Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2134 days ago
Perl script to extract sequence by Ids from multifasta file !
...my ($id) = $seq =~ /^>*(\S+)/; # parse ID as first word in FASTA header if (exists($ids{$id})) { $seq =~ s/^>*.+\n//; # remove FASTA header $seq =~ s/\n//g; #...2105 days ago
2084 days ago
Perl script to extract a sequence from multifasta with range !
...; { local $/=">"; while() { chomp; next unless /\w/; s/>$//gs; my @chunk = split /\n/; my $header = shift @chunk; my $...2075 days ago
2013 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1624 days ago
Installing ggplot2 and its dependencies on Ubuntu !
...essor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sy...1559 days ago
To convert just one specific read group to fastq
...e 2>> log.txt" # Merge all the BAM files into one. samtools merge -f all.bam bam/*.bam # Investigate the readgroups in the header. echo "" echo "SAM file header:" samtools view -H all.bam...1551 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ sudo apt install libpar-packer-perl Reading package lists......1520 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1005 days ago