Quickstart

Most features in pysradb are accessible both from the command-line and as a python package. pysradb usage on the two platforms will be displayed by selecting the corresponding tab below.

::: note ::: title Note :::

If you have any questions along the way, please head over to the python-api-usage{.interpreted-text role=”doc”} or the cmdline{.interpreted-text role=”doc”} for more information. You may also wish to refer to the commands{.interpreted-text role=”doc”} :::

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Notebooks

A Google Colaboratory version of most used commands are available in this Colab Notebook . Colab runs Python 3.6 while pysradb requires Python 3.7+ and hence the notebooks no longer run on Colab, but can be downloaded and run locally.

The following notebooks document all the possible features of pysradb:

1. Python API

2. Downloading datasets from SRA - command line

3. Parallely download multiple datasets - Python API

4. Converting SRA-to-fastq - command line (requires conda)

5. Downloading subsets of a project - Python API

6. Download BAMs

7. Metadata for multiple SRPs

8. Multithreaded fastq downloads using Aspera Client

9. Searching SRA/GEO/ENA

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Metadata

pysradb makes it very easy to obtain metadata from SRA/EBI:

::: tabbed Console

$ pysradb metadata SRP265425

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
df = db.metadata("SRP265425")
df

:::

Output: :

study_accession experiment_accession    experiment_title    experiment_desc organism_taxid  organism_name   library_name    library_strategy    library_source  library_selection   library_layout  sample_accession    sample_title    instrument  instrument_model    instrument_model_desc   total_spots total_size  run_accession   run_total_spots run_total_bases
SRP265425   SRX8434255  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 63-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745319      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1311358 83306910    SRR11886735 1311358 109594216
SRP265425   SRX8434254  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 62-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745320      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 2614109 204278682   SRR11886736 2614109 262305651
SRP265425   SRX8434253  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 61-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745318      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 2286312 183516004   SRR11886737 2286312 263304134
SRP265425   SRX8434252  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 60-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745317      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 5202567 507524965   SRR11886738 5202567 781291588
SRP265425   SRX8434251  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 38-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745315      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 3313960 356104406   SRR11886739 3313960 612430817
SRP265425   SRX8434250  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 37-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745316      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 5155733 565882351   SRR11886740 5155733 954342917
SRP265425   SRX8434249  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 36-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745313      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1324589 175619046   SRR11886741 1324589 216531400
SRP265425   SRX8434248  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 35-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745314      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1639851 198973268   SRR11886742 1639851 245466005
SRP265425   SRX8434247  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 68-2020-05-07   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745312      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 3921389 210198580   SRR11886743 3921389 332935558
SRP265425   SRX8434246  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 66-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745311      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 14295475    2150005008  SRR11886744 14295475    2967829315
SRP265425   SRX8434245  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 65-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745310      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 5124692 294846140   SRR11886745 5124692 431819462
SRP265425   SRX8434244  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 64-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745309      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 2986306 205666872   SRR11886746 2986306 275400959
SRP265425   SRX8434243  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 34-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745308      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1182690 59471336    SRR11886747 1182690 86350631
SRP265425   SRX8434242  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 33-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745307      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 6031816 749323230   SRR11886748 6031816 928054297

Additionally to obtain locations of .fastq/.sra files and other metadata:

pysradb makes it very easy to obtain metadata from SRA/EBI:

::: tabbed Console

$ pysradb metadata SRP265425 --detailed

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
df = db.metadata("SRP265425", detailed=True)
df

:::

Output: :

