Extracting all information about a sample when using xtract from e-utilities

Question

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: SAMPLEs are within an EXPERIMENT tag). I read in the e-utilities guide 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.

Answer 1

You can give pysradb a shot.

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]