A perl script I'm writing needs to parse a file that has continuation lines like a Makefile. i.e. lines that begin with whitespace are part of the previous line.
I wrote the code below but don't feel like it is very clean or perl-ish (heck, it doesn't even use "redo"!)
There are many edge cases: EOF at odd places, single-line files, files that start or end with a blank line (or non-blank line, or continuation line), empty files. All my test cases (and code) are here: http://whatexit.org/tal/flatten.tar
Can you write cleaner, perl-ish, code that passes all my tests?
#!/usr/bin/perl -w
use strict;
sub process_file_with_continuations {
my $processref = shift #_;
my $nextline;
my $line = <ARGV>;
$line = '' unless defined $line;
chomp $line;
while (defined($nextline = <ARGV>)) {
chomp $nextline;
next if $nextline =~ /^\s*#/; # skip comments
$nextline =~ s/\s+$//g; # remove trailing whitespace
if (eof()) { # Handle EOF
$nextline =~ s/^\s+/ /;
if ($nextline =~ /^\s+/) { # indented line
&$processref($line . $nextline);
}
else {
&$processref($line);
&$processref($nextline) if $nextline ne '';
}
$line = '';
}
elsif ($nextline eq '') { # blank line
&$processref($line);
$line = '';
}
elsif ($nextline =~ /^\s+/) { # indented line
$nextline =~ s/^\s+/ /;
$line .= $nextline;
}
else { # non-indented line
&$processref($line) unless $line eq '';
$line = $nextline;
}
}
&$processref($line) unless $line eq '';
}
sub process_one_line {
my $line = shift #_;
print "$line\n";
}
process_file_with_continuations \&process_one_line;
How about slurping the whole file into memory and processing it using regular expressions. Much more 'perlish'. This passes your tests and is much smaller and neater:
#!/usr/bin/perl
use strict;
use warnings;
$/ = undef; # we want no input record separator.
my $file = <>; # slurp whole file
$file =~ s/^\n//; # Remove newline at start of file
$file =~ s/\s+\n/\n/g; # Remove trailing whitespace.
$file =~ s/\n\s*#[^\n]+//g; # Remove comments.
$file =~ s/\n\s+/ /g; # Merge continuations
# Done
print $file;
If you don't mind loading the entire file in memory, then the code below passes the tests.
It stores the lines in an array, adding each line either to the previous one (continuation) or at the end of the array (other).
#!/usr/bin/perl
use strict;
use warnings;
my #out;
while( <>)
{ chomp;
s{#.*}{}; # suppress comments
next unless( m{\S}); # skip blank lines
if( s{^\s+}{ }) # does the line start with spaces?
{ $out[-1] .= $_; } # yes, continuation, add to last line
else
{ push #out, $_; } # no, add as new line
}
$, = "\n"; # set output field separator
$\ = "\n"; # set output record separator
print #out;
Related
I am trying to read from a file and print out the location of duplicate words on each line.I have stored each line in an array, but I am not sure if this is the right way to start.
while (my $fileLine = <$fh>){
my #lineWords = split /\s+/, $fileLine;
print "#\n"
}
#!/usr/bin/perl
use strict;
use warnings;
while (<DATA>){
chomp; # remove end of line chars
my #wordsInLine = split /\s+/, $_;
#wordsInLine = map {lc($_)} #wordsInLine; # convert words to lowercase
my( $word, %wordsInLine, $n );
for $word (#wordsInLine) {
$wordsInLine{$word}++; # use hash %wordsInLine to count occurences of words
}
for $word (#wordsInLine) {
$n++;
if( (my $count = $wordsInLine{$word}||0) > 1 ) {
print "line $.: Word $n \"$word\" is repeated $count times\n";
delete($wordsInLine{$word}); # do not generate more than one report
# about the same word in single line
}
}
}
__DATA__
This this is a sample sentence
A that That THAT !
I wrote this code and it works fine, it should find lines in which there's no string like 'SID' and append a pipe | at the beginning of the line, so like this: find all lines in which there's no 'SID' and append a pipe | at the beginning of the line. But how I wrote it, I can just output the lines which were changed and have a pipe. What I actually want: leave the file as it is and just append the pipes to the lines which match. Thank you.
