Results for "long-read-based"
Bio-Scripts
# To follow these instructions, we'll assume your system admins have already installed these essentials: # Debian/Ubuntu system admins should run: sudo apt-get install -y...2172 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import req...1164 days ago
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 #Pa...1129 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $myDir = "/home/anjana/seqs"; # Output d...
2943 days ago
Read lines from input file – print lines that match a regular expression
#!/usr/bin/perl use strict; use warnings; my $line; #read the line-by-line for each line ask if it matches the regex print it if it matches while($line = ){...2944 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::Escape...2943 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needleman-Wuns...2933 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 $fh2,"2902 days ago
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2899 days ago
Perl subroutine to read and write files
# Input output (InOut) the file # usage: # @array = InOut('read',$file) # $string = InOut('read',$file) # InOut('write',$file,\$string) # InOut('write',$file,\@array)...2893 days ago
