Calculate some statistics for a DNA alignment with Perl
...ormat => 'fasta', -file => 't/data/nei_gojobori_test.aln'); my $alnobj = $in->next_aln; my ($seq1id,$seq2id) = map { $_->display_id } $alnobj->e...2702 days ago
Check overlapping range with Perl
#!/usr/bin/perl use strict; use warnings; my @ranges = 0; push @ranges, $ranges[-1] + 1 + int rand 200 for 1..10000; my @tests = map int rand $ranges[-1], 0..1000000; matc...2680 days ago
Genetic Algorithms demonstration with word DNA in Perl
...y: select only survivors from the population, # then use map to have only the fitness come through my @weights = map { $_->{fitness} } grep { $_->...($_) > 1 && length($_) < $max_entry_length } map { uc } @dictionary; # bui...2425 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # User need to set the reference multifasta file name he...2193 days ago
Perl subroutine to read genome/reads fasta file !
...ub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) o...>/){ if(defined $id && defined $seq){ $map{$id} = $seq; $seq="";.../; } else { $seq=$seq.$_; } } $map{$id} = $seq; close(IN); r...2186 days ago
Long reads mapper bash script !
.../bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.f.../anaconda3/bin/samtools graphMapLoc=/home/urbe/Tools/graphmap/...ovided" echo "#USAGE: runMapper.sh minimap2 ref.fa reads.f...fi elif [ $toolName == "minimap2" ]; then echo "Mapping w...2176 days ago
Perl script to create a consensus of nucleotide sequences !
...T=>[], C=>[], G=>[] ); s/\s//g for @mi; my ($w) = sort {$b $a} map {length} @mi; # set w to t.... my %h = ( a=>0, t=>0, c=>0, g=>0 ); my @mi_letters = map { [split '', uc $_] } @mi;...2085 days ago
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