regex.Matcher;
import java.util.regex.Pattern;


// Check if input match a pattern


Pattern curPat = Pattern.compile( "tanvir"+ "(.)+" + "tanvir");
Matcher mymatcher;

String input="tanvirAAAAAAAtanvir";
mymatcher = curPat.matcher( input );

if(mymatcher.find())
{
        System.out.println("Matched pattern: "+ input );
                   
}
// List all hit with position in input string
m=  ConstantValue.patReplicaFantom.matcher(colNameUnReadable) ;
 while (m.find()) {
                        System.out.print("Start index: " + m.start());
                        System.out.print(" End index: " + m.end());
                        System.out.println(" Found: " + m.group());
 }

// Split a input according to pattern


Pattern patFastaHeade = Pattern.compile("[>_]+"); 
String text=">aaaa";
String tmp[];
tmp = patFastaHeade.split(text);
for( int i=0; i < tmp.length ; i++) }
              System.out.println( tmp[i] );
}

Comments

Popular posts from this blog

MATLAB cross validation

// use built-in function samplesize = size( matrix , 1); c = cvpartition(samplesize,  'kfold' , k); % return the indexes on each fold ///// output in matlab console K-fold cross validation partition              N: 10    NumTestSets: 4      TrainSize: 8  7  7  8       TestSize: 2  3  3  2 ////////////////////// for i=1 : k    trainIdxs = find(training(c,i) ); %training(c,i);  // 1 means in train , 0 means in test    testInxs  = find(test(c,i)       ); % test(c,i);       // 1 means in test , 0 means in train    trainMatrix = matrix (  matrix(trainIdxs ), : );    testMatrix  = matrix (  matrix(testIdxs  ), : ); end //// now calculate performance %%  calculate performance of a partiti...

R tutorial

Install R in linux ============ In CRAN home page, the latest version is not available. So, in fedora, Open the terminal yum list R  --> To check the latest available version of r yum install R --> install R version yum update R --> update current version to latest one 0 find help ============ ?exact topic name (  i.e.   ?mean ) 0.0 INSTALL 3rd party package  ==================== install.packages('mvtnorm' , dependencies = TRUE , lib='/home/alamt/myRlibrary/')   #  install new package BED file parsing (Always use read.delim it is the best) library(MASS) #library(ggplot2) dirRoot="D:/research/F5shortRNA/TestRIKEN/Rscripts/" dirData="D:/research/F5shortRNA/TestRIKEN/" setwd(dirRoot) getwd() myBed="test.bed" fnmBed=paste(dirData, myBed, sep="") # ccdsHh19.bed   tmp.bed ## Read bed use read.delim - it is the  best mybed=read.delim(fnmBed, header = FALSE, sep = "\t", quote = ...

SLURM tutorial : Basic commands

Main website for learning SLRUM http://slurm.schedmd.com/tutorials.html Submit a job with name and outputfile name(This will overwrite the parameters in shell file header ) sbatch   -J   job1  -o   job1.out  --partition=batch    myscript.sh   Basic shell script for job #!/bin/sh # #SBATCH --job-name=testJob #SBATCH --time=01:00:00 #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --partition=dragon-default # # Display all variables set by slurm env | grep "^SLURM" | sort # cd /projects/dragon/FANTOM5/processed_data_feature ## All my commands for job will go here date;time; mkdir t1 How to submit a batch job sbatch myscript.sh How to check the list of jobs of a user squeue -u user1 squeue -u user1 -l # it will show in details   How to check the whole history and status of a job   scontrol show job=JOBID   How to use one particular node in interactive mode. Useful when all...