As you have several sequences to download, I think it will be quite easy to add this command into a little bash script to process all of them. For this, you can use Entrez Direct as mentioned by dc Why not always use Entrez Direct? While it is fine for a small number of sequences, it can be slow to download a large number of sequences. Entrez Direct by default will download uncompressed data so you will end up spending more time downloading a larger file instead of downloading a smaller, compressed file from FTP more quickly.
If you were to use Entrez Direct for this purpose, I'd not bother with a bash script and use epost to first post the entire list of accessions and then pipe it to efetch as shown below:. You can also get this link directly, by using Chrome's developer tools F12 , viewing the Network tab, then loading the page in 1.
Sorry, I can't post a comment with my reputation score. However, your command is downloading all sequences from the input file into a single fasta file.
I believe that if you have a big bunch of sequences, it could be a little bit tricky after to manipulate that kind of file. Just by curiosity, do you have a trick to create one sequence per file using efetch? Sign up to join this community. The best answers are voted up and rise to the top. Stack Overflow for Teams — Collaborate and share knowledge with a private group. Create a free Team What is Teams? Learn more.
This script lets you find out what TaxIDs to pass to ngd , and will write a simple one-item-per-linefile to pass in to it. It utilises the ete3 toolkit, so refer to their site to install the dependencyif it's not already satisfied. You can query the database using a particular TaxID, or a scientific name. The primary function of thescript is to return all the child taxa of the specified parent taxa. The script has various optionsfor what information is written in the output.
On first use, a small sqlite database will be created in your home directoryby default change the location with the --database flag. You can update this databaseby using the --update flag. Note that if the database is not in your home directory,you must specify it with --database or a new database will be created in your homedirectory.
Fasta Sequence Example Ncbi Previous post. How to download gene sequence from NCBI? This post will show you how to create a FASTA file for submitting single- and multiple-nucleotide sequences. So this is a set of scripts that focuses on the actual genome downloading. Usage To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following: Downloading multiple groups is also possible: If you're on a reasonably fast connection, you might want to try running multiple downloads in parallel: To download all fungal GenBank genomes from NCBI in GenBank format, run: To download all viral RefSeq genomes in FASTA format, run: It is possible to download multiple formats by supplying a list of formats or simply download all formats: Ncbi To download only completed bacterial RefSeq genomes in GenBank format, run: It is possible to download multiple assembly levels at once by supplying a list: To download only bacterial reference genomes from RefSeq in GenBank format, run: To download bacterial RefSeq genomes of the genus Streptomyces , run: Note : This is a simple string match on the organism name provided by NCBI only.
You can also use this with a slight trick to download genomes of a certain species as well: Note : The quotes are important. Multiple genera is also possible: You can also put genus names into a file, one organism per line, e.
This can be handy if you need to matcha value in the middle of the NCBI organism name, like so: Note : The above command will download all bacterial genomes containing 'coelicolor' anywhere in theirorganism name from RefSeq.
It is also possible to download multiple species taxids or taxids by supplying the numbers in a comma-separated list: Note : The above command will download the reference genomes for cat and human. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown. The Overflow Blog.
Podcast Who is building clouds for the independent developer? Exploding turkeys and how not to thaw your frozen bird: Top turkey questions Featured on Meta. Now live: A fully responsive profile. Reducing the weight of our footer. Related Hot Network Questions. Question feed. Stack Overflow works best with JavaScript enabled.
Accept all cookies Customize settings.
0コメント