Results for "omim genbank embl"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisai...yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text) seqs = seqs['genb...1193 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...'Fasta'); $out = Bio::SeqIO->newFh('-format' => 'Genbank'); print $out $_ while ;...2973 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cannot open $gb_report for reading: $!"; # Flag for multiline translation...2974 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...2973 days ago
Download the genome from NCBI using bash script/command
...enome # Look for genome assembly summary and extract the URL #...h.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t".../ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"...ov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"...2589 days ago
Download the gff files from NCBI using bash script/command
...e_gff # Look for genome assembly summary and extract the URL #...h.gov/genomes/refseq/fungi/assembly_summary.txt' | awk '{FS="\t".../ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"...ov/genomes/refseq/protozoa/assembly_summary.txt' | awk '{FS="\t"...2580 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2320 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options]...tps://www.uniprot.org/help/uniprotkb - UniProtKB/TrEMBL Aminoacid yes https...OG Profile - http://eggnog5.embl.de - dbCAN2 Pr...999 days ago
Bash command to explore assembly summary genbank !
wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt pip3 install csvkit csvcut -t -K 1 -c 'excluded_from_refseq' assembly_summary_genbank.txt \ | tail -n +2 | tr ";" "\n" \ | sed -e 's/^ //' -e 's/ $//' | grep -v '""' \ | sort | uniq -c | sort -nr825 days ago
