Results for "read depth"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has m...dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read(...1120 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPl...gs(TRUE)[2] fastANI_visual_file=commandArgs(TRUE)[3] library(genoPlotR) #Read...1085 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every seque...t"; # Go to sequence directory and open it (i.e, read contents) chdir($myDir) || d...: $!"; # Open $myDir foreach $seqFile (sort readd...
2900 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 = ){ chomp...2901 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See:...fixed MATCH and MISMATCH scores we will use values read from BLOSUM50) my $MATCH...any gap my %BLOSUM50 = (); my @aalist = (); # read...2890 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 $fh2,"2859 days ago
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2856 days ago
Perl subroutine to read and write files
# Input output (InOut) the file # usage: # @array = InOut('read',$file) # $string = InOut('read',$file) # InOut('write',$file,\$string) # InOut('write',$file...ing); sub InOut { my($bit,$file,$data) = @_; if($bit eq 'read'...2850 days ago
- #!/usr/local/bin/perl -w # NOTE: YOU MUST CHANGE THE LINE ABOVE TO POINT TO # THE FU...r sequence. This database is not human-readable, and can get...j, $k, $key) = (0, 0, 0, ""); $seq = ""; #Read...
2677 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2601 days ago
