Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna1005 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring...1005 days ago
1005 days ago
Perl onliner to check the ids in two files !
perl -lane 'BEGIN{open(A,"ids2.txt"); while(){chomp; $k{$_}++}} if (defined($k{$F[0]})) {print "$_\t$F[0]\t1"} else {print "$_\tNA\t0"}; ' ids1.txt > aaa.xls982 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$...########################################## | 100% perl-xml-parser-2.44 | 165 KB |...########################################## | 100% perl-gd-2.68 | 112 KB |...978 days ago
Perl script to rename the fasta file !
#Script #1 #!/usr/bin/perl -w use strict; #USAGE #perl extractPattern.pl kmerfasta > uniref100_result_broad my %kHash; local $/ = '>'; my $infile2 = "$ARGV[0]"; # Kmer fasta open( FH2, '913 days ago
Extract all fasta sequences except ids !
awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' genomic.fna > filtered_without_omi...9.fa out=omi_kmer19_formated.fa fastawrap=19 #Extract and number the kmers perl storeKmer.pl omi_kmer19_forma...883 days ago
bash script to extract sequence by ids !
Use a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input: cat > in.fasta BGI_novel_T016313 Solyc03g025570.2.1 TTCAAG...878 days ago
878 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.html870 days ago