Looking for some help with this perl regex.
I need to extract (3) items from this filename: abc101.name.aue-abc_p002.20110124.csv
abc101.name.aue-abc_p002.20110124.csv
where item (3) in this example 002, can also be a max of 4 digits, 0002
Here's my non working regex:
while (my $line=<>) {
chomp $line;
if ($line =~ m/abc(d{3}).name.(w{3})_p([0-9]).[0-9].csv/) {
print $1;
print $2;
print $3;
}
}
while (my $line=<>) {
chomp $line;
if ($line =~ /^abc(\d{3})\.name\.(\w{3})-abc_p(\d{1,4})\.\d+.csv$/) {
print $1;
print $2;
print $3;
}
}
You are missing a few plus signs (or { } quantifiers) and escaping the dots:
abc(d{3})\.name\.(w{3})_p([0-9]{3,4})\.[0-9]+\.csv/
Untested: /^abc(\d{3})\.name\.([a-z]{3})-abc_p(\d{1,4})\.\d+\.csv$/
Related
I am VERY new to perl, and to programming in general.
I have been searching for the past couple of days on how to count the number of pattern matches; I have had a hard time understanding others solutions and applying them to the code I have already written.
Basically, I have a sequence and I need to find all the patterns that match [TC]C[CT]GGAAGC
I believe I have that part down. but I am stuck on counting the number of occurrences of each pattern match. Does anyone know how to edit the code I already have to do this? Any advice is welcomed. Thanks!
#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;
# open fasta file for reading
unless( open( FASTA, "<", '/scratch/Drosophila/dmel-all-chromosome- r6.02.fasta' )) {
die "Can't open dmel-all-chromosome-r6.02.fasta for reading:", $!;
}
#split the fasta record
local $/ = ">";
#scan through fasta file
while (<FASTA>) {
chomp;
if ( $_ =~ /^(.*?)$(.*)$/ms) {
my $header = $1;
my $seq = $2;
$seq =~ s/\R//g; # \R removes line breaks
while ( $seq =~ /([TC]C[CT]GGAAGC)/g) {
print $1, "\n";
}
}
}
Update, I have added in
my #matches = $seq =~ /([TC]C[CT]GGAAGC)/g;
print scalar #matches;
In the code below. However, it seems to be outputting 0 in front of each pattern match, instead of outputting the total sum of all pattern matches.
while (<FASTA>) {
chomp;
if ( $_ =~ /^(.*?)$(.*)$/ms) {
my $header = $1;
my $seq = $2;
$seq =~ s/\R//g; # \R removes line breaks
while ( $seq =~ /([TC]C[CT]GGAAGC)/g) {
print $1, "\n";
my #matches = $seq =~ /([TC]C[CT]GGAAGC)/g;
print scalar #matches;
}
}
}
Edit: I need the output to list ever pattern match found. I also need it to find the total number of matches found. For example:
CCTGGAAGC
TCTGGAAGC
TCCGGAAGC
3 matches found
counting the number of occurrences of each pattern match
my #matches = $string =~ /pattern/g
#matches array will contain all the matched parts. You can then do below to get the count.
print scalar #matches
Or you could directly write
my $matches = () = $string =~ /pattern/
I would suggest you to use the former as you might need to check "what was matched" in future (perhaps for debugging?).
Example 1:
use strict;
use warnings;
my $string = 'John Doe John Done';
my $matches = () = $string =~ /John/g;
print $matches; #prints 2
Example 2:
use strict;
use warnings;
my $string = 'John Doe John Done';
my #matches = $string =~ /John/g;
print "#matches"; #prints John John
print scalar #matches; #prints 2
Edit:
while ( my #matches = $seq =~ /([TC]C[CT]GGAAGC)/g) {
print $1, "\n";
print "Count of matches:". scalar #matches;
}
As you have written the code, you have to count the matches yourself:
local $/ = ">";
my $count = 0;
#scan through fasta file
while (<FASTA>) {
chomp;
if ( $_ =~ /^(.*?)$(.*)$/ms) {
my $header = $1;
my $seq = $2;
$seq =~ s/\R//g; # \R removes line breaks
while ( $seq =~ /([TC]C[CT]GGAAGC)/g) {
print $1, "\n";
$count = $count +1;
}
}
}
print "Fount $count matches\n";
should do the job.
