Results for "Usage"
Bio-Scripts
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse comman...1099 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...if ( defined( $param{help} ) ) { print_usage(); exit(0); } if (...efined( $param{returnType} ) ) ) { print_usage(); exit(1); } $param...print $message; } } sub print_usage { print...2914 days ago
Blast result parser with Perl and Bioperl
...ady for import into a spreadsheet program for browsing and further analysis. # use strict; use warnings; use Bio::SearchIO; # Usage information die "Usage: $0 \n", if (@ARGV != 3);...2912 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
#!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n". " -h: help\n"....pt_m); use Bio::SeqIO; use Getopt::Std; getopts('hm:') || die "$usage\n"; die "$usage\n" if (defin...2912 days ago
- #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "
2912 days ago
- ...6156/ my $chr = shift; my $pos = shift; my $size = shift; my $usage = "Example: perl extract_seq_..."ERROR: You must pass three arguments: chr. num., position, and size.\n$usage"; } chomp $size; my...
2908 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biologica...8, Pg. 19 # Needleman-Wunsch global alignment algo (GOTHO 1982 mod) # usage statement die "usage: $0...2904 days ago
Count GC Content in nucleotide sequence with Perl
#!/usr/bin/perl -w ### Usage: get_gc_content.pl...--------------------- if ($#ARGV == -1) { usage(); exit; } $fasta_file...&process_it; close(IN); close(OUT); sub usage { $0 get_gc_content.pl...2904 days ago
Perl script to extract lines with matching ids !!
#!/usr/bin/perl use strict; use warnings; my %patterns; #USAGE: perl extactByIds.pl Idsfile1 file2 > Result # Open file and get patterns to search for open(my $fh2,"2873 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extractSeqbyID.pl LIST...2873 days ago
