I have the following string below that I need to split up but I need to keep the separator with the second portion of the string. So that I end up with:
$a = 'State of mind is primary';
$b = '\098\455\098evertyhing else is secondary.-Eckhart Tolle '
My attempt:
my $string = 'State of mind is primary\098\455\098evertyhing else is secondary. -Eckhart Tolle';
my $separator = '\098\455\098';
my ($a, $b) = split($separator, $string);
print "$a\n";
print "$b\n";
How can I accomplish this with perl split?
Split on the 0-length string that precedes the sequence.
my ($x, $y) = split(/(?=\\098\\455\\098)/, $string);
Use a positive lookahead.
(I've simplified your separator to remove one potential source of confusion)
#!/usr/bin/perl
use strict;
use warnings;
use feature 'say';
my $string = 'State of mind is primaryXXXevertyhing else is secondary. -Eckhart Tolle';
my $separator = 'XXX';
my ($first, $second) = split /(?=$separator)/, $string;
say "$first / $second";
And the output:
$ perl split
State of mind is primary / XXXevertyhing else is secondary. -Eckhart Tolle
Don't use split() use pattern matching.
EDIT I guess you really meant \ not octal characters:
my $string = "State of mind is primary\\098\\455\\098\everything else is secondary. -Eckhart Tolle";
my($a, $b) = ($string =~ /^(.+)(\\098\\455\\098.+)$/);
print "A: '$a'\n";
print "B: '$b'\n";
output:
A: 'State of mind is primary'
B: '\098\455\098ertyhing else is secondary. -Eckhart Tolle'
Related
Here is the script of user Suic for calculating molecular weight of fasta sequences (calculating molecular weight in perl),
#!/usr/bin/perl
use strict;
use warnings;
use Encode;
for my $file (#ARGV) {
open my $fh, '<:encoding(UTF-8)', $file;
my $input = join q{}, <$fh>;
close $fh;
while ( $input =~ /^(>.*?)$([^>]*)/smxg ) {
my $name = $1;
my $seq = $2;
$seq =~ s/\n//smxg;
my $mass = calc_mass($seq);
print "$name has mass $mass\n";
}
}
sub calc_mass {
my $a = shift;
my #a = ();
my $x = length $a;
#a = split q{}, $a;
my $b = 0;
my %data = (
A=>71.09, R=>16.19, D=>114.11, N=>115.09,
C=>103.15, E=>129.12, Q=>128.14, G=>57.05,
H=>137.14, I=>113.16, L=>113.16, K=>128.17,
M=>131.19, F=>147.18, P=>97.12, S=>87.08,
T=>101.11, W=>186.12, Y=>163.18, V=>99.14
);
for my $i( #a ) {
$b += $data{$i};
}
my $c = $b - (18 * ($x - 1));
return $c;
}
and the protein.fasta file with n (here is 2) sequences:
seq_ID_1 descriptions etc
ASDGDSAHSAHASDFRHGSDHSDGEWTSHSDHDSHFSDGSGASGADGHHAH
ASDSADGDASHDASHSAREWAWGDASHASGASGASGSDGASDGDSAHSHAS
SFASGDASGDSSDFDSFSDFSD
>seq_ID_2 descriptions etc
ASDGDSAHSAHASDFRHGSDHSDGEWTSHSDHDSHFSDGSGASGADGHHAH
ASDSADGDASHDASHSAREWAWGDASHASGASGASG
When using: perl molecular_weight.pl protein.fasta > output.txt
in terminal, it will generate the correct results, however it also presents an error of "Use of unitialized value in addition (+) at molecular_weight.pl line36", which is just localized in line of "$b += $data{$i};" how to fix this bug ? Thanks in advance !
You probably have an errant SPACE somewhere in your data file. Just change
$seq =~ s/\n//smxg;
into
$seq =~ s/\s//smxg;
EDIT:
Besides whitespace, there may be some non-whitespace invisible characters in the data, like WORD JOINER (U+2060).
If you want to be sure to be thorough and you know all the legal symbols, you can delete everything apart from them:
$seq =~ s/[^ARDNCEQGHILKMFPSTWYV]//smxg;
Or, to make sure you won't miss any (even if you later change the symbols), you can populate a filter regex dynamically from the hash keys.
