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:

 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]

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:

 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]

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

Mokita

Java is case sensitive.
Now give yourself a kick.

[prometheuzz]

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:

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

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

[prometheuzz]

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

Mokita

Try this:

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]

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:

"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]

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]

...
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+)"