I need to sort lowercase strings based on the vowels appearing in the given strings that are inputted from a file. I need to print the sorted list of strings on the command prompt.
i.e. the vowel will be the substring of vowels appearing in stringA (vowelA), and vowelB the corresponding substring of stringB. StringA appears before stringB in the output if the substring vowelA appears before vowelB in the ascending ASCII order.
What I have currently:
#!/usr/bin/perl -w
use warnings;
use strict;
open my $INFILE, '<', $ARGV[0] or die $!;
while( my $line = <$INFILE> ) {
sub sort_vowels {
my $vowels_a = $a;
my $vowels_b = $b;
$vowels_a =~ s/[^aeiou]//g; # only vowels
$vowels_b =~ s/[^aeiou]//g;
return $vowels_a cmp $vowels_b; # compare the substrings
}
}
print sort { sort_vowels }; # print the sorted strings
close $INFILE;
Sample Input:
albacore
albatross
vermeil
panacea
apparate
parmesan
candelabra
fanfare
false
beans
This should output:
apparate
fanfare
panacea
albatross
albacore
false
parmesan
candelabra
beans
vermeil
The error I'm getting:
syntax error at sort_strings.pl line 22, near "};"
Execution of sort_strings.pl aborted due to compilation errors.
Not sure where I went wrong. Any help would be greatly appreciated!
Perhaps print sort { sort_vowels } <$INFILE>; is what you're looking for.
while and foreach loops allow you to work with a single element at a time, but sort requires an entire list as it's input.
Well, if you consider a vowels-only version of the string a key to the sort order of the words, then you can process each word like so:
push #{ $hash{ lc ( $word =~ s/[^aeiou]//igr ) } }, $word;
Starting with Perl 5.14 the /r flag returns the result. Same could be done this way, pre-5.14:
push #{ $hash{ lc( join( '', $word =~ m/([aeiou]+)/ig )) } }, $word;
Then outputting the order is only a matter of getting a sorted set of keys and dereffing the list of words stored within those keys:
say foreach map { #{ $hash{ $_ } } } sort keys %hash;
Related
use strict;
use warnings;
my $tmp = join "\n", <DATA>;
my #biblables = ();
List items will be fetched and storing into #biblables in a while loop
while($tmp=~m/\\bibitem\[([^\[\]]*)\]{([^\{\}]*)}/g)
{
push(#biblables, "\\cite{$2}, ");
}
print #biblables;
While printing this we are getting the output like as:
\cite{BuI2001},\cite{BuI2002},\cite{BuI2003},\cite{BuI2004},\cite{BuI2005},\cite{BuI2006},
However we need the output like this
\cite{BuI2001},\cite{BuI2002},\cite{BuI2003},\cite{BuI2004},\cite{BuI2005},\cite{BuI2006}.
Hence we can use post regex to insert dot at the end of the listitem in array
while($tmp=~m/\\bibitem\[([^\[\]]*)\]{([^\{\}]*)}/g)
{
my $post = $';
if($post!~m/\\bibitem\[([^\[\]]*)\]{([^\{\}]*)}/)
{ push(#biblables, "\\cite{$2}."); }
else { push(#biblables, "\\cite{$2}, "); }
}
print #biblables;
Could you please advise me if there is short way to get this output
#
__DATA__
\bibitem[{BuI (2001)}]{BuI2001}
\bibitem[{BuII (2002)}]{BuI2002}
\bibitem[{BuIII (2003)}]{BuI2003}
\bibitem[{BuIV (2004)}]{BuI2004}
\bibitem[{BuV (2005)}]{BuI2005}
\bibitem[{BuVI (2006)}]{BuI2006}
You can add the comma and period after the fact:
while($tmp=~m/\\bibitem\[([^\[\]]*)\]{([^\{\}]*)}/g){
push(#biblables, "\\cite{$2}");
}
print join ', ', #biblables;
print ".\n";
If you read from a filehandle you can use eof to determine that you are on the last line, at which point you replace the comma by the dot in the last element. This allows you to build the array completely in the loop, as required.
use warnings;
use strict;
open my $fh, '<', 'bibitems.txt';
my #biblabels;
while (<$fh>) {
push #biblabels, "\\cite{$2}," if /\\bibitem\[([^\[\]]*)\]{([^\{\}]*)}/;
$biblabels[-1] =~ tr/,/./ if eof;
}
print "$_ " for #biblabels;
print "\n";
This prints your desired output.