HTH Georg
my #count = ($seq =~ /([TC]C[CT]GGAAGC)/g);
print scalar #count ;
I have a problem I cannot understand. I have this string:
gene_id "siRNA_Z27kG1_20543"transcript_id "siRNA_Z27kG1_20543_X_1";tss_id "TSS124620"
And I want to change the gene_id. So, I have the following code:
if ($line =~ /;transcript_id "([A-Za-z0-9:\-._]*)(_[oxOX][_.][0-9]*)";/) {
$num = $2;
$line =~ s/gene_id "([A-Za-z0-9:\-._]*)";/gene_id "$1$num";/g;
print $new $line."\n";
}
The aim of my code is to change siRNA_Z27kG1_20543 for siRNA_Z27kG1_20543_X_1. However, my code does not produce that output. Why? I can't understand that.
My regex needs to be as it is because I match other strings (this time with success).
#!/usr/bin/perl
use strict;
use warnings;
my $string = q{gene_id "siRNA_Z27kG1_20543"transcript_id "siRNA_Z27kG1_20543_X_1";tss_id "TSS124620"};
if($string =~ m|transcript_id "([A-Za-z0-9:\-._]*)(_[oxOX][_.][0-9]*)"|){
my $replace_with = qq{gene_id "$1$2"};
$string =~ s/gene_id (\"\w+\")/$replace_with/g;
}
print "$string";
Output: gene_id "siRNA_Z27kG1_20543_X_1"transcript_id "siRNA_Z27kG1_20543_X_1";tss_id "TSS124620"
Demo
Remove the semicolon at the start of the pattern as it is not present in the string :-
if ($line =~ /transcript_id "([A-Za-z0-9:\-._]*)(_[oxOX][_.][0-9]*)";/) {
$num = $2;
$line =~ s/gene_id "([A-Za-z0-9:\-._]*)";/gene_id "$1$num";/g;
print $new $line."\n";
}
I am splitting sentences at individual space characters, and then matching these terms against keys of hashes. I am getting matches only if the terms are 100% similar, and I am struggling to find a perfect regex that could match several occurrences of the same word. Eg. Let us consider I have a term 'antagon' now it perfectly matches with the term 'antagon' but fails to match with antagonists, antagonistic or pre-antagonistic, hydro-antagonist etc. Also I need a regex to match occurrences of words like MCF-7 with MCF7 or MC-F7 silencing the effect of special characters and so on.
This is the code that I have till now; thr commented part is where I am struggling.
(Note: Terms in the hash are stemmed to root form of a word).
use warnings;
use strict;
use Drug;
use Stop;
open IN, "sample.txt" or die "cannot find sample";
open OUT, ">sample1.txt" or die "cannot find sample";
while (<IN>) {
chomp $_;
my $flag = 0;
my $line = lc $_;
my #full = ();
if ( $line =~ /<Sentence.*>(.*)<\/Sentence>/i ) {
my $string = $1;
chomp $string;
$string =~ s/,/ , /g;
$string =~ s/\./ \. /g;
$string =~ s/;/ ; /g;
$string =~ s/\(/ ( /g;
$string =~ s/\)/ )/g;
$string =~ s/\:/ : /g;
$string =~ s/\::/ :: )/g;
my #array = split / /, $string;
foreach my $word (#array) {
chomp $word;
if ( $word =~ /\,|\;|\.|\(|\)/g ) {
push( #full, $word );
}
if ( $Stop_words{$word} ) {
push( #full, $word );
}
if ( $Values{$word} ) {
my $term = "<Drug>$word<\/Drug>";
push( #full, $term );
}
else {
push( #full, $word );
}
# if($word=~/.*\Q$Values{$word}\E/i)#Changed this
# {
# $term="<Drug>$word</$Drug>";
# print $term,"\n";
# push(#full,$term);
# }
}
}
my $mod_str = join( " ", #full );
print OUT $mod_str, "\n";
}
I need a regex to match occurances of words like MCF-7 with MCF7 or
MC-F7
The most straightforward approach is just to strip out the hyphenss i.e.