#!usr/bin/perl
use strict;
use warnings;
use autodie;
my $fh;
open $fh, '<', 'file1.csv';
my $out = 'file2.csv';
open(FILE, '>', $out);
my $myline = "";
while (my $line = <$fh>) {
chomp $line;
unless ($line =~ m/^SID/) {
$line =~ m/^(.*)$/;
$myline = "\|$1";
}
print FILE $myline . "\n";
}
close $fh;
close FILE;
my file example:
SID,bla
foo bar <- my code adds the pipe to the beginning of this line
output should be like this:
SID,bla
| foo bar
but in my case I only print $myline, I know:
| foo bar
The line
$line =~ m/^(.*)$/
is misguided: all it does is put the contents of $line into $1, so the following statement
$myline = "\|$1"
may as well be
$myline = "|$line"
(The pipe | doesn't need escaping unless it is part of a regular expression.)
Since you are printing $myline at the end of your loop you are never seeing the contents of unmodified lines.
You can fix that by printing $line or $myline according to which one contains the required output, like this
while (my $line = <$fh>) {
chomp $line;
if ($line =~ m/^SID/) {
print "$line\n";
}
else {
my $myline = "|$line";
print "$myline\n";
}
}
or, much more simply, by dropping the intermediate variable and using the default $_ for the input lines, like this
while (<$fh>) {
print '|' unless /^SID/;
print;
}
Note that I have also removed the chomp as it just means you have to put the newline back on the end of the string when you print it.
Instead of creating a new variable $myline, use the one you already have:
while (my $line =<$fh>) {
$line = '|' . $line if $line !~ /^SID/;
print FILE $line;
}
Also, you can use lexical filehandle for the output file as well. Moreover, you should check the return value of open:
open my $OUT, '>', $out or die $!;
the below script is basically catching the second column and counting the values. The only minor issue I have is that the file has empty lines at the end (it's how the values are being exported) and because of these empty lines the script is miscounting. Any ideas please? Thanks.
my $sum_column_b = 0;
open my $file, "<", "file_to_count.txt" or die($!);
while( my $line = <$file>) {
$line =~ m/\s+(\d+)/; #regexpr to catch second column values
$sum_column_b += $1;
}
print $sum_column_b, "\n";
I think the main issue has been established, you are using $1 when it is not conditionally tied to the regex match, which causes you to add values when you should not. This is an alternative solution:
$sum_column_b += $1 if $line =~ m/\s+(\d+)/;
Typically, you should never use $1 unless you check that the regex you expect it to come from succeeded. Use either something like this:
if ($line =~ /(\d+)/) {
$sum += $1;
}
Or use direct assignment to a variable:
my ($num) = $line =~ /(\d+)/;
$sum += $num;
Note that you need to use list context by adding parentheses around the variable, or the regex will simply return 1 for success. Also note that, like Borodin says, this will give an undefined value when the match fails, and you must add code to check for that.
This can be handy when capturing several values:
my #nums = $line =~ /(\d+)/g;
The main problem is that if the regex does not match, then $1 will hold the value it received in the previous successful match. So every empty line will cause the previous line to be counted again.
An improvement would be:
my $sum_column_b = 0;
open my $file, "<", "file_to_count.txt" or die($!);
while( my $line = <$file>) {
next if $line =~ /^\s*$/; # skip "empty" lines
# ... maybe skip other known invalid lines
if ($line =~ m/\s+(\d+)/) { #regexpr to catch second column values
$sum_column_b += $1;
} else {
warn "problematic line '$line'\n"; # report invalid lines
}
}
print $sum_column_b, "\n";
The else-block is of course optional but can help noticing invalid data.
Try putting this line just after the while line:
next if ( $line =~ /^$/ );
Basically, loop around to the next line if the current line has no content.
#!/usr/bin/perl
use warnings;
use strict;
my $sum_column_b = 0;
open my $file, "<", "file_to_count.txt" or die($!);
while (my $line = <$file>) {
next if (m/^\s*$/); # next line if this is unsignificant
if ($line =~ m/\s+(\d+)/) {
$sum_column_b += $1;
}
}
print "$sum_column_b\n";
I have a file which I want to take all the lines which starts with CDS and a line below.
This lines are like:
CDS 297300..298235
/gene="ENSBTAG00000035659"
I found this in your site:
open(FH,'FILE');
while ($line = <FH>) {
if ($line =~ /Pattern/) {
print "$line";
print scalar <FH>;
}
}
and it works great when the CDS is only a line.
Sometimes in my file is like
CDS join(complement(416559..416614),complement(416381..416392),
complement(415781..416087))
/gene="ENSBTAG00000047603"
or with more lines in the CDS.
How can I take only the CDS lines and the next line of the ID???
please i need your help!
Thank you in advance.
