Perl/Scripts

The following is a compilation of useful one-line scripts for Perl. The original was compiled by Tom Christiansen, however, I have converted it into the wiki format and have added more examples (always adding more).

Edit a file from the CLI using Perl

perl -p -i.bak -e 's|before|after|' filename  # backup of original file 'filename.bak'

perl -p -i -e 's|before|after|ig' filename

-p: Execute the command for every line of the file.
-i: Invokes in place editing. If a backup extension is provided, a backup of the original file will be made with the extension provided. e.g. -i.bak.
-e: Invoke command.

Perl one-liners

run contents of "my_file" as a program

perl my_file

run debugger "stand-alone"

perl -d -e 42

run program, but with warnings

perl -w my_file

run program under debugger

perl -d my_file

just check syntax, with warnings

perl -wc my_file

useful at end of "find foo -print"

perl -nle unlink

simplest one-liner program

perl -e 'print "hello world!\n"'

add first and penultimate columns

perl -lane 'print $F[0] + $F[-2]'

just lines 15 to 17

perl -ne 'print if 15 .. 17' *.pod

in-place edit of *.c files changing all foo to bar

perl -p -i.bak -e 's/\bfoo\b/bar/g' *.c

command-line that prints the first 50 lines (cheaply)

perl -pe 'exit if $. > 50' f1 f2 f3 ...

delete first 10 lines

perl -i.old -ne 'print unless 1 .. 10' foo.txt

change all the isolated oldvar occurrences to newvar

perl -i.old -pe 's{\boldvar\b}{newvar}g' *.[chy]

command-line that reverses the whole file by lines

perl -e 'print reverse <>' file1 file2 file3 ....

find palindromes

perl -lne 'print if $_ eq reverse' /usr/dict/words

command-line that reverse all the bytes in a file

perl -0777e 'print scalar reverse <>' f1 f2 f3 ...

command-line that reverses the whole file by paragraphs

perl -00 -e 'print reverse <>' file1 file2 file3 ....

increment all numbers found in these files

perl i.tiny -pe 's/(\d+)/ 1 + $1 /ge' file1 file2 ....

command-line that shows each line with its characters backwards

perl -nle 'print scalar reverse $_' file1 file2 file3 ....

delete all but lines between START and END

perl -i.old -ne 'print unless /^START$/ .. /^END$/' foo.txt

binary edit (careful!)

perl -i.bak -pe 's/Mozilla/Slopoke/g' /usr/local/bin/netscape

look for dup words

perl -0777 -ne 'print "$.: doubled $_\n" while /\b(\w+)\b\s+\b\1\b/gi'

command-line that prints the last 50 lines (expensively)

perl -e '@lines = <>; print @lines[ $#lines .. $#lines-50' f1 f2 f3 ...

using the ternary operator:

echo "|E..|"|perl -ne 'printf("%s\n",substr($_,1,1)=~/[A-Z]/?substr($_,1,1):"_");'
# prints "E" if that substr is A-Z
# else prints "_"

The tr/// operator

The "tr///" operator performs a substitution on the individual characters in a string.

Simple example:

#!/usr/bin/perl -w
use strict;
my $text = 'some cheese';
$text =~ tr/ce/XY/;
print "$text\n";

More examples:

$x =~ tr/a/b/;          # replace each "a" with a "b".
$x =~ tr/ /_/;          # convert spaces to underlines.
$x =~ tr/aeiou/AEIOU/;  # capitalise vowels.
$x =~ tr/79/97/;        # exchange "7" and "9".

The only characters that have special meaning to "tr///" are the backslash and the dash. The latter indicates a range of characters:

$x =~ tr/0-9/QERTYUIOPX/; # Digits to letters.
$x =~ tr/A-Z/a-z/;        # Convert to lowercase.

Actually, the slash also has a special meaning to "tr///". The slash is called the "delimiter", because it indicates the "limit" on the list of characters to substitute. However, we can use most kinds of punctuation in place of the slash. For example:

$x =~ tr!aeiou!AEIOU!;
$x =~ tr:aeiou:AEIOU:;

Note that we can also use parentheses, but the syntax changes a little because parentheses include the idea of containment:

$x =~ tr(aeiou)(AEIOU);
$x =~ tr<aeiou><AEIOU>;

The semantics (meaning) don't change; only the syntax (way of writing it) changes. But even though the delimiter is arbitrary, we still talk about it as "tr///".