run_accession   study_accession experiment_accession    experiment_title    experiment_desc organism_taxid  organism_name   library_name    library_strategy    library_source  library_selection   library_layout  sample_accession    sample_title    instrument  instrument_model    instrument_model_desc   total_spots total_size  run_total_spots run_total_bases run_alias   sra_url_alt1    sra_url_alt2    sra_url experiment_alias    isolate collected_by    collection_date geo_loc_name    host    host_disease    isolation_source    lat_lon BioSampleModel  sra_url_alt3    ena_fastq_http  ena_fastq_http_1    ena_fastq_http_2    ena_fastq_ftp   ena_fastq_ftp_1 ena_fastq_ftp_2
SRR11886735 SRP265425   SRX8434255  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 63-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745319      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1311358 83306910    1311358 109594216   IonXpress_063_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam  gs://sra-pub-src-9/SRR11886735/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886735/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   https://sra-download.ncbi.nlm.nih.gov/traces/sra0/SRR/011608/SRR11886735        GC-20   NA  02-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/035/SRR11886735/SRR11886735.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/035/SRR11886735/SRR11886735.fastq.gz
SRR11886736 SRP265425   SRX8434254  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 62-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745320      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 2614109 204278682   2614109 262305651   IonXpress_062_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam  gs://sra-pub-src-16/SRR11886736/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-download.ncbi.nlm.nih.gov/traces/sra46/SRZ/011886/SRR11886736/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta  https://sra-download.ncbi.nlm.nih.gov/traces/sra50/SRR/011608/SRR11886736       GC-51   NA  14-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886736/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/036/SRR11886736/SRR11886736.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/036/SRR11886736/SRR11886736.fastq.gz
SRR11886737 SRP265425   SRX8434253  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 61-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745318      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 2286312 183516004   2286312 263304134   IonXpress_061_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam  gs://sra-pub-src-16/SRR11886737/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-download.ncbi.nlm.nih.gov/traces/sra29/SRZ/011886/SRR11886737/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta  https://sra-download.ncbi.nlm.nih.gov/traces/sra17/SRR/011608/SRR11886737       GC-24   NA  07-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886737/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/037/SRR11886737/SRR11886737.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/037/SRR11886737/SRR11886737.fastq.gz
SRR11886738 SRP265425   SRX8434252  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 60-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745317      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 5202567 507524965   5202567 781291588   IonXpress_060_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam  gs://sra-pub-src-15/SRR11886738/IonXpress_060_R_2020_04_22_15_56_22_user_GCEID_S5_58_SARS_CoV2_SA4.bam.1    https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRZ/011886/SRR11886738/IonXpress_060_R_2020_04_22_15_56_22_user_GCEID_S5_58_SARS_CoV2_SA4.bam    https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRR/011608/SRR11886738       GC-23   NA  08-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886738/IonXpress_060_R_2020_04_22_15_56_22_user_GCEID_S5_58_SARS_CoV2_SA4.bam.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/038/SRR11886738/SRR11886738.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/038/SRR11886738/SRR11886738.fastq.gz
SRR11886739 SRP265425   SRX8434251  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 38-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745315      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 3313960 356104406   3313960 612430817   IonXpress_038_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam  gs://sra-pub-src-13/SRR11886739/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886739/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   https://sra-download.ncbi.nlm.nih.gov/traces/sra24/SRR/011608/SRR11886739       GC-11b  NA  24-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/039/SRR11886739/SRR11886739.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/039/SRR11886739/SRR11886739.fastq.gz
SRR11886740 SRP265425   SRX8434250  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 37-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745316      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 5155733 565882351   5155733 954342917   IonXpress_037_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam  gs://sra-pub-src-5/SRR11886740/IonXpress_037_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886740/IonXpress_037_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/011608/SRR11886740       GC-14b  NA  28-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/040/SRR11886740/SRR11886740.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/040/SRR11886740/SRR11886740.fastq.gz
SRR11886741 SRP265425   SRX8434249  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 36-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745313      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1324589 175619046   1324589 216531400   IonXpress_036_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam  gs://sra-pub-src-11/SRR11886741/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886741/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   https://sra-download.ncbi.nlm.nih.gov/traces/sra57/SRR/011608/SRR11886741       GC-12   NA  24-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/041/SRR11886741/SRR11886741.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/041/SRR11886741/SRR11886741.fastq.gz