The oef returns true if the next read will return end-of-file. This means that you've just read the last line, which got put on the array if it matched. This function is rarely needed but here it seems to find a fitting purpose. Note that eof and eof() behave a little differently. Please see the eof page.
If the other capture in the regex is meant to be used change the above to if (...) { ... }. Note that what is in {} is in Latex called citation keys, while the (optional) labels are things inside []. I'd go with the array name of #citkeys for clarity.
If you're determine to add the comma's and dots to the elements when
matching in the regex while loop, it can be done like this.
Since you don't know the total matches yet, just keep a reference to
the most recently pushed element.
Then append the , or . as needed.
Code
use strict;
use warnings;
$/ = undef;
my $tmp = <DATA>;
my #biblables = ();
my $ref = undef;
while( $tmp =~ /\\bibitem\[([^\[\]]*)\]{([^\{\}]*)}/g )
{
$$ref .= ", " if defined $ref;
$ref = \$biblables[ push(#biblables,"\\cite{$2}") ];
}
$$ref .= "." if defined $ref;
print #biblables;
__DATA__
\bibitem[{BuI (2001)}]{BuI2001}
\bibitem[{BuII (2002)}]{BuI2002}
\bibitem[{BuIII (2003)}]{BuI2003}
\bibitem[{BuIV (2004)}]{BuI2004}
\bibitem[{BuV (2005)}]{BuI2005}
\bibitem[{BuVI (2006)}]{BuI2006}
Output
\cite{BuI2001}, \cite{BuI2002}, \cite{BuI2003}, \cite{BuI2004}, \cite{BuI2005}, \cite{BuI2006}.
I am making a hash from regex expression. I run my program below and I have a check at the end to see if my hash made ok. But I keep getting an error for the value., I get this ARRAY(0x1a1c740), when it should be 437768. Keys can display ok. I didnt do split because i need the key to be the first part of a species name. This is what i am matching.
# "aaaaaaaaaa","aaaaaaaaaa","437768","Cryptophyta sp. CR-MAL06",0
Thanks very much for your help that you may give.
use strict;
use warnings;
open (my $in_fh,"$ARGV[0]") or die "Failed to open file: $!\n";
open (my $out_fh, ">genus.txt");
my %hash;
while ( my $line = <$in_fh> ) {
#
# "aaaaaaaaaa","aaaaaaaaaa","437768","Cryptophyta sp. CR-MAL06",0
#
if ($line =~ m/\"+\w+\"+\,+\"+\w+\"+\,+\"+(\d+)\"+\,+\"+(\w+)+.+/) {
my $v = $1;
my $k = $2;
$hash{$k} = [$v];
}
}
if (exists $hash{'Cryptophyta'}) {
print $out_fh $hash{'Cryptophyta'};
}
else {
print $out_fh "NO\n";
}
close $in_fh;
close $out_fh;
Change this line:
$hash{$k} = [$v];
to
$hash{$k} = $v;
[$v] is a reference to an array but you want to store a scalar.
[ ] creates an array, assigns the result of the enclosed expression to that array, and returns a reference to the array. It is that reference you are printing.
You were probably trying to support multiple matches. Two problems:
You continually create a new array with one element. Replace
$hash{$k} = [ $v ];
with
push #{ $hash{$k} }, $v;
You print the reference to the array rather than the contents of the array. Replace
print $out_fh $hash{'Cryptophyta'};
with
print $out_fh join(', ', #{ $hash{'Cryptophyta'} });
I am writing a simple program which capitalizes each word in a sentence. It gets a multi-line input. I then loop through the input lines, split each word in the line, capitalize it and then join the line again. This works fine if the input is one sentence, but as soon as I input two lines my program crashes (and if I wait too long my computer freezes.)