my $ignore_these = "[-_']"
$word =~ s{$ignore_these}{}g;
I am not sure what is stored in your Value hash, so its hard to tell what you expect to happen
if($word=~/.*\Q$Values{$word}\E/i)
However, the kind of thing I imagin you want is (simplified your code somewhat)
#!/usr/bin/perl
use strict;
use warnings;
use utf8;
use 5.10.0;
use Data::Dumper;
while (<>) {
chomp $_;
my $flag = 0;
my $line = lc $_;
my #full = ();
if ( $line =~ /<Sentence.*>(.*)<\/Sentence>/i ) {
my $string = $1;
chomp $string;
$string =~ s/([,\.;\(\)\:])/ $1 /g; # squished these together
$string =~ s/\:\:/ :: )/g; # typo in original
my #array = split /\s+/, $string; # split on one /or more/ spaces
foreach my $word (#array) {
chomp $word;
my $term=$word;
my $word_chars = "[\\w\\-_']";
my $word_part = "antagon";
if ($word =~ m{$word_chars*?$word_part$word_chars+}) {
$term="<Drug>$word</Drug>";
}
push(#full,$term); # push
}
}
my $mod_str = join( " ", #full );
say "<Sentence>$mod_str</Sentence>";
}
This gives me the following output, which is my best guess at what you expect:
$ cat tmp.txt
<Sentence>This in antagonizing the antagonist's antagonism pre-antagonistically.</Sentence>
$ cat tmp.txt | perl x.pl
<Sentence>this in <Drug>antagonizing</Drug> the <Drug>antagonist's</Drug> <Drug>antagonism</Drug> <Drug>pre-antagonistically</Drug> .</Sentence>
$
perl -ne '$things{$1}++while s/([^ ;.,!?]*?antagon[^ ;.,!?]++)//;END{print "$_\n" for sort keys %things}' FILENAME
If the file contains the following:
he was an antagonist
antagonize is a verb
why are you antagonizing her?
this is an alpha-antagonist
This will return:
alpha-antagonist
antagonist
antagonize
antagonizing
Below is the a regular (not one-liner) version:
#!/usr/bin/perl
use warnings;
use strict;
open my $in, "<", "sample.txt" or die "could not open sample.txt for reading!";
open my $out, ">", "sample1.txt" or die "could not open sample1.txt for writing!";
my %things;
while (<$in>){
$things{$1}++ while s/([^ ;.,!?]*?antagon[^ ;.,!?]++)//
}
print $out "$_\n" for sort keys %things;
You may want to take another look at your assumptions on your approach. What it sounds like to me is that you are looking for words which are within a certain distance of a list of words. Take a look at the Levenshtein distance formula to see if this is something you want. Be aware, however, that computing this might take exponential time.
DESCR: "10GE SR"
i need match this above part which is part of my rest of the string. Im using regex in perl.
i tried
if ($line =~ /DESCR: \"([a-zA-Z0-9)\"/) {
print "$1\n";
}
but im not able to understand how to consider spaces inside my string. these spaces can occur any where within the quotes. can someone help me out.
$str = 'DESCR: "10GE SR"';
if ($str =~ /DESCR: \"([a-zA-Z0-9\s]+)\"/) {
print "$1\n";
}
Take a look, this pattern can match double quoted in string:
if ($line =~ /DESCR: \"((?:[^\\"]|\\.)*)\"/) {
print "$1\n";
}
It may be simpler:
if ( $line =~ /DESCR: "([^"]+)"/ ) {
print "$1\n";
}
My code...
$option = "[1]";
if ($option =~ m/^\[\d\]$/) {print "Activated!"; $str=$1;}
I need a way to drop off the square brackets from $option. $str = $1 does not work for some reason. Please advise.
To get $1 to work you need to capture the value inside the brackets using parentheses, i.e:
if ($option =~ m/^\[(\d)\]$/) {print "Activated!"; $str=$1;}
if ($option =~ m/^\[(\d)\]$/) { print "Activated!"; $str=$1; }
Or
if (my ($str) = $option =~ m/^\[(\d)\]$/) { print "Activated!" }
Or
if (my ($str) = $option =~ /(\d)/) { print "Activated!" }
..and a bunch of others. You forgot to capture your match with ()'s.
EDIT:
if ($option =~ /(?<=^\[)\d(?=\]$)/p && (my $str = ${^MATCH})) { print "Activated!" }
Or
my $str;
if ($option =~ /^\[(\d)(?{$str = $^N})\]$/) { print "Activated!" }
Or
if ($option =~ /^\[(\d)\]$/ && ($str = $+)) { print "Activated!" }
For ${^MATCH}, $^N, and $+, perlvar.
I love these questions : )