SRR11886742 SRP265425   SRX8434248  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 35-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745314      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1639851 198973268   1639851 245466005   IonXpress_035_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam  gs://sra-pub-src-11/SRR11886742/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886742/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRR/011608/SRR11886742       GC-13   NA  23-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/042/SRR11886742/SRR11886742.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/042/SRR11886742/SRR11886742.fastq.gz
SRR11886743 SRP265425   SRX8434247  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 68-2020-05-07   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745312      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 3921389 210198580   3921389 332935558   IonXpress_068_R_2020_05_07_11_47_51_user_GCEID-S5-60-SARS_CoV2_SA4.bam  gs://sra-pub-src-17/SRR11886743/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRZ/011886/SRR11886743/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta  https://sra-download.ncbi.nlm.nih.gov/traces/sra54/SRR/011608/SRR11886743       GC-55   NA  24-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886743/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/043/SRR11886743/SRR11886743.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/043/SRR11886743/SRR11886743.fastq.gz
SRR11886744 SRP265425   SRX8434246  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 66-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745311      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 14295475    2150005008  14295475    2967829315  IonXpress_066_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.fastq    gs://sra-pub-src-11/SRR11886744/IonXpress_066_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.fastq.1  https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886744/IonXpress_066_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.fastq.1   https://sra-download.ncbi.nlm.nih.gov/traces/sra20/SRR/011608/SRR11886744       GC-26   NA  07-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/044/SRR11886744/SRR11886744.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/044/SRR11886744/SRR11886744.fastq.gz
SRR11886745 SRP265425   SRX8434245  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 65-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745310      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 5124692 294846140   5124692 431819462   IonXpress_065_R_2020_04_22_11_10_56_user_GCEID-S5-57-SARS_CoV2_SA4.bam  gs://sra-pub-src-16/SRR11886745/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-download.ncbi.nlm.nih.gov/traces/sra69/SRZ/011886/SRR11886745/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta  https://sra-download.ncbi.nlm.nih.gov/traces/sra19/SRR/011608/SRR11886745       GC-25   NA  10-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886745/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/045/SRR11886745/SRR11886745.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/045/SRR11886745/SRR11886745.fastq.gz
SRR11886746 SRP265425   SRX8434244  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 64-2020-04-22   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745309      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 2986306 205666872   2986306 275400959   IonXpress_064_R_2020_04_22_15_56_22_user_GCEID-S5-58-SARS_CoV2_SA4.bam  gs://sra-pub-src-17/SRR11886746/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-download.ncbi.nlm.nih.gov/traces/sra59/SRZ/011886/SRR11886746/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta  https://sra-download.ncbi.nlm.nih.gov/traces/sra47/SRR/011608/SRR11886746       GC-21   NA  03-Apr-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886746/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/046/SRR11886746/SRR11886746.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/046/SRR11886746/SRR11886746.fastq.gz
SRR11886747 SRP265425   SRX8434243  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 34-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745308      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 1182690 59471336    1182690 86350631    IonXpress_034_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam  gs://sra-pub-src-16/SRR11886747/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1  https://sra-download.ncbi.nlm.nih.gov/traces/sra77/SRZ/011886/SRR11886747/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta  https://sra-download.ncbi.nlm.nih.gov/traces/sra13/SRR/011608/SRR11886747       GC-11a  NA  24-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886747/Wuhan_Hu_1_NC_045512_21500_and_subgenomics_SA4.fasta.1   http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/047/SRR11886747/SRR11886747.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/047/SRR11886747/SRR11886747.fastq.gz
SRR11886748 SRP265425   SRX8434242  Ampliseq of SARS-CoV-2  Ampliseq of SARS-CoV-2  2697049 Severe acute respiratory syndrome coronavirus 2 33-2020-04-03   AMPLICON    VIRAL RNA   RT-PCR  SINGLE  SRS6745307      Ion Torrent S5 XL   Ion Torrent S5 XL   ION_TORRENT 6031816 749323230   6031816 928054297   IonXpress_033_R_2020_04_03_10_09_05_user_GCEID-S5-55-SARS_CoV2_SA4.bam  gs://sra-pub-src-15/SRR11886748/IonXpress_033_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1    https://sra-download.ncbi.nlm.nih.gov/traces/sra43/SRZ/011886/SRR11886748/IonXpress_033_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam    https://sra-download.ncbi.nlm.nih.gov/traces/sra66/SRR/011608/SRR11886748       GC-14a  NA  28-Mar-2020 Australia: Victoria Homo sapiens    COVID-19    swab    NA  Pathogen.cl https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR11886748/IonXpress_033_R_2020_04_03_10_09_05_user_GCEID_S5_55_SARS_CoV2_SA4.bam.1 http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR118/048/SRR11886748/SRR11886748.fastq.gz         era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR118/048/SRR11886748/SRR11886748.fastq.gz