You'd need to make %Data and the filter regex global, so the filter is available in the main loop. As a beneficial side effect, you don't need to re-initialize the data hash every time you enter calc_mass().
use strict;
use warnings;
my %Data = (A=>71.09,...);
my $Filter_regex = eval { my $x = '[^' . join('', keys %Data) . ']'; qr/$x/; };
...
$seq =~ s/$Filter_regex//smxg;
(This filter works as long as the symbols are single character. For more complicated ones, it may be preferable to match for the symbols and collect them from the sequence, instead of removing unwanted characters.)
[perl 5.8.8]
I have a sequence of names of things like:
names='foobar1304,foobar1305,foobar1306,foobar1307'
where the names differ only by a contiguous string of digits somewhere in the name. The strings of digits in any sequence are all of the same length, and the digit strings form a continuous numeric sequence with no skips, e.g. 003,004,005.
I want a compact representation like:
compact_name='foobar1304-7'
(The compact form is just a name, so it's exact form is negotiable.)
There will usually only be <10 things, though some sets might span a decade, e.g.
'foobaz2205-11'
Is there some concise way to do this in perl? I'm not a big perl hacker, so be a little gentle...
Bonus points for handling embedded sequences like:
names='foobar33-pqq,foobar34-pqq,foobar35-pqq'
The ideal script would neatly fall back to 'firstname2301-lastname9922' in case it can't identify a sequence in the names.
I am not sure I got your specification, but it works somehow:
#!/usr/bin/perl
use warnings;
use strict;
use Test::More;
sub compact {
my $string = shift;
my ($name, $value) = split /=/, $string;
$name =~ s/s$// or die "Cannot create compact name for $name.\n"; #/ SO hilite bug
$name = 'compact_' . $name;
$value =~ s/^'|'$//g; #/ SO hilite bug
my #values = split /,/, $value; #/ SO hilite bug
my ($prefix, $first, $suffix) = $values[0] =~ /^(.+?)([0-9]+)(.*)$/;
my $last = $first + $#values;
my $same = 0;
$same++ while substr($first, 0, $same) eq substr($last, 0, $same);
$last = substr $last, $same - 1;
for my $i ($first .. $first + $#values) {
$values[$i - $first] eq ($prefix . $i . $suffix)
or die "Invalid sequence at $values[$i-$first].\n";
}
return "$name='$prefix$first-$last$suffix'";
}
is( compact("names='foobar1304,foobar1305,foobar1306,foobar1307'"),
"compact_name='foobar1304-7'");
is( compact("names='foobaz2205,foobaz2206,foobaz2207,foobaz2208,foobaz2209,foobaz2210,foobaz2211'"),
"compact_name='foobaz2205-11'");
is( compact("names='foobar33-pqq,foobar34-pqq,foobar35-pqq'"),
"compact_name='foobar33-5-pqq'");
done_testing();
Someone sure will post an more elegant solution, but the following
use strict;
use warnings;
my $names='foobar1308-xy,foobar1309-xy,foobar1310-xy,foobar1311-xy';
my #names = split /,/,$names;
my $pfx = lcp(#names);
my #nums = map { m/$pfx(\d*)/; $1 } #names;
my $first=shift #nums;
my $last = pop #nums;
my $suf=$names[0];
$suf =~ s/$pfx\d*//;
print "$pfx\{$first-$last}$suf\n";
#https://gist.github.com/3309172
sub lcp {
my $match = shift;
substr($match, (($match ^ $_) =~ /^\0*/, $+[0])) = '' for #_;
$match;
}
prints:
foobar13{08-11}-xy
I have an input variable, say $a. $a can be either number or string or mix of both.
My question is how can I strip off the variable to separate numeric digits and alphabetic characters?
Example;
$a can be 'AB9'
Here I should be able to store 'AB' in one variable and '9' in other.
How can I do that?
Check this version, it works with 1 or more numeric and alphabetic characters in a variable.
