How to regex extract something from a string

Question

I have this line:

[1] "RPKM_AB123_Gm12878_control.extended.bed_28m_control_500 and RPKM_AB156_GM12878-50ng_test.extended.bed_28m_test_500"

and I want to extract AB123_Gm12878_control and AB156_GM12878-50ng from the string.

I have tried this and it isn't working yet.

if ($_ =~ /.*"RPKM_([\w.]+).extended.+\s\w+\sRPKM_([\w.]+).extended.+"/){
   print $1,"\t",$2,"\t";
}

Can someone point out where I did it wrong? Thanks!

Jerry · Accepted Answer · 2013-09-25 18:15:55Z

3

".*RPKM_([\w.]+).extended.+\s\w+\sRPKM_([\w.]+).extended.+"
                                        ^^^^^

This character class is not accepting - which the string your matching against contains.

Try putting the hyphen in:

".*RPKM_([\w.]+)\.extended.+\s\w+\sRPKM_([\w.-]+)\.extended.+"

Also, it's good to escape the periods.

answered Sep 25, 2013 at 18:15

Jerry

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4 Comments

amon Over a year ago

The periods, on the other hand, should probably not be in the charclasses.

Jerry Over a year ago

@amon Probably. No idea whether the OP has strings where the parts to be extracted contain these...

olala Over a year ago

Also, about the period, in this particular case I don't need to include period in the final output. I read somewhere that they don't escape period.Is it necessary to escape it?

Jerry Over a year ago

@user2157668 It's safer to, so you don't end up with unexpected results!

mpapec · Accepted Answer · 2013-09-25 18:34:10Z

1

You can simplify regex and match all occurrences using /g

if ( my($m1, $m2) = /RPKM_([^.]+)/g ) {
  print $m1,"\t",$m2,"\t";
}

answered Sep 25, 2013 at 18:34

mpapec

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