Answers.Body: <p>As suggested by somebody, the datasets tools from NCBI  is blazing fast:</p>
  <pre><code>datasets download genome taxon 187492  --include protein
  </code></pre>
  <p><a href="https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/" rel="nofollow noreferrer">NCBI Datasets Tool</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-03T17:58:51.313Z
Answers.Text: Thanks for sharing this, its really useful.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-03T22:41:28.373Z
Answers.Text: If you do get chance @TheAugust please mark your answer as "accepted" (helps with site stats). I recommend upvoting the answer because its efficiency allows local blast (and other methods) to interrogate data when remote NCBI blast is inefficient. NCBI servers do have a restricted access policy for some of their services.
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-03T16:46:23.990Z
Answers.LastActivityDate: 2023-11-03T16:46:23.990Z
Answers.UserDisplayName: The August
Body: <p>I'm trying to get ALL Proteins for a Taxonomic ID from Entrez using Esearch/Efetch and the following command:</p>
  <pre><code>esearch -db &quot;protein&quot; -query &quot;txid374666[Organism]&quot; | efetch -format fasta &gt; txid_374666.fasta
  </code></pre>
  <p>Can somebody tell if this command will get ALL proteins or not? Besides, this appears to be a bit slow.</p>
  <p>Can somebody point out any Biopython workflow, particularly how to get ALL Proteins</p>
  <p>Thanks</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-01T15:38:28.907Z
Comments.Text: That would work - except for the precise search term used. The issue is the NCBI server may time out, certainly if this was Blast it would do. Doing a single command line would prevent checking. Personally I would use a script to check what was downloaded with the `esearch` output (which will certainly work). If I get chance I will provide a full answer, e.g. search term stuff.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-01T16:06:57.823Z
Comments.Text: Thanks for your response. I'll await your answer
Comments.UserDisplayName: The August
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-01T16:30:16.543Z
Comments.Text: I've to download a huge lot of sequences for hundreds of bacterial genus (not species)  for a metaproteomics study. Which method will work best for me? esearch/efetch, python scripting , anything else?
Comments.UserDisplayName: The August
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-01T16:44:10.323Z
Comments.Text: If I've time I will answer in detail about how I'd do this. In general further details would help (even if not me answering), i.e. how many different species are needed? This sounds like a script more than a one liner.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-01T17:35:19.747Z
Comments.Text: Around 700 genus are there, and under each jenus on an average 3 species. I'm trying to download using esearch/efetch . I belong to University, where I've good internet speed , yet, the link is breaking very often
Comments.UserDisplayName: The August
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-03T08:16:40.813Z
Comments.Text: Hi there, not sure if it can help but I asked a similar question some times ago here : https://stackoverflow.com/questions/74727918/handle-500-server-error-type-during-api-request-using-rentrez/75055203#75055203. I am using R however. General idea was that it was taking too long so I had to deal with server errors using a try/catch/sleep function.
Comments.UserDisplayName: Paul Endymion
Tags: <sequence><entrez><biopython><efetch>
Title: Getting ALL Protein entries from Entrez for a particular taxonomic id
ThreadText: # Getting ALL Protein entries from Entrez for a particular taxonomic id
  
  (Asked by: username_0 on 2023-11-01)
  
  I'm trying to get ALL Proteins for a Taxonomic ID from Entrez using Esearch/Efetch and the following command:
  
  ```
  esearch -db "protein" -query "txid374666[Organism]" | efetch -format fasta > txid_374666.fasta
  
  ```
  
  Can somebody tell if this command will get ALL proteins or not? Besides, this appears to be a bit slow.
  
  Can somebody point out any Biopython workflow, particularly how to get ALL Proteins
  
  Thanks
  
  **Tags:** sequence, entrez, biopython, efetch
  
  > **Comments:**
  > **username_1**: That would work - except for the precise search term used. The issue is the NCBI server may time out, certainly if this was Blast it would do. Doing a single command line would prevent checking. Personally I would use a script to check what was downloaded with the `esearch` output (which will certainly work). If I get chance I will provide a full answer, e.g. search term stuff.  
  > **username_0**: Thanks for your response. I'll await your answer  
  > **username_0**: I've to download a huge lot of sequences for hundreds of bacterial genus (not species)  for a metaproteomics study. Which method will work best for me? esearch/efetch, python scripting , anything else?  
  > **username_1**: If I've time I will answer in detail about how I'd do this. In general further details would help (even if not me answering), i.e. how many different species are needed? This sounds like a script more than a one liner.  
  > **username_0**: Around 700 genus are there, and under each jenus on an average 3 species. I'm trying to download using esearch/efetch . I belong to University, where I've good internet speed , yet, the link is breaking very often  
  > **username_2**: Hi there, not sure if it can help but I asked a similar question some times ago here : https://stackoverflow.com/questions/74727918/handle-500-server-error-type-during-api-request-using-rentrez/75055203#75055203. I am using R however. General idea was that it was taking too long so I had to deal with server errors using a try/catch/sleep function.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2023-11-03. Score: 3 | Accepted answer
  
  As suggested by somebody, the datasets tools from NCBI is blazing fast:
  
  ```
  datasets download genome taxon 187492  --include protein
  
  ```
  
  [NCBI Datasets Tool](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/)
  
  > **Comments:**
  > **username_1**: Thanks for sharing this, its really useful.  
  > **username_1**: If you do get chance @username_0 please mark your answer as "accepted" (helps with site stats). I recommend upvoting the answer because its efficiency allows local blast (and other methods) to interrogate data when remote NCBI blast is inefficient. NCBI servers do have a restricted access policy for some of their services.  
  
  ---
  
  