Assuming the "next line" always contains /gene=, one can use the flip-flop operator.
while (<>) {
print if m{^CDS} ... m{/gene=};
}
Otherwise, you need to parse the CDS line. It might be sufficient to count parens.
my $depth = 0;
my $print_next = 0;
while (<>) {
if (/^CDS/) {
print;
$depth = tr/(// - tr/)//;
$print_next = 1;
}
elsif ($depth) {
print;
$depth += tr/(// - tr/)//;
}
elsif ($print_next) {
print;
$print_next = 0;
}
}
You need to break the input into outdented paragraphs. Outdented paragraphs start a non-space character in their first line and start with space characters for the rest.
Try:
#!/usr/bin/env perl
use strict;
use warnings;
# --------------------------------------
my $input_file = shift #ARGV;
my $para = undef; # holds partial paragraphs
open my $in_fh, '<', $input_file or die "could not open $input_file: $!\n";
while( my $line = <$in_fh> ){
# paragraphs are outdented, that is, start with a non-space character
if( $line =~ m{ \A \S }msx ){
# don't do if very first line of file
if( defined $para ){
# If paragraph starts with CDS
if( $para =~ m{ \A CDS \b }msx ){
process_CDS( $para );
}
# delete the old paragraph
$para = undef;
}
}
# add the line to the paragraph,
$para .= $line;
}
close $in_fh or die "could not close $input_file: $!\n";
# the last paragraph is not handle inside the loop, so do it now
if( defined $para ){
# If paragraph starts with CDS
if( $para =~ m{ \A CDS \b }msx ){
process_CDS( $para );
}
}
I am new to perl and would like to do what I think is some basic string manipulation to DNA sequences stored in an rtf file.
Essentially, my file reads (file is in FASTA format):
>LM1
AAGTCTGACGGAGCAACGCCGCGTGTATGAAGAAGGTTTTCGGATCGTAA
AGTACTGTCCGTTAGAGAAGAACAAGGATAAGAGTAACTGCTTGTCCCTT
GACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGG
TAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGCGC
GCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCCCCGGCTTAACCGGGGAG
GGTCATTGGAAACTGGAAGACTGGAGTGCAGAAGAGGAGAGTGGAATTCC
ACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAG
GCGACTCTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCA
AACAGGATTAGATACCCTGGTAGTCCACGCCGT
What I would like to do is read into my file and print the header (header is >LM1) then match the following DNA sequence GTGCCAGCAGCCGC and then print the preceding DNA sequence.
So my output would look like this:
>LM1
AAGTCTGACGGAGCAACGCCGCGTGTATGAAGAAGGTTTTCGGATCGTAA
AGTACTGTCCGTTAGAGAAGAACAAGGATAAGAGTAACTGCTTGTCCCTT
GACGGTATCTAACCAGAAAGCCACGGCTAACTAC
I have written the following program:
#!/usr/bin/perl
use strict; use warnings;
open(FASTA, "<seq_V3_V6_130227.rtf") or die "The file could not be found.\n";
while(<FASTA>) {
chomp($_);
if ($_ =~ m/^>/ ) {
my $header = $_;
print "$header\n";
}
my $dna = <FASTA>;
if ($dna =~ /(.*?)GTGCCAGCAGCCGC/) {
print "$dna";
}
}
close(FASTA);
The problem is that my program reads the file line by line and the output I am receiving is the following:
>LM1
GACGGTATCTAACCAGAAAGCCACGGCTAACTAC
Basically I don't know how to assign the entire DNA sequence to my $dna variable and ultimately don't know how to avoid reading the DNA sequence line by line. Also I am getting this warning:
Use of uninitialized value $dna in pattern match (m//) at stacked.pl line 14, line 1113.
If anyone could give me some help with writing better code or point me in the correct direction it would be much appreciated.