#!/usr/bin/perl
use strict;
use Data::Dumper;
my $var = '11a';
my (#digits, #alphabetics);
while ($var =~ /([a-zA-Z]+)/g) {
push #alphabetics, $1;
}
while ($var =~ /(\d+)/g) {
push #digits, $1;
}
print Dumper(\#alphabetics);
print Dumper(\#digits);
Here's one way to express it very shortly:
my ($digits) = $input =~ /(\d+)/;
my ($alpha) = $input =~ /([a-z]+)/i;
say 'digits: ' . ($digits // 'none');
say 'non-digits: ' . ($alpha // 'none');
It's important to use the match operator in list context here, otherwise it would return if the match succeeded.
If you want to get all occurrences in the input string, simply change the scalar variables in list context to proper arrays:
my #digits = $input =~ /(\d+)/g;
my #alpha = $input =~ /([a-z]+)/gi;
say 'digits: ' . join ', ' => #digits;
say 'non-digits: ' . join ', ' => #alpha;
For my $input = '42AB17C', the output is
digits: 42, 17
non-digits: AB, C
With this sentence:
my $sent = "Mapping and quantifying mammalian transcriptomes RNA-Seq";
We want to get all possible consecutive pairs of words.
my $var = ['Mapping and',
'and quantifying',
'quantifying mammalian',
'mammalian transcriptomes',
'transcriptomes RNA-Seq'];
Is there a compact way to do it?
Yes.
my $sent = "Mapping and quantifying mammalian transcriptomes RNA-Seq";
my #pairs = $sent =~ /(?=(\S+\s+\S+))\S+/g;
A variation that (perhaps unwisely) relies on operator evaluation order but doesn't rely on fancy regexes or indices:
my #words = split /\s+/, $sent;
my $last = shift #words;
my #var;
push #var, $last . ' ' . ($last = $_) for #words;
This works:
my #sent = split(/\s+/, $sent);
my #var = map { $sent[$_] . ' ' . $sent[$_ + 1] } 0 .. $#sent - 1;
i.e. just split the original string into an array of words, and then use map to iteratively produce the desired pairs.
I don't have it as a single line, but the following code should give you somewhere to start. Basically does it with a push and a regext with /g.
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
$Data::Dumper::Indent = 1;
my $t1 = 'aa bb cc dd ee ff';
my $t2 = 'aa bb cc dd ee';
foreach my $txt ( $t1, $t2 )
{
my #a;
push( #a, $& ) while( $txt =~ /\G\S+(\s+\S+|)\s*/g );
print Dumper( \#a );
}
One liner thanks to the syntax from #ysth
my #a = $txt =~ /\G(\S+(?:\s+\S+|))\s*/g;
My regex is slightly different in that if you have an odd number of words, the last word still gets an entry.
I have a string in Perl that is 23 digits long. I need to cut it apart into different pieces. First 2 digits in one variable, next 3 in another variable, next 4 into another variable, etc. Basically the 23 digits needs to end up as 6 separate variables (2,3,4,4,3,7) characters, in that order.
Any ideas how I can cut the string up like this?
There are lots of ways to do it, but the shortest is probably unpack:
my $string = '1' x 23;
my #values = unpack 'A2A3A4A4A3A7', $string;
If you need separate variables, you can use a list assignment:
my ($v1, $v2, $v3, $v4, $v5, $v6) = unpack 'A2A3A4A4A3A7', $string;
Expanding on Alex's method, rather than specify each start and end, use the list you gave of lengths.
#!/usr/bin/env perl
use strict;
use warnings;
my $string = "abcdefghijklmnopqrstuvw";
my $pos = 0;
my #split = map {
my $start = $pos;
my $end = $_;
$pos += $end;
substr( $string, $start, $end);
} (2,3,4,4,3,7);
print "$_\n" for #split;
This said you probably should look at unpack which is used for fixed width fields. I have no experience with it though.
You could use a regex, viz:
$string =~ /\d{2}\d{3}\d{4}\d{4}\d{3}\d{7}/
and capture each part by surrounding with brackets ().
You then find each capture in the variables $1, $2 ...
or get them all in the returned list
See perldoc perlre
You want to use perldoc substr.
$substring = substr($string, $start, $length);
I'd also use `map' on a list of [start, length] pairs to make your life easier:
$string = "123456789";
#values = map {substr($string, $_->[0], $_->[1])} ([1, 3], [4, 2] , ...);
Here's a sub that will do it, using the already discussed unpack.
sub string_slices {
my $str = shift;
return unpack( join( 'A', '', #_ ), $str );
}