I want to remove the words Z or ZN and LVT from the strings present in my file but I couldn't get it. Can someone check my code.
Input
abchsfk/jshflka/ZN (cellLVT)
asjkfsa/sfklfkshfsf/Z (mobLVT)
asjhfdjkfd/sjfdskjfhdk/hsakfshf/Z (celLVT)
asjhdjs/jhskjds/ZN (abcLVT)
shdsjk/jhskd/ZN (xyzLVT)
Output
abchsfk/jshflka cell
asjkfsa/sfklfkshfsf mob
asjhfdjkfd/sjfdskjfhdk/hsakfshf cel
asjhdjs/jhskjds abc
shdsjk/jhskd xyz
CODE:
if ($line =~ /LVT/ && ($line =~ /ZN/ || $line =~ /Z/) )
#### matches the words LVT and ( Z or ZN)
{
my #names = split / /, $line; ##### splits the line
$names[2] =~ s/\/Z|/ZN//g; #### remove Z or ZN
$names[3] =~ s/\(|LVT\)//g ; #### remove LVT & braces
print OUT " $names[2] $names[3] \n"; #### print
}
The problem is the order of matching: s/\/Z|\/ZN//g (the second backslash is missing in your code!). You should match the longer string first, otherwise Z will match and N won't be deleted.
There's even easier way, though: Just use \/ZN?:
#!/usr/bin/perl
use warnings;
use strict;
while (my $line = <DATA>) {
if ($line =~ /LVT/ && $line =~ /ZN?/) {
my #names = split ' ', $line;
$names[0] =~ s/\/ZN?//g;
$names[1] =~ s/\(|LVT\)//g;
print "$names[0] $names[1]\n";
}
}
__DATA__
abchsfk/jshflka/ZN (cellLVT)
asjkfsa/sfklfkshfsf/Z (mobLVT)
asjhfdjkfd/sjfdskjfhdk/hsakfshf/Z (celLVT)
asjhdjs/jhskjds/ZN (abcLVT)
shdsjk/jhskd/ZN (xyzLVT)
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 need to write a script which does the following:
$ cat testdata.txt
this is my file containing data
for checking pattern matching with a patt on the back!
only one line contains the p word.
$ ./mygrep5 pat th testdata.txt
this is my file containing data
for checking PATTERN MATCHING WITH a PATT ON THe back!
only one line contains the p word.
I have been able to print the line which is amended with the "a" capitalized as well. I have no idea how to only take what is needed.
I have been messing around (below is my script so far) and all I manage to return is the "PATT ON TH" part.
#!/usr/bin/perl
use strict;
use warnings;
use feature 'say';
use Data::Dump 'pp';
my ($f, $s, $t) = #ARGV;
my #output_lines;
open(my $fh, '<', $t);
while (my $line = <$fh>) {
if ($line =~ /$f/ && $line =~ /$s/) {
$line =~ s/($f.+?$s)/$1/g;
my $sub_phrase = uc $1;
$line =~ s/$1/$sub_phrase/g;
print $line;
}
#else {
# print $line;
#}
}
close($fh);
which returns: "for checking pattern matching with a PATT ON THe back!"
How can I fix this problem?
It sounds like you want to capitalize from pat to th except for instances of a surrounded by spaces. The easiest way is to uppercase the whole thing, and then fix any instances of A surrounded by spaces.
sub capitalize {
my $s = shift;
my $uc = uc($s);
$uc =~ s/ \s \K A (?=\s) /a/xg;
return $uc;
}
s{ ( \Q$f\E .* \Q$s\E ) }{ capitalize($1) }xseg;
The downside is that will replacing any existing A surrounded by spaces with a. The following is more complicated, but it doesn't suffer from that problem:
sub capitalize {
my $s = shift;
my #parts = $s =~ m{ \G ( \s+ | \S+ ) }xg;
for (#parts) {
$_ = uc($_) if $_ ne "a";
}
return join('', #parts);
}
s{ ( \Q$f\E .* \Q$s\E ) }{ capitalize($1) }xseg;
The rest of the code can be simplified:
#!/usr/bin/perl
use strict;
use warnings;
sub capitalize { ... }
my $f = shift;
my $s = shift;
while (<>) {
s{ ( \Q$f\E .* \Q$s\E ) }{ capitalize($1) }xseg;
print;
}
So, if you want to match each sequence that starts with pat and ends with th, non-greedily, and uppercase that sequence, you can simply use an expression on the right side of your substitution:
$line =~ s/($f.+?$s)/uc($1)/eg;
And that's it.
I want to print a line of a file if it contains string A and it doesnt contain string B (also splitting into newlines at each colon). What is the proper syntax? Here is what I tried ( I want it print lines containing "bash" but to not print lines containing numbers):
my $file = passwdtest;
open(FH, "$file");
foreach (<FH>) {
print join("\n", split(/:/, "$_")) if ($_ =~ /bash/ and $_ != /\d+/);
};
close FH;
$_ != /\d+/
is short for
$_ != ($_ =~ /\d+/)
Instead of != you need !~
if ($_ =~ /bash/ and $_ !~ /\d+/);
Isn't that just:
if (/bash/ && ! /\d+/)
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.
How can I count the amount of spaces at the start of a string in Perl?
I now have:
$temp = rtrim($line[0]);
$count = ($temp =~ tr/^ //);
But that gives me the count of all spaces.
$str =~ /^(\s*)/;
my $count = length( $1 );
If you just want actual spaces (instead of whitespace), then that would be:
$str =~ /^( *)/;
Edit: The reason why tr doesn't work is it's not a regular expression operator. What you're doing with $count = ( $temp =~ tr/^ // ); is replacing all instances of ^ and with itself (see comment below by cjm), then counting up how many replacements you've done. tr doesn't see ^ as "hey this is the beginning of the string pseudo-character" it sees it as "hey this is a ^".
You can get the offset of a match using #-. If you search for a non-whitespace character, this will be the number of whitespace characters at the start of the string:
#!/usr/bin/perl
use strict;
use warnings;
for my $s ("foo bar", " foo bar", " foo bar", " ") {
my $count = $s =~ /\S/ ? $-[0] : length $s;
print "'$s' has $count whitespace characters at its start\n";
}
Or, even better, use #+ to find the end of the whitespace:
#!/usr/bin/perl
use strict;
use warnings;
for my $s ("foo bar", " foo bar", " foo bar", " ") {
$s =~ /^\s*/;
print "$+[0] '$s'\n";
}
Here's a script that does this for every line of stdin. The relevant snippet of code is the first in the body of the loop.
#!/usr/bin/perl
while ($x = <>) {
$s = length(($x =~ m/^( +)/)[0]);
print $s, ":", $x, "\n";
}
tr/// is not a regex operator. However, you can use s///:
use strict; use warnings;
my $t = (my $s = " \t\n sdklsdjfkl");
my $n = 0;
++$n while $s =~ s{^\s}{};
print "$n \\s characters were removed from \$s\n";
$n = ( $t =~ s{^(\s*)}{} ) && length $1;
print "$n \\s characters were removed from \$t\n";
Since the regexp matcher returns the parenthesed matches when called in a list context, CanSpice's answer can be written in a single statement:
$count = length( ($line[0] =~ /^( *)/)[0] );
This prints amount of white space
echo " hello" |perl -lane 's/^(\s+)(.*)+$/length($1)/e; print'
3