Bash oneliner to extract all ids from a multifasta file
#List of ids - one per line in allIds.txt $ awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa # You can play with this f=!l[$1 ] if wanted to extract or not extract the ids1535 days ago
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Install Python locally on shared Linux server !
#Install python to local directory #Firstly, I create a folder in my home directory, download the python source and extract it mkdir ~/python cd ~/python wget https://www....2095 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids = (); open FILE, $idsfile; while() { chomp; $ids{$_} += 1;...2092 days ago
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Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600 contigs.fasta > contigs-gt300-lte600.fasta my $minlen = shift...2062 days ago
To convert just one specific read group to fastq
..."" echo "Number of alignments with read group: GROUP-SRR1972919" samtools view -c -r GROUP-SRR1972919 all.bam # Reverting the process is to extract reads, tagged with readgroups...1539 days ago
Perl script to reads and extract webpage contents !
use 5.010; use strict; use warnings; use WWW::Mechanize; my ($url) = @ARGV; die "Usage: $0 URL\n" if not $url; my $w = WWW::Mechanize->new; $w->get($url); say $w->content; #Run #jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com1510 days ago
Pack a perl program with their dependencies on Ubuntu !
.../bioinformaticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents jit@jit-H...@jit.aber Explore taxdump files !By Jit 37 days ago extracttaxdumpreadmetaxonomyncbi...1508 days ago