Here is my code
#input = <STDIN>;
foreach(#input)
{
#reset #words
#words= ();
#readability
$lines =$_;
#split sentence
#words = split( / /, $lines );
#capitalize each word
foreach(#words){
$words[$k] = ucfirst;
$k++;
}
#join sentences again
$lines = join(' ', #words);
#create output line
$output[$i]=$lines;
$i++;
}
#print the result
print "\nResult:\n";
foreach(#output){
print $output[$j],"\n";
$j++;
}
Could someone please tell me why it crashes?
use strict (and be told about not properly handled variables like your indices)
use for var (array) to get a usable item without an index (Perl isn't Javascript)
What isn't there can't be wrong (e.g. push instead of index)
In code:
use strict; # always!
my #input = <STDIN>; # the loop need in- and output
my #output = ();
for my $line (#input) # for makes readability *and* terseness easy
{
chomp $line; # get rid of eol
#split sentence
my #words = split( / /, $line );
#capitalize each word
for my $word (#words){ # no danger of mishandling indices
$word = ucfirst($word);
}
#join sentences again
$line = join(' ', #words);
#create output line
push #output, $line;
}
#print the result
print "\nResult:\n";
for my $line (#output){
print $line, "\n";
}
The problem is that you are using global variables throughout, so they are keeping their values across iterations of the loop. You have reset #words to an empty list even though you didn't need to - it is overwritten when you assign the result of split to it - but $k is increasing endlessly.
$k is initially set to undef which evaluates as zero, so for the first sentence everything is fine. But you leave $k set to the number of elements in #words so it starts from there instead of from zero for the next sentence. Your loop over #words becomes endless because you are assigning to (and so creating) $words[$k] so the array is getting longer as fast as you are looping through it.
The same problem applies to $i and $j, but execution never gets as far as reusing those.
Alshtough this was the only way of working in Perl 4, over twenty years ago, Perl 5 has made programming very much nicer to write and debug. You can now declare variables with my, and you can use strict which (among other things) insists that every variable you use must be declared, otherwise your program won't compile. There is also use warnings which is just as invaluable. In this case it would have warned you that you were using an undefined variable $k etc. to index the arrays.
If I apply use strict and use warnings, declare all of your variables and initialise the counters to zero then I get a working program. It's still not very elegant, and there are much better ways of doing it, but the error has gone away.
use strict;
use warnings;
my #input = <STDIN>;
my #output;
my $i = 0;
foreach (#input) {
# readability
my $lines = $_;
# split sentence
my #words = split ' ', $lines;
# capitalize each word
my $k = 0;
foreach (#words) {
$words[$k] = ucfirst;
$k++;
}
# join sentences again
$lines = join ' ', #words;
#create output line
$output[$i] = $lines;
$i++;
}
print "\nResult:\n";
my $j = 0;
foreach (#output) {
print $output[$j], "\n";
$j++;
}
I am aiming to extract a string from start to an end word, (dIonly is start and should be the end workset [including these parenthesis]; furthermore I would like to print the output into a file named report.
I have had problems with lookbehind, as the variable length was not implemented.
Now I reversed the string, to do lookahead. However, something is still not working.
I need to start from dIonly which means I have to reverse the string to circumvent the problem described above, as there are many workset(( in the whole string, which means I can't start from there...
Thank you! I edited the script now. What I need to do is reverse the string. I did that by splitting the string with a space as delimiter into a list, then reversed it, and put it into a string again. Just to split it into a list again at the delimiter 'solution' as my output will have several strings of which I want to extract dIonly to workset (this only works once the string is reversed as otherwise I would encouter worksets that I do not want and extract a different string, as dIonly is a distinct part of the pattern of the solution from which I can work forward to the second workset (which itself is the first workset with 2 parenthesis). Then I want to print it to a new output file. Any suggestions welcome!
This is a sample of the data:
... denotes that it continues after
..... maxRiskC(cA, 3)) c workset((RiskCA(cA, 3), RiskCB(cB, 2), maxRiskC(cA, 3))) c RiskCA(cA, 3) c RiskCB(cB, 2)) ***********
equation (built-in equation for symbol <=) 6 <= 40 ---> true
Solution 4 (state 31) states: 40 rewrites: 8421 in 5357394502ms cpu
(1464ms real) (0) rewrites/second) G:Game --> workset(empty) c playA
c dIonly c
.....