Using the pos function:
use strict;
use warnings;
my $dna = "";
my $seq = "GTGCCAGCAGCCGC";
while (<DATA>) {
if (/^>/) {
print;
} else {
if (/^[AGCT]/) {
$dna .= $_;
}
}
}
if ($dna =~ /$seq/g) {
print substr($dna, 0, pos($dna) - length($seq)), "\n";
}
__DATA__
>LM1
AAGTCTGACGGAGCAACGCCGCGTGTATGAAGAAGGTTTTCGGATCGTAA
AGTACTGTCCGTTAGAGAAGAACAAGGATAAGAGTAACTGCTTGTCCCTT
GACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGG
TAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGCGC
GCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCCCCGGCTTAACCGGGGAG
GGTCATTGGAAACTGGAAGACTGGAGTGCAGAAGAGGAGAGTGGAATTCC
ACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAG
GCGACTCTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCA
AACAGGATTAGATACCCTGGTAGTCCACGCCGT
You can process a file with multiple entries like so:
while (<DATA>) {
if (/^>/) {
if ($dna =~ /$seq/g) {
print substr($dna, 0, pos($dna) - length($seq)), "\n";
$dna = "";
}
print;
} elsif (/^[AGCT]/) {
$dna .= $_;
}
}
if ($dna && $dna =~ /$seq/g) {
print substr($dna, 0, pos($dna) - length($seq)), "\n";
}
Your while statement reads until the end of file. That means at every loop iteration, $_ is the next line in <FASTA>. So $dna = <FASTA> isn't doing what you think it is. It is reading more than you probably want it to.
while(<FASTA>) { #Reads a line here
chomp($_);
if ($_ =~ m/^>/ ) {
my $header = $_;
print "$header\n";
}
$dna = <FASTA> # reads another line here - Causes skips over every other line
}
Now, you need to read the sequence into your $dna. You can update your while loop with an else statement. So if its a head line, print it, else, we add it to $dna.
while(<FASTA>) {
chomp($_);
if ($_ =~ m/^>/ ) {
# It is a header line, so print it
my $header = $_;
print "$header\n";
} else {
# if it is not a header line, add to your dna sequence.
$dna .= $_;
}
}
After the loop, you can do your regex.
Note: This solution assumes there is only 1 sequence in the fasta file. If you have more than one, your $dna variable will have all the sequences as one.
Edit: Adding simple a way to handle multiple sequences
my $dna = "";
while(<FASTA>) {
chomp($_);
if ($_ =~ m/^>/ ) {
# Does $dna match the regex?
if ($dna =~ /(.*?)GTGCCAGCAGCCGC/) {
print "$1\n";
}
# Reset the sequence
$dna = "";
# It is a header line, so print it
my $header = $_;
print "$header\n";
} else {
# if it is not a header line, add to your dna sequence.
$dna .= $_;
}
}
# Check the last sequence
if ($dna =~ /(.*?)GTGCCAGCAGCCGC/) {
print "$1\n";
}
I came up with a solution using BioSeqIO (and the trunc method from BioSeq from the BioPerl distribution. I also used index to find the subsequence rather than using a regular expression.
This solution does not print out the id, (line begins with >), if the subsequence was not found or if the subsequence begins at the first postion, (and thus no preceding characters).
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
my $in = Bio::SeqIO->new( -file => "fasta_junk.fasta" ,
-format => 'fasta');
my $out = Bio::SeqIO->new( -file => '>test.dat',
-format => 'fasta');
my $lookup = 'GTGCCAGCAGCCGC';
while ( my $seq = $in->next_seq() ) {
my $pos = index $seq->seq, $lookup;
# if $pos != -1, ($lookup not found),
# or $pos != 0, (found $lookup at first position, thus
# no preceding characters).
if ($pos > 0) {
my $trunc = $seq->trunc(1,$pos);
$out->write_seq($trunc);
}
}
__END__
*** fasta_junk.fasta
>LM1
AAGTCTGACGGAGCAACGCCGCGTGTATGAAGAAGGTTTTCGGATCGTAA
AGTACTGTCCGTTAGAGAAGAACAAGGATAAGAGTAACTGCTTGTCCCTT
GACGGTATCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGG
TAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGCGC
GCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCCCCGGCTTAACCGGGGAG
GGTCATTGGAAACTGGAAGACTGGAGTGCAGAAGAGGAGAGTGGAATTCC
ACGTGTAGCGGTGAAATGCGTAGATATGTGGAGGAACACCAGTGGCGAAG
GCGACTCTCTGGTCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCA
AACAGGATTAGATACCCTGGTAGTCCACGCCGT
*** contents of test.dat
>LM1
AAGTCTGACGGAGCAACGCCGCGTGTATGAAGAAGGTTTTCGGATCGTAAAGTACTGTCC
GTTAGAGAAGAACAAGGATAAGAGTAACTGCTTGTCCCTTGACGGTATCTAACCAGAAAG
CCACGGCTAACTAC
read the whole file into memory then look for the regexp
while(<FASTA>) {
chomp($_);
if ($_ =~ m/^>/ ) {
my $header = $_;
print "$header\n";
} else {
$dna .= $_;
}
}
if ($dna =~ /(.*?)GTGCCAGCAGCCGC/) {
print $1;
}