Results for "format"
Bio-Scripts
Download genome using NCBI esearch command line !
..."CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI f...1095 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...1095 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 us...Bio::SeqIO->newFh('-file' => "$inFile" , '-format' => 'Fasta'); $out = Bio::Se...2910 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...%param = ( query => undef, outputFile => undef, database => undef, returnType => undef, maxRecords => undef, format => undef, verbose...2910 days ago
Blast result parser with Perl and Bioperl
...ysis. # use strict; use warnings; use Bio::SearchIO; # Usage information die "Usage: $0 \n", if...V; print "Parsing the BLAST result ..."; my $in = Bio::SearchIO->new(-format => 'blast', -file => $infile)...2908 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...('hm:') || die "$usage\n"; die "$usage\n" if (defined($opt_h)); my $format = "fasta"; my @seqArr = ();...$file = shift) { my $seqio_obj = Bio::SeqIO->new(-file => $file, -format => $format); while (my $...2908 days ago
Extract a range from genome file with perl.
...$end_pos = $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 $...2621 days ago
- ...ned($filter_length) || $filter_length !~ /\d+/; ### ### Get the length of each sequence: ### my $in = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta'); my @seq_lengths...
2698 days ago
- ...rl modules # DB_File and GD.pm, available from CPAN. # For usage information, run this program with the...ot against a second sequence with option -j. is a fasta format file from which the...
2687 days ago
Perl script to remove the duplicate sequences from multifasta file
...y $file = "myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqIO->new(-file => ">$file.uniq", -format => "fasta"); while(my $seq...2684 days ago
