Results for "GenBank"
Bio-Scripts
Python script to download covid genome !
...to sign up import requests import yaml seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text) seqs = seqs['genbank-sequences'] print("got %d se...1128 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...'-format' => 'Fasta'); $out = Bio::SeqIO->newFh('-format' => 'Genbank'); print $out $_ while ;...2908 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; 1 means transla...2909 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::Es...2908 days ago
Download the genome from NCBI using bash script/command
...i.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_fungi # -for bacteria curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt...2524 days ago
Download the gff files from NCBI using bash script/command
...i.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_fungi # -for bacteria curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt...2515 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_file2255 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 -nr760 days ago