Converting between accession numbers

pysradb provides a suite of commands for interoperability between conversion numbers.

Convert SRP to SRX

::: tabbed Console

$ pysradb srp-to-srx SRP098789

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
df = db.srp-to-srx("SRP098789")
df

:::

Output: :

study_accession experiment_accession    experiment_title        experiment_desc organism_taxid  organism_name   library_strategy        library_source  library_selection       sample_accession        sample_title    instrument      total_spots     total_size      run_accession   run_total_spots run_total_bases study_accesssion
SRP098789       SRX2536428      GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Homo sapiens; RNA-Seq       GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Homo sapiens; RNA-Seq       9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956378      Illumina HiSeq 2500     69422931        1545681856      SRR5227313      69422931        3540569481      SRP098789
SRP098789       SRX2536427      GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-seq; Homo sapiens; OTHER   GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-seq; Homo sapiens; OTHER   9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956377      Illumina HiSeq 2500     58065134        1302369810      SRR5227312      58065134        2961321834      SRP098789
SRP098789       SRX2536426      GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Homo sapiens; RNA-Seq       GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Homo sapiens; RNA-Seq       9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956376      Illumina HiSeq 2500     63720205        1416818619      SRR5227311      63720205        3249730455      SRP098789
SRP098789       SRX2536425      GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-seq; Homo sapiens; OTHER   GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-seq; Homo sapiens; OTHER   9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956375      Illumina HiSeq 2500     66363585        1482728577      SRR5227310      66363585        3384542835      SRP098789
SRP098789       SRX2536424      GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; Homo sapiens; RNA-Seq      GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; Homo sapiens; RNA-Seq      9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956374      Illumina HiSeq 2500     40062613        904488287       SRR5227309      40062613        2043193263      SRP098789
SRP098789       SRX2536423      GSM2476017: 1.5 ?M PF-067446846, 60 min, rep 5 -riboseq; Homo sapiens; OTHER    GSM2476017: 1.5 ?M PF-067446846, 60 min, rep 5 -riboseq; Homo sapiens; OTHER    9606    Homo sapiens    OTHER   TRANSCRIPTOMIC other    SRS1956373      Illumina HiSeq 2500     65591217        1499668100      SRR5227308      65591217        3345152067      SRP098789
SRP098789       SRX2536422      GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; Homo sapiens; RNA-Seq      GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; Homo sapiens; RNA-Seq      9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956372      Illumina HiSeq 2500     66480991        1564636133      SRR5227307      66480991        3390530541      SRP098789
SRP098789       SRX2536421      GSM2476015: 1.5 ?M PF-067446846, 60 min, rep 4 -riboseq; Homo sapiens; OTHER    GSM2476015: 1.5 ?M PF-067446846, 60 min, rep 4 -riboseq; Homo sapiens; OTHER    9606    Homo sapiens    OTHER   TRANSCRIPTOMIC other    SRS1956371      Illumina HiSeq 2500     57588015        1357395400      SRR5227306      57588015        2936988765      SRP098789
SRP098789       SRX2536420      GSM2476014: vehicle, 60 min rep 3; Homo sapiens; OTHER  GSM2476014: vehicle, 60 min rep 3; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956370      Illumina HiSeq 2000    48405034 1530784033      SRR5227305      48405034        2420251700      SRP098789
SRP098789       SRX2536419      GSM2476013: vehicle, 60 min rep 2; Homo sapiens; OTHER  GSM2476013: vehicle, 60 min rep 2; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956369      Illumina HiSeq 2000    47139057 1489018603      SRR5227304      47139057        2356952850      SRP098789
SRP098789       SRX2536418      GSM2476012: vehicle, 60 min rep 1; Homo sapiens; OTHER  GSM2476012: vehicle, 60 min rep 1; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956368      Illumina HiSeq 2000    50956178 1495757884      SRR5227303      50956178        2547808900      SRP098789
SRP098789       SRX2536417      GSM2476011: 0.3 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     GSM2476011: 0.3 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956367      Illumina HiSeq 2000     44258180        1404548468      SRR5227302      44258180        2212909000      SRP098789
SRP098789       SRX2536416      GSM2476010: 0.3 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     GSM2476010: 0.3 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956366      Illumina HiSeq 2000     49129512        1536091510      SRR5227301      49129512        2456475600      SRP098789
SRP098789       SRX2536415      GSM2476009: 0.3 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     GSM2476009: 0.3 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956365      Illumina HiSeq 2000     30043362        903983724       SRR5227300      30043362        1502168100      SRP098789
SRP098789       SRX2536414      GSM2476008: 1.5 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     GSM2476008: 1.5 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956364      Illumina HiSeq 2000     48766213        1530350854      SRR5227299      48766213        2438310650      SRP098789
SRP098789       SRX2536413      GSM2476007: 1.5 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     GSM2476007: 1.5 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956363      Illumina HiSeq 2000     49334392        1475414353      SRR5227298      49334392        2466719600      SRP098789
SRP098789       SRX2536412      GSM2476006: 1.5 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     GSM2476006: 1.5 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956362      Illumina HiSeq 2000     60381365        1801283052      SRR5227297      60381365        3019068250      SRP098789
SRP098789       SRX2536411      GSM2476005: vehicle, 10 min rep 3; Homo sapiens; OTHER  GSM2476005: vehicle, 10 min rep 3; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956361      Illumina HiSeq 2000    52737784 1644829192      SRR5227296      52737784        2636889200      SRP098789
SRP098789       SRX2536410      GSM2476004: vehicle, 10 min rep 2; Homo sapiens; OTHER  GSM2476004: vehicle, 10 min rep 2; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956360      Illumina HiSeq 2000    46137148 1455541408      SRR5227295      46137148        2306857400      SRP098789
SRP098789       SRX2536409      GSM2476003: vehicle, 10 min rep 1; Homo sapiens; OTHER  GSM2476003: vehicle, 10 min rep 1; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956359      Illumina HiSeq 2000    76002122 1552821132      SRR5227294      76002122        3800106100      SRP098789
SRP098789       SRX2536408      GSM2476002: 0.3 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     GSM2476002: 0.3 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956358      Illumina HiSeq 2000     42709138        1338829352      SRR5227293      42709138        2135456900      SRP098789
SRP098789       SRX2536407      GSM2476001: 0.3 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     GSM2476001: 0.3 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956357      Illumina HiSeq 2000     60552437        1875910244      SRR5227292      60552437        3027621850      SRP098789
SRP098789       SRX2536406      GSM2476000: 0.3 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     GSM2476000: 0.3 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956356      Illumina HiSeq 2000     41143319        843881081       SRR5227291      41143319        2057165950      SRP098789
SRP098789       SRX2536405      GSM2475999: 1.5 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     GSM2475999: 1.5 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956355      Illumina HiSeq 2000     40462973        1287284933      SRR5227290      40462973        2023148650      SRP098789
SRP098789       SRX2536404      GSM2475998: 1.5 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     GSM2475998: 1.5 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956354      Illumina HiSeq 2000     41657461        1360366732      SRR5227289      41657461        2082873050      SRP098789
SRP098789       SRX2536403      GSM2475997: 1.5 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     GSM2475997: 1.5 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956353      Illumina HiSeq 2000     42082855        916745706       SRR5227288      42082855        2104142750      SRP098789

