Extracting information from String (regex, Beanshell)

Mokita

Hello,

I am working with Taverna to build a workflow. Taverna has a beanshell where I can program in java. I am having some problems in writing a script. I want to extract information from a string, separated by newline. For this i am using regex.

The String is given:

P48534
EXP value is: e-10
Q0543
EXP value is: 4e-07

My script look like this in Beanshell:

Expand|Select|Wrap|Line Numbers

  import java.util.regex.Matcher;

import java.util.regex.Pattern;
 
Pattern pGI = Pattern.compile("(^.*?$)");

Pattern pEvaLue = Pattern.compile("is: (.*)$");

Matcher mGI;

Matcher mEvalue;

StringBuffer temp = new StringBuffer();

String [] line = BlastReport.split("\n");

int arraysize = line.length; 
 
for (int i=0; i<(arraysize-1); i+=2){

    String sGI = line[i];

    String sEvalue = line[i+1];    

    mGI = pGI.matcher(sGI);

    mEvalue = pEvalue.matcher(sEvalue);

    String gi="";
 
    if (mGI.find()){

        gi =mGI.group(1);

    }

    if (mEvalue.find()){

        String eval = mEvalue.group(1);

        if(eval.startsWith("e")){

            eval= "1".concat(eval);

        }

        Double d = new Double (eval);

        double Evalue = d.doubleValue();

        if (Evalue<=0.02){

            temp.append(gi + "\n");

        }

    }

}
 
String result = temp.toString().trim();

The error message is: "Attempt to resolve method: matcher() on undefined variable or class name: pEvalue: at Line: 16: pEvalue .matcher(sEvalue)"

Can someone tell me why is giving me this error and how can i fix it.

Thank you in advance,

Mokita

prometheuzz

Quote:

Originally Posted by Mokita

Hello,

I am working with Taverna to build a workflow. Taverna has a beanshell where I can program in java. I am having some problems in writing a script. I want to extract information from a string, separated by newline. For this i am using regex.

The String is given:

P48534
EXP value is: e-10
Q0543
EXP value is: 4e-07

...

It looks like you're trying to capture the text after the is:, right?
Try this:

Expand|Select|Wrap|Line Numbers

  String text = "P48534\nEXP value is: e-10\nQ0543\nEXP value is: 4e-07";

Pattern pattern = Pattern.compile("(?<=is:\\s)[^\\n]+");

Matcher matcher = pattern.matcher(text);
 
while(matcher.find()) {

  System.out.println(matcher.group());

}

r035198x

Which one is your line 16?

Mokita

My line 16 is:
mEvalue = pEvalue.matcher(sEvalue);

Mokita

r035198x

Quote:

Originally Posted by Mokita

My line 16 is:
mEvalue = pEvalue.matcher(sEvalue);

Mokita

Java is case sensitive.
Now give yourself a kick.

prometheuzz

Quote:

Originally Posted by Mokita

My line 16 is:
mEvalue = pEvalue.matcher(sEvalue);

Mokita

That splitting of your String and increasing with 2 in your for loop looks dangerous. Perhaps I (or someone else) can suggest a better approach. But then you first need to explain what is you're trying to do.

So given the String:

Expand|Select|Wrap|Line Numbers

"P48534\nEXP value is: e-10\nQ0543\nEXP value is: 4e-07"

what is it you're trying to extract and/or group?

prometheuzz

Quote:

Originally Posted by Mokita

My line 16 is:
mEvalue = pEvalue.matcher(sEvalue);

Mokita

Try this:

Expand|Select|Wrap|Line Numbers

 String text = "P48534\nEXP value is: e-10\nQ0543\nEXP value is: 4e-07";

Pattern pattern = Pattern.compile("([A-Z]\\d+).*\\n?.*((?<=is:\\s)[^\\n]+)");

Matcher matcher = pattern.matcher(text);
 
System.out.println(text+"\n");
 
while(matcher.find()) {

  String id = matcher.group(1);

  String sVal = matcher.group(2);

  sVal = sVal.startsWith("e") ? 1+sVal : sVal;

  double dVal = Double.parseDouble(sVal);

  System.out.println(id+"\t"+dVal);

}

Mokita

Quote:

Originally Posted by prometheuzz

That splitting of your String and increasing with 2 in your for loop looks dangerous. Perhaps I (or someone else) can suggest a better approach. But then you first need to explain what is you're trying to do.

So given the String:

Expand|Select|Wrap|Line Numbers

"P48534\nEXP value is: e-10\nQ0543\nEXP value is: 4e-07"

what is it you're trying to extract and/or group?

I am trying to do a workflow with taverna, which has a beanshell, where i can write a script in it.
In my workflow i will have the output of a blast search, GI number, which are the P23234 or Q12344 or A12443 or only numbers and also a E-value, which is the EXP vaule is: e-10.
From that output i want to extract the GI numbers which have an e-value<= 0.02. The way i thought i could extract was with regular expressions in java, but the way i wrote the script it is not working.

I think it is more clear what i want to do, but if you need more explanation please ask.

Mokita

r035198x

Quote:

Originally Posted by Mokita

I am trying to do a workflow with taverna, which has a beanshell, where i can write a script in it.
In my workflow i will have the output of a blast search, GI number, which are the P23234 or Q12344 or A12443 or only numbers and also a E-value, which is the EXP vaule is: e-10.
From that output i want to extract the GI numbers which have an e-value<= 0.02. The way i thought i could extract was with regular expressions in java, but the way i wrote the script it is not working.

I think it is more clear what i want to do, but if you need more explanation please ask.

Mokita

I don't think regex is best for this (I could be wrong of course). You are not searching for a pattern (which is where I mostly use my regex) but you are searching for numbers within some range.
P.S I hope you managed to correct the spelling mistake for that variable.

Mokita

Hello

I want to thank you for your help, it is working. I also want to ask you a quick question.
How can i change group 1 ([A-Z]\\d+) to catch: P00DF3 or 1234653 or Q5647GJD or A4658DF
It is not catching the ones with letters in the midle.

Thank you again,

Mokita

prometheuzz

Quote:

Originally Posted by Mokita

...
How can i change group 1 ([A-Z]\\d+) to catch: P00DF3 or 1234653 or Q5647GJD or A4658DF
It is not catching the ones with letters in the midle.

Thank you again,

Mokita

Try replacing "([A-Z]\\d+)" with "(\\w+)"

Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

re: Extracting information from String (regex, Beanshell)

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