"tr///" returns the number of replacements it made:

my $salary = '$1,000,000.00';   # Dollar sign: use single quote!
my $ego = ($salary =~ tr/0/0/); # Count the zeros in salary.

One more thing: "tr///" has an alias: "y///". This is to please users of sed, which uses the "y///" command do to basically what "tr///" does. In Perl, "tr///" and "y///" do exactly the same thing; use whichever you like. Remember: there is more than one way to do it (TIMTOWTDI).

$text =~ tr/0-9/A-J/;   # Convert digits to letters.
$text =~  y/0-9/A-J/;   # Does exactly the same thing.

Options

"tr///" can take the following options:

c   # complement (invert) the search-list.
d   # delete found but un-replaced characters.
s   # squash duplicate replaced characters.

These options are specified after the final delimiter, like this:

$x =~ tr/abc/xyz/s;    # Note the "s" at the end.
$x =~ tr(abc)(xyz)s;   # Same thing, but with parentheses.
$x =~ tr/abc/xy/ds;    # Multiple options.
# In the last case, the "z" is missing. You'll see why shortly.

In the last example, we specified both the "d" and the "s" options. The order of the options is not important (i.e., "sd"="ds").

Examples:

#!/usr/bin/perl -w
use strict;

##### The "s" option #####
my $text = 'good cheese';
$text =~ tr/eo/eu/s;
print "$text\n";
# Output is: gud chese

##### The "d" option #####
my $big = 'vowels are useful';
$big =~ tr/aeiou/AEI/d;
print "$big\n";
# The first three vowels are made uppercase.
# The other two, which have no replacement
# character, are deleted because of the "d".

Average numbers

A program that reads numbers and outputs the average. Here is one such program:

#!/usr/bin/perl -w
use strict;
my $line;
my $sum=0;
my $n=0;
while(defined($line=<STDIN>)){
  $sum+=$line;
  $n++;
}
my $average=$sum/$n;
print "The average is $sum/$n = $average\n";

Misc

Change columns in each line of files:

perl -e '$sep=",";while(<>){s/\Q$sep\E/\t/g;print $_;}' file.csv >file.tab

Change tab-separated data to use a different delimiter:

perl -e '$sep=",";while(<>){s/\t/$sep/g;print $_;}' file.tab >file.csv

Remove spaces in a line:

perl -e 'while(<>){s/ //g;print $_;}' foo

Change all characters to upper case:

perl -e 'while(<>){print uc($_);}' foo

Change a FASTA file into tabular format:

perl -e '$count=0;$len=0;while(<>){s/\r?\n//;s/\t/ /g;if(s/^>//){ \
   if($. !=1){print "\n"}s/ |$/\t/;$count++;$_ .="\t";} \
   else{s/ //g;$len +=length($_)}print $_;}print "\n";' foo.fsa >foo.tab

Change a tabular file into FASTA format:

perl -e '$len=0;while(<>){s/\r?\n//;@F=split /\t/,$_;print ">$F[0]"; \
   if(length($F[1])){print" $F[1]"}print "\n";$s=$F[2];$len+=length($s); \
   $s=~s/.{60}(?=.)/$&\n/g;print "$s\n";}' foo.tab >foo.fsa

Change from one biological format to another:

perl -MBio::SeqIO -e '$informat="genbank";$outformat="fasta";$count=0; \
   for $infile (@ARGV){$in=Bio::SeqIO->newFh(-file =>$infile, -format =>$informat); \
   $out=Bio::SeqIO->newFh(-format =>$outformat); \
   while(<$in>){print $out $_;$count++;}}' foo.gbk >foo.fsa