|

Convert GSE to SRP

::: tabbed Console

$ pysradb srp-to-srx SRP098789

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
df = db.srp-to-srx("SRP098789")
df

:::

Output: :

study_accession experiment_accession    experiment_title        experiment_desc organism_taxid  organism_name   library_strategy        library_source  library_selection       sample_accession        sample_title    instrument      total_spots     total_size      run_accession   run_total_spots run_total_bases study_accesssion
SRP098789       SRX2536428      GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Homo sapiens; RNA-Seq       GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Homo sapiens; RNA-Seq       9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956378      Illumina HiSeq 2500     69422931        1545681856      SRR5227313      69422931        3540569481      SRP098789
SRP098789       SRX2536427      GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-seq; Homo sapiens; OTHER   GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-seq; Homo sapiens; OTHER   9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956377      Illumina HiSeq 2500     58065134        1302369810      SRR5227312      58065134        2961321834      SRP098789
SRP098789       SRX2536426      GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Homo sapiens; RNA-Seq       GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Homo sapiens; RNA-Seq       9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956376      Illumina HiSeq 2500     63720205        1416818619      SRR5227311      63720205        3249730455      SRP098789
SRP098789       SRX2536425      GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-seq; Homo sapiens; OTHER   GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-seq; Homo sapiens; OTHER   9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956375      Illumina HiSeq 2500     66363585        1482728577      SRR5227310      66363585        3384542835      SRP098789
SRP098789       SRX2536424      GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; Homo sapiens; RNA-Seq      GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; Homo sapiens; RNA-Seq      9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956374      Illumina HiSeq 2500     40062613        904488287       SRR5227309      40062613        2043193263      SRP098789
SRP098789       SRX2536423      GSM2476017: 1.5 ?M PF-067446846, 60 min, rep 5 -riboseq; Homo sapiens; OTHER    GSM2476017: 1.5 ?M PF-067446846, 60 min, rep 5 -riboseq; Homo sapiens; OTHER    9606    Homo sapiens    OTHER   TRANSCRIPTOMIC other    SRS1956373      Illumina HiSeq 2500     65591217        1499668100      SRR5227308      65591217        3345152067      SRP098789
SRP098789       SRX2536422      GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; Homo sapiens; RNA-Seq      GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; Homo sapiens; RNA-Seq      9606    Homo sapiens    RNA-Seq TRANSCRIPTOMIC  cDNA    SRS1956372      Illumina HiSeq 2500     66480991        1564636133      SRR5227307      66480991        3390530541      SRP098789
SRP098789       SRX2536421      GSM2476015: 1.5 ?M PF-067446846, 60 min, rep 4 -riboseq; Homo sapiens; OTHER    GSM2476015: 1.5 ?M PF-067446846, 60 min, rep 4 -riboseq; Homo sapiens; OTHER    9606    Homo sapiens    OTHER   TRANSCRIPTOMIC other    SRS1956371      Illumina HiSeq 2500     57588015        1357395400      SRR5227306      57588015        2936988765      SRP098789
SRP098789       SRX2536420      GSM2476014: vehicle, 60 min rep 3; Homo sapiens; OTHER  GSM2476014: vehicle, 60 min rep 3; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956370      Illumina HiSeq 2000    48405034 1530784033      SRR5227305      48405034        2420251700      SRP098789
SRP098789       SRX2536419      GSM2476013: vehicle, 60 min rep 2; Homo sapiens; OTHER  GSM2476013: vehicle, 60 min rep 2; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956369      Illumina HiSeq 2000    47139057 1489018603      SRR5227304      47139057        2356952850      SRP098789
SRP098789       SRX2536418      GSM2476012: vehicle, 60 min rep 1; Homo sapiens; OTHER  GSM2476012: vehicle, 60 min rep 1; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956368      Illumina HiSeq 2000    50956178 1495757884      SRR5227303      50956178        2547808900      SRP098789
