Answers.Body: <p>You can give <a href="https://github.com/saketkc/pysradb" rel="nofollow noreferrer">pysradb</a> a shot.</p>
  <pre class="lang-bash prettyprint-override"><code>study_accession experiment_accession experiment_title                                                   experiment_desc              
                                        organism_taxid  organism_name           library_strategy library_source  library_selection library_layout sample_accession sample_title instrument           total_spots total_size  run_accession run_total_spots run_total_bases
  SRP178555       SRX5243234             GSM3560726: 97-gem-Day3-OEA115; Caenorhabditis elegans; RNA-Seq    GSM3560726: 97-gem-Day3-OEA115; Caenorhabditis elegans; RNA-Seq  6239            Caenorhabditis elegans  RNA-Seq          TRANSCRIPTOMIC  cDNA              SINGLE         SRS4245909                    Illumina HiSeq 2500  19052916     446793895  SRR8435699    19052916         971698716    
  SRP178555       SRX5243233             GSM3560725: 97-gem-Day3-OEA087; Caenorhabditis elegans; RNA-Seq    GSM3560725: 97-gem-Day3-OEA087; Caenorhabditis elegans; RNA-Seq  6239            Caenorhabditis elegans  RNA-Seq          TRANSCRIPTOMIC  cDNA              SINGLE         SRS4245908                    Illumina HiSeq 2500  18156224     428457264  SRR8435698    18156224         925967424 
  .. [truncated]
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-16T20:45:54.253Z
Answers.LastActivityDate: 2020-09-16T20:45:54.253Z
Answers.UserDisplayName: Saket Choudhary
Body: <p>I would like to extract all information about each <code>SAMPLE</code> after running the following query (run the query and add a <code>| grep SAMPLE</code> for clarification on what I mean by <code>SAMPLE</code>):</p>
  <p><code>esearch -db sra -query PRJNA514750 | efetch -format xml</code></p>
  <p>I tried the following:</p>
  <p><code>esearch -db sra -query PRJNA514750 | efetch -format xml | xtract -pattern EXPERIMENT -element SAMPLE</code></p>
  <p>but this returns nothing (PS: <code>SAMPLE</code>s are within an <code>EXPERIMENT</code> tag). I read in the <a href="https://www.ncbi.nlm.nih.gov/books/NBK25497/" rel="nofollow noreferrer">e-utilities guide</a> that <code>-pattern</code> will divide the data into rows, and <code>-element</code> into columns, so I'm presuming that this didn't work because <code>SAMPLE</code> has multiple tags within it. So I then tried:</p>
  <pre><code>esearch -db sra -query PRJNA514750 | efetch -format xml | xtract -pattern SAMPLE -element random_SAMPLE_tag
  </code></pre>
  <p>where <code>random_SAMPLE_tag</code> is any tag within <code>SAMPLE</code>.</p>
  <p>Here's a concrete example:</p>
  <pre><code>esearch -db sra -query PRJNA514750 | efetch -format xml | xtract -pattern SAMPLE -element TITLE
  </code></pre>
  <p>This works, but I want to get all the information about each <code>SAMPLE</code>, and I do not know beforehand what the tags within it are (I manually got <code>TITLE</code> in this case), and since I want to get this info for a quite a few studies, I can't manually check this.</p>
  
Tags: <phylogenetics><e-utilities>
Title: Extracting all information about a sample when using xtract from e-utilities
ThreadText: # Extracting all information about a sample when using xtract from e-utilities
  
  (Asked by: username_0 on 2020-08-06)
  
  I would like to extract all information about each `SAMPLE` after running the following query (run the query and add a `| grep SAMPLE` for clarification on what I mean by `SAMPLE`):
  
  `esearch -db sra -query PRJNA514750 | efetch -format xml`
  
  I tried the following:
  
  `esearch -db sra -query PRJNA514750 | efetch -format xml | xtract -pattern EXPERIMENT -element SAMPLE`
  
  but this returns nothing (PS: `SAMPLE`s are within an `EXPERIMENT` tag). I read in the [e-utilities guide](https://www.ncbi.nlm.nih.gov/books/NBK25497/) that `-pattern` will divide the data into rows, and `-element` into columns, so I'm presuming that this didn't work because `SAMPLE` has multiple tags within it. So I then tried:
  
  ```
  esearch -db sra -query PRJNA514750 | efetch -format xml | xtract -pattern SAMPLE -element random_SAMPLE_tag
  
  ```
  
  where `random_SAMPLE_tag` is any tag within `SAMPLE`.
  
  Here's a concrete example:
  
  ```
  esearch -db sra -query PRJNA514750 | efetch -format xml | xtract -pattern SAMPLE -element TITLE
  
  ```
  
  This works, but I want to get all the information about each `SAMPLE`, and I do not know beforehand what the tags within it are (I manually got `TITLE` in this case), and since I want to get this info for a quite a few studies, I can't manually check this.
  
  **Tags:** phylogenetics, e-utilities
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-09-16. Score: 1
  
  You can give [pysradb](https://github.com/saketkc/pysradb) a shot.
  
  ```bash
  study_accession experiment_accession experiment_title                                                   experiment_desc              
                                        organism_taxid  organism_name           library_strategy library_source  library_selection library_layout sample_accession sample_title instrument           total_spots total_size  run_accession run_total_spots run_total_bases
  SRP178555       SRX5243234             GSM3560726: 97-gem-Day3-OEA115; Caenorhabditis elegans; RNA-Seq    GSM3560726: 97-gem-Day3-OEA115; Caenorhabditis elegans; RNA-Seq  6239            Caenorhabditis elegans  RNA-Seq          TRANSCRIPTOMIC  cDNA              SINGLE         SRS4245909                    Illumina HiSeq 2500  19052916     446793895  SRR8435699    19052916         971698716    
  SRP178555       SRX5243233             GSM3560725: 97-gem-Day3-OEA087; Caenorhabditis elegans; RNA-Seq    GSM3560725: 97-gem-Day3-OEA087; Caenorhabditis elegans; RNA-Seq  6239            Caenorhabditis elegans  RNA-Seq          TRANSCRIPTOMIC  cDNA              SINGLE         SRS4245908                    Illumina HiSeq 2500  18156224     428457264  SRR8435698    18156224         925967424 
  .. [truncated]
  
  ```
  
  
  ---
  
  