Results for "multiple fasta"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # ht...("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().spl...1131 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" /...-query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleo...-query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for ali...-q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequence...1096 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Outp...e.r-project.org #Parse command line arguments query_fasta=commandArgs(TRUE)[1] subject_fasta=commandArgs(TRUE)[2] fastANI_visual_file=commandArgs(TRU...1096 days ago
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $in...'-file' => "$inFile" , '-format' => 'Fasta'); $out = Bio::SeqIO->newFh(...2911 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::E...2911 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...l -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n". " -h: he...ce ? to the ambigous characters.\n" . "If multiple files are given, sequences...sage\n" if (defined($opt_h)); my $format = "fasta"; my @seqArr = (); @ARGV...2909 days ago
- #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "
2909 days ago
Count GC Content in nucleotide sequence with Perl
#!/usr/bin/perl -w ### Usage: get_gc_content.pl...if ($#ARGV == -1) { usage(); exit; } $fasta_file = $ARGV[0]; $out_file = "gc_out.txt"; unless ( open(IN, "$fasta_file") ) { print "Go...2900 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::...m); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extra..."\n>"; open OUT, ">$out" or die; open FILE, "$fasta" or die; while () { tri...2870 days ago
- #USAGE: CI_normal(matrix[,c(x:y)],97.5) - multiple column from a normal distribution #USAGE: CI_tdist(matrix[,c(x:y)],97.5) - multi...
2866 days ago