SRP098789       SRX2536417      GSM2476011: 0.3 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     GSM2476011: 0.3 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956367      Illumina HiSeq 2000     44258180        1404548468      SRR5227302      44258180        2212909000      SRP098789
SRP098789       SRX2536416      GSM2476010: 0.3 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     GSM2476010: 0.3 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956366      Illumina HiSeq 2000     49129512        1536091510      SRR5227301      49129512        2456475600      SRP098789
SRP098789       SRX2536415      GSM2476009: 0.3 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     GSM2476009: 0.3 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956365      Illumina HiSeq 2000     30043362        903983724       SRR5227300      30043362        1502168100      SRP098789
SRP098789       SRX2536414      GSM2476008: 1.5 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     GSM2476008: 1.5 ?M PF-067446846, 60 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956364      Illumina HiSeq 2000     48766213        1530350854      SRR5227299      48766213        2438310650      SRP098789
SRP098789       SRX2536413      GSM2476007: 1.5 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     GSM2476007: 1.5 ?M PF-067446846, 60 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956363      Illumina HiSeq 2000     49334392        1475414353      SRR5227298      49334392        2466719600      SRP098789
SRP098789       SRX2536412      GSM2476006: 1.5 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     GSM2476006: 1.5 ?M PF-067446846, 60 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956362      Illumina HiSeq 2000     60381365        1801283052      SRR5227297      60381365        3019068250      SRP098789
SRP098789       SRX2536411      GSM2476005: vehicle, 10 min rep 3; Homo sapiens; OTHER  GSM2476005: vehicle, 10 min rep 3; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956361      Illumina HiSeq 2000    52737784 1644829192      SRR5227296      52737784        2636889200      SRP098789
SRP098789       SRX2536410      GSM2476004: vehicle, 10 min rep 2; Homo sapiens; OTHER  GSM2476004: vehicle, 10 min rep 2; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956360      Illumina HiSeq 2000    46137148 1455541408      SRR5227295      46137148        2306857400      SRP098789
SRP098789       SRX2536409      GSM2476003: vehicle, 10 min rep 1; Homo sapiens; OTHER  GSM2476003: vehicle, 10 min rep 1; Homo sapiens; OTHER  9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956359      Illumina HiSeq 2000    76002122 1552821132      SRR5227294      76002122        3800106100      SRP098789
SRP098789       SRX2536408      GSM2476002: 0.3 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     GSM2476002: 0.3 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956358      Illumina HiSeq 2000     42709138        1338829352      SRR5227293      42709138        2135456900      SRP098789
SRP098789       SRX2536407      GSM2476001: 0.3 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     GSM2476001: 0.3 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956357      Illumina HiSeq 2000     60552437        1875910244      SRR5227292      60552437        3027621850      SRP098789
SRP098789       SRX2536406      GSM2476000: 0.3 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     GSM2476000: 0.3 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956356      Illumina HiSeq 2000     41143319        843881081       SRR5227291      41143319        2057165950      SRP098789
SRP098789       SRX2536405      GSM2475999: 1.5 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     GSM2475999: 1.5 ?M PF-067446846, 10 min, rep 3; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956355      Illumina HiSeq 2000     40462973        1287284933      SRR5227290      40462973        2023148650      SRP098789
SRP098789       SRX2536404      GSM2475998: 1.5 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     GSM2475998: 1.5 ?M PF-067446846, 10 min, rep 2; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956354      Illumina HiSeq 2000     41657461        1360366732      SRR5227289      41657461        2082873050      SRP098789
SRP098789       SRX2536403      GSM2475997: 1.5 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     GSM2475997: 1.5 ?M PF-067446846, 10 min, rep 1; Homo sapiens; OTHER     9606    Homo sapiens    OTHER   TRANSCRIPTOMIC  other   SRS1956353      Illumina HiSeq 2000     42082855        916745706       SRR5227288      42082855        2104142750      SRP098789