#!/usr/bin/perl
# perl -d ./perl_debugger.pl
use strict;
use Data::Dumper qw(Dumper);
use File::Slurp;
my #a_linesorig;
my #a_out;
my #a_str;
my $line;
my $reversedline;
my #a_linesrev;
my #reversedarray;
my $reversedline;
my $str;
open(my $fh, "<", "data.txt")
or die "cannot open < data.txt: $!";
my $line = read_file('data.txt');
#a_linesorig = split(' ', $line);
#a_linesrev = reverse(#a_linesorig);
$reversedline = join(' ', #a_linesrev); # joins the reversed list to a single string again
#reversedarray = split( /solution/, $reversedline ); # should split huge string into a list from one solution to next
foreach $str (#reversedarray) {
if ($str =~ /\bdIonly:\b(.*?)\bworkset\b/g);
print Dumper \$str;
print (#a_out, "$str");
}
close $fh
or die "can't close file: $!";
open(my $fh, ">", "output.txt")
or die "cannot open > output.txt: $!";
foreach $str (#a_out)
{
print ($fh "$str\n");
}
close $fh
or die "can't close file: $!";
Take off the reverse, it will reverse letters also and not individual words, for that scalar.
You can try it with a greedy match since you are only interested in the last workset:
while (my $line = <$input>) {
chomp $line;
if ($line =~ /.*workset(.*dIonly)/) {
# do something with results
say $fh "'$1'";
}
}
And if you need to reverse before writing to the file, you can do:
while (my $line = <$input>) {
chomp $line;
if ($line =~ /.*workset(.*dIonly)/) {
say $fh join " ",reverse (split / /,$1);
}
}
I need to find match between two tab delimited files files like this:
File 1:
ID1 1 65383896 65383896 G C PCNXL3
ID1 2 56788990 55678900 T A ACT1
ID1 1 56788990 55678900 T A PRO55
File 2
ID2 34 65383896 65383896 G C MET5
ID2 2 56788990 55678900 T A ACT1
ID2 2 56788990 55678900 T A HLA
what I would like to do is to retrive the matching line between the two file. What I would like to match is everyting after the gene ID
So far I have written this code but unfortunately perl keeps giving me the error:
use of "Use of uninitialized value in pattern match (m//)"
Could you please help me figure out where i am doing it wrong?
Thank you in advance!
use strict;
open (INA, $ARGV[0]) || die "cannot to open gene file";
open (INB, $ARGV[1]) || die "cannot to open coding_annotated.var files";
my #sample1 = <INA>;
my #sample2 = <INB>;
foreach my $line (#sample1) {
my #tab = split (/\t/, $line);
my $chr = $tab[1];
my $start = $tab[2];
my $end = $tab[3];
my $ref = $tab[4];
my $alt = $tab[5];
my $name = $tab[6];
foreach my $item (#sample2){
my #fields = split (/\t/,$item);
if ( $fields[1] =~ m/$chr(.*)/
&& $fields[2] =~ m/$start(.*)/
&& $fields[4] =~ m/$ref(.*)/
&& $fields[5] =~ m/$alt(.*)/
&& $fields[6] =~ m/$name(.*)/
) {
print $line, "\n", $item;
}
}
}
On its surface your code seems to be fine (although I didn't debug it). If you don't have an error I cannot spot, could be that the input data has RE special character, which will confuse the regular expression engine when you put it as is (e.g. if any of the variable has the '$' character). Could also be that instead of tab you have spaces some where, in which case you'll indeed get an error, because your split will fail.
In any case, you'll be better off composing just one regular expression that contains all the fields. My code below is a little bit more Perl Idiomatic. I like using the implicit $_ which in my opinion makes the code more readable. I just tested it with your input files and it does the job.
use strict;
open (INA, $ARGV[0]) or die "cannot open file 1";
open (INB, $ARGV[1]) or die "cannot open file 2";
my #sample1 = <INA>;
my #sample2 = <INB>;
foreach (#sample1) {
(my $id, my $chr, my $start, my $end, my $ref, my $alt, my $name) =
m/^(ID\d+)\s+(\w+)\s+(\w+)\s+(\w+)\s+(\w+)\s+(\w+)\s+(\w+)/;
my $rex = "^ID\\d+\\s+$chr\\s+$start\\s+$end\\s+$ref\\s+$alt\\s+$name\\s+";
#print "$rex\n";
foreach (#sample2) {
if( m/$rex/ ) {
print "$id - $_";
}
}
}
Also, how regular is the input data? Do you have exactly one tab between the fields? If that is the case, there is no point to split the lines into 7 different fields - you only need two: the ID portion of the line, and the rest. The first regex would be
(my $id, my $restOfLine) = m/^(ID\d+)\s+(.*)$/;
And you are searching $restOfLine within the second file in a similar technique as above.