Arrays as Queues

use strict;
my @queue;
unshift(@queue,"Customer 1"); # @queue is now ("Customer 1")
unshift(@queue,"Customer 2"); # @queue is now ("Customer 2" "Customer 1")
unshift(@queue,"Customer 3");
          # @queue is now ("Customer 3" "Customer 2" "Customer 1")
my $item=pop(@queue);         # @queue is now ("Customer 3" "Customer 2")
print "Servicing $item\n";    # prints:  Servicing Customer 1\n
$item=pop(@queue);            # @queue is now ("Customer 3")
print "Servicing $item\n";    # prints:  Servicing Customer 2\n

use strict;
my @notAqueue;
unshift(@notAqueue,"Customer 0","Customer 1");
          # @queue is now ("Customer 0","Customer 1")
unshift(@notAqueue,"Customer 2");
          # @queue is now ("Customer 2","Customer 0","Customer 1")

Transpose matrix

Note: The following could be used to transpose a CSV file.

#!/bin/sh
# Example CSV file
# FROM:
#  a1,a2,a3
#  b1,b2,b3
# TO:
#  a1,b1
#  a2,b2
#  a3,b3

perl -e '$unequal=0;$_=<>;s/\r?\n//;@out_rows=split(/\,/, $_);\
$num_out_rows=$#out_rows+1;while(<>){s/\r?\n//;@F=split(/\,/,$_);\
foreach $i (0 .. $#F){$out_rows[$i] .="\,$F[$i]";}\
if($num_out_rows !=$#F+1){$unequal=1;}} END\
{foreach $row (@out_rows){print"$row\n"} \
warn "\nWARNING! Rows in input had different numbers of columns\n" \
if $unequal;warn "\nTransposed table: result has $. columns and $num_out_rows rows\n\n" }' $1

Perl and bioinformatics

Complement every base in the file foo.fsa:

perl -pe 'tr/ATCG/TAGC/' foo.fsa

Add first and fourth columns:

perl -ane 'print $F[0] + $F[3], "\n"' datafile

Only print lines 15 - 17:

perl -ne 'print if 15 .. 17' *.gff

Count lines:

perl -ne '$counter++;END{print "$counter lines";}' datafile

Split a multi-sequence FASTA file into individual files:

perl -ne 'BEGIN{$/=">";} if(/^\s*(\S+)/){open(F,">$1.fsa")||warn"$1 write failed:$!\n";chomp;print F ">",$_}'

Perl and MySQL

This section will just list a bunch of random examples. They are useful to give you an idea of what you can do with Perl, MySQL, and the CLI.

Note: These examples were taken from my course in Comparative Microbial Genomics at CBS (in Denmark).

mysql -B -e "update cmp_genomics.features set note='' where user=USER() and note not like 'tcs%' or note is null"
foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
   foreach type (ecf s54 s70)
     cat source/$accession.proteins.$type.sigmas.hmmsearch | \
     perl -ne 'next unless /^CDS_(\d+)\-(\d+)_DIR([\-\+]+)\s+([0-9\-\.e]+)\s+([0-9\-\.e]+)\s+/;\
        my($start,$stop,$dir,$score,$evalue)=($1,$2,$3,$4,$5);\
        next unless $score>0;\
        print "update cmp_genomics.features set note=\"Sigma Factor '$type'\" \
           where start=$start and stop=$stop and user=user() and accession=\"'$accession'\";\n";'\
     |mysql
   end
end

mysql -B -e "update cmp_genomics.features set note='' where user=USER() and note not like 'sigma%' or note is null"
foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
   foreach type (RRreciever HisKA_1 HisKA_2 HisKA_3 HWE_HK)
     cat source/$accession.$type.TCS.hmmsearch | \
     perl -ne 'next unless /^CDS_(\d+)\-(\d+)_DIR([\-\+]+)\s+([0-9\-\.e]+)\s+([0-9\-\.e]+)\s+/;\
        my($start,$stop,$dir,$score,$evalue)=($1,$2,$3,$4,$5);\
        next unless $score>0; \
        print "update cmp_genomics.features set note=\"TCS '$type'\" \
           where start=$start and stop=$stop and user=user() and accession=\"'$accession'\";\n";'\
     |mysql -B
   end
end