---

|

Downloading sequencing data

pysradb can alse be used to download either .fastq or .sra filesboth from ENA and SRA.

Downloading via accession number

::: tabbed Console

$ pysradb download SRP098789

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
db.download("SRP098789")

:::

|

It is also possible to pipe the dataframe from [metadata]{.title-ref} or [search]{.title-ref} to download, after filtering the dataframe entries:

::: tabbed Console

$ pysradb metadata SRP276671 --detailed | pysradb download

:::

::: tabbed Python

from pysradb.sraweb import SRAweb
db = SRAweb()
df = db.sra_metadata('SRP016501', detailed=True)
db.download(df=df)

:::

|

Ultrafast fastq downloads

With aspera-client installed, pysradb canan perform ultra fast downloads:

To download all original fastqs with [aspera-client]{.title-ref} installed utilizing 8 threads:

::: tabbed Console

$ pysradb download -t 8 --use_ascp -p SRP002605

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
db.download("SRP098789", use_ascp=True, threads=8)

:::

Refer to the notebook for (shallow) time benchmarks.

---

|

Search

Retrieving metadata by accession number

::: tabbed Console

$ pysradb metadata SRP276671

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
df = db.sra_metadata('SRP016501')
df

:::

Output: :

study_accession experiment_accession    experiment_title        experiment_desc organism_taxid  organism_name   library_strategy        library_source  library_selection       sample_accession        sample_title    instrument      total_spots     total_size      run_accession   run_total_spots run_total_bases
SRP276671       SRX8978626      hCov-19/Canada/ON/VIDO01/2020 (EPI ISL 413015)  hCov-19/Canada/ON/VIDO01/2020 