If your files are huge and performance is an issue, you should consider putting the first regular expressions (or strings) in a map. That will give you O(n*log(m)) where n and m are the number of lines in each file.
Finally, I have a similar challenge when I need to compare logs. The logs are supposed to be identical, with the exception of a time mark at the beginning of each line. But more importantly: most lines are the same and in order. If this is what you have, and it make sense for you, you can:
First remove the IDxxx from each line: perl -pe "s/ID\d+ +//" file >cleanfile
Then use BeyondCompare or Windiff to compare the files.
I played a bit with your code. What you wrote there was actually three loops:
one over the lines of the first file,
one over the lines of the second file, and
one over all fields in these lines. You manually unrolled this loop.
The rest of this answer assumes that the files are strictly tab-seperated and that any other whitespace matters (even at the end of fields and lines).
Here is a condensed version of the code (assumes open filehandles $file1, $file2, and use strict):
my #sample2 = <$file2>;
SAMPLE_1:
foreach my $s1 (<$file1>) {
my (undef, #fields1) = split /\t/, $s1;
my #regexens = map qr{\Q$_\E(.*)}, #fields1;
SAMPLE_2:
foreach my $s2 (#sample2) {
my (undef, #fields2) = split /\t/, $s2;
for my $i (0 .. $#regexens) {
$fields2[$i] =~ $regexens[$i] or next SAMPLE_2;
}
# only gets here if all regexes matched
print $s1, $s2;
}
}
I did some optimisations: precompiling the various regexes and storing them in an array, quoting the contents of the fields etc. However, this algorithm is O(n²), which is bad.
Here is an elegant variant of that algorithm that knows that only the first field is different — the rest of the line has to be the same character for character:
my #sample2 = <$file2>;
foreach my $s1 (<$file1>) {
foreach my $s2 (#sample2) {
print $s1, $s2 if (split /\t/, $s1, 2)[1] eq (split /\t/, $s2, 2)[1];
}
}
I just test for string equality of the rest of the line. While this algorithm is still O(n²), it outperforms the first solution roughly by an order of magnitude simply by avoiding braindead regexes here.
Finally, here is an O(n) solution. It is a variant of the previous one, but executes the loops after each other, not inside each other, therefore finishing in linear time. We use hashes:
# first loop via map
my %seen = map {reverse(split /\t/, $_, 2)}
# map {/\S/ ? $_ : () } # uncomment this line to handle empty lines
<$file1>;
# 2nd loop
foreach my $line (<$file2>) {
my ($id2, $key) = split /\t/, $line, 2;
if (defined (my $id1 = $seen{$key})) {
print "$id1\t$key";
print "$id2\t$key";
}
}
%seen is a hash that has the rest of the line as a key and the first field as a value. In the second loop, we retrieve the rest of the line again. If this line was present in the first file, we reconstruct the whole line and print it out. This solution is better than the others and scales well up- and downwards, because of its linear complexity
How about:
#!/usr/bin/perl
use File::Slurp;
use strict;
my ($ina, $inb) = #ARGV;
my #lines_a = File::Slurp::read_file($ina);
my #lines_b = File::Slurp::read_file($inb);
my $table_b = {};
my $ln = 0;
# Store all lines in second file in a hash with every different value as a hash key
# If there are several identical ones we store them also, so the hash values are lists containing the id and line number
foreach (#lines_b) {
chomp; # strip newlines
$ln++; # count current line number
my ($id, $rest) = split(m{[\t\s]+}, $_, 2); # split on whitespaces, could be too many tabs or spaces instead
if (exists $table_b->{$rest}) {
push #{ $table_b->{$rest} }, [$id, $ln]; # push to existing list if we already found an entry that is the same
} else {
$table_b->{$rest} = [ [$id, $ln] ]; # create new entry if this is the first one
}
}
# Go thru first file and print out all matches we might have
$ln = 0;
foreach (#lines_a) {
chomp;
$ln++;
my ($id, $rest) = split(m{[\t\s]+}, $_, 2);
if (exists $table_b->{$rest}) { # if we have this entry print where it is found
print "$ina:$ln:\t\t'$id\t$rest'\n " . (join '\n ', map { "$inb:$_->[1]:\t\t'$_->[0]\t$rest'" } #{ $table_b->{$rest} }) . "\n";
}
}