rm -f source/all.16s.fsa  # in case any exist (from previous runs)
foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
   mysql -B -N -D cmp_genomics -e "SELECT SUBSTR(seq,start,stop-start+1) AS sequence,\
     REPLACE(substring_index(genomes.organism,' ',4),' ','_') AS name,dir from genomes,features \
     WHERE genomes.accession=features.accession AND genomes.user=features.user AND \
     features.user=user() AND featuretype='rRNA' AND features.accession='$accession'" | \
   perl -ane '$F[0]=reverse($F[0]) if $F[2] eq "-";$F[0]=~tr/ATGC/TACG/ if $F[2] eq "-";\
     print ">$F[1]\n"; \
     for($x=0;$x<length($F[0]);$x=$x+60){print substr($F[0],$x,60),"\n";}last;' \
   >> source/all.16s.fsa
end
less source/all.16s.fsa

cat CP000034.codon-usage.aa.list \
| perl -ane 'next unless $F[1] =~ /^[A-Z]+/;print "\t$F[1]"; ' \
> aa.dat
mysql -B -N -e 'select accession,organism from cmp_genomics.genomes where user=USER()' \
> organism.names
foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
  cat $accession.codon-usage.aa.list \
  |perl -ane 'BEGIN{foreach(`cat organism.names`) \
       {chomp;@A=split(/\t+/,$_);$NAMES{$A[0]}=$A[1];}} \
       next unless $F[1]=~/^[A-Z]+/;$FREQ{$F[1]}=$F[3];push @AA,$F[1]; \
       END{print "\n";print "$NAMES{'$accession'}";foreach $aa(@AA){print "\t",$FREQ{$aa};}}' \
  >> aa.dat
end

mysql -e "delete from localization where user=USER() and type='signalp'" cmp_genomics
foreach accession (AE017042 AE016879 AL111168 AL645882 AP008232 AP009048 BA000021 CP000034)
  perl -ne 'if(/^CDS_(\d+)-(\d+)_DIR([+-])\s+0.\d+\s+\d+\s+[YN]\s+0.\d+\s+\d+\s+[YN]\s+[10].\d+\s+\d+\s+Y\s+[10].\d+\s+Y\s+[10].\s+\s+Y\s+CDS_\d+-\d+_DIR[+-]\s+Q\s+[10].\d+\s+[10]\s+Y\s+[10].\d+\s+Y/) \
     {print "INSERT INTO localization (user,protid,type) \
          SELECT USER() AS user, ft.id AS protid, \"signalp\" AS type \
          FROM features AS ft \
          WHERE ft.user=USER() AND \
          ft.accession=\"'$accession'\" AND \
          ft.start=$1 and ft.stop=$2 AND \
          ft.dir=\"$3\";\n";}' $accession.signalp \
  |mysql -D cmp_genomics
end

perl -e 'foreach $i(1..11){open IN,"col$i";while(<IN>){chomp;($a,$c)=split(/\t+/,$_);$DATA{$a}{$i}=$c;}close IN;} \
     END{foreach $a(reverse sort keys %DATA){foreach $i(1..11){$DATA{$a}{$i}=0 if $DATA{$a}{$i} eq "" and $i>1; \
     print $DATA{$a}{$i};print "\t" if $i<11;}print "\n";}}' \
> final.dat

R
postscript('final.ps')
source("/path/to/heatmap.R")
data<-as.matrix(read.table('final.dat',row.names=1,header=TRUE,sep="\t"))
pal<-maPalette(low=rgb(10,10,10,maxColorValue=10),
               high=rgb(0,0,10,maxColorValue=10),
               mid=rgb(5,5,10,maxColorValue=10),, k=1024)
par(oma=c(0,0,0,0.5))
data<-scale(data)
new_heatmap(data,cexCol=1,cexRow=1,colors=pal)
dev.off()
quit(save="no")

External links

Perl/Scripts

Contents

Edit a file from the CLI using Perl

Perl one-liners

The tr/// operator

Options

Average numbers

Misc

Arrays as Queues

Transpose matrix

Perl and bioinformatics

Perl and MySQL

External links

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Tools