882 days ago
Commands to get the detail of disk usage on Linux !
#A simplistic approach would be du -shc /home/* du -shc /home/jnarayan #To sort it: du -smc /home/* | sort -n #There is also a wellknown Perl script that has the option of mailing disk usage reports per user: durep http://www.ubuntugeek.com/create-disk-usage-reports-with-durep.html831 days ago
Command line to print disk usage on Linux terminal !
#Print disk usage - perl du -h |perl -e'%h=map{/.\s/;99**(ord$&&7)-$`,$_}`du -h`;die@h{sort%h}' #Bash du -k * | sort -nr | cut -f2 | xargs -d '\n' du -sh #Base du -scBM | sort -n #More du -s * | sort -rn | cut -f2- | xargs -d "\n" du -sh830 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr783 days ago
Identify genome-wide synteny with LASTZ alignment
....chain.filter AAChr1.txt FFChr1.txt chr1.chain.filter.tnet.synnet.axt axtSort chr1.chain.filter.tnet.synnet.axt chr1.chain.filter.tnet.synnet.Sort.axt axtToMaf chr1.chain.filte...532 days ago
Perl script to parse VCF file !
...mosome_counts; for my $entry (@vcf_entries) { $chromosome_counts{$entry->{CHROM}}++; } print "Chromosome counts:\n"; for my $chromosome (sort keys %chromosome_counts) {...109 days ago
Perl script to parse blast results and plot basic stats !
#!/usr/bin/perl use strict; use warnings; use List::Util qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./parse_blast.pl blast_result.txt\n...109 days ago
Perl script to calculate the basic stats of the assembled genome !
...ength = $seq->length; $total_length += $length; $num_contigs++; push @contig_lengths, $length; } # Sort contig lengths in descending order @contig_lengths = sort { $b $a } @contig_lengths;...109 days ago
Python script for basic stats of the assembled genome !
...length = len(record.seq) total_length += length num_contigs += 1 contig_lengths.append(length) # Sort contig lengths in descending order contig_lengths.sort(reverse=True) # Calculate...109 days ago