Results for "Fasta"
Bio-Scripts
Python script to download covid genome !
...x['gene-region'] == "complete": nm = x['accession'] print("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().spl...1127 days ago
Download genome using NCBI esearch command line !
...cleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for ali...fastANI -q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequence...1092 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...1092 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 u...>newFh('-file' => "$inFile" , '-format' => 'Fasta'); $out = Bio::SeqIO->newFh(...2907 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...2907 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
#!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n". " -h: help\n"....die "$usage\n"; die "$usage\n" if (defined($opt_h)); my $format = "fasta"; my @seqArr = (); @ARGV...2905 days ago
- #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "
2905 days ago
Count GC Content in nucleotide sequence with Perl
...-------------------- if ($#ARGV == -1) { usage(); exit; } $fasta_file = $ARGV[0]; $out_file = "gc_out.txt"; unless ( open(IN, "$fasta_file") ) { print "Go...2897 days ago
Perl script to extract fasta sequence by matching name/ids !!
...se Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta $ARGV[2] or die "use extra...close LINE; $/ = "\n>"; open OUT, ">$out" or die; open FILE, "$fasta" or die; while () { tri...2866 days ago
Extract a range from genome file with perl.
...$ARGV[2]; my $in = Bio::SeqIO->new ( -file => $in_file, -format => 'fasta'); my $out = Bio::SeqIO->new( -file => ">$in_file.out", -format => 'fasta'); while (my $seq = $in-...2618 days ago
