Talk:Perl

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
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 ~/Ex3/source/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 ~/Ex3/source/$accession.codon-usage.aa.list \
  | perl -ane 'BEGIN { foreach (`cat organism.names`) \
                       {chomp; @A = split (/\t+/,$_);$NAMES{$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 ( "/home/people/kiil/Exercises/files/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")

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 ">", $_ }'

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

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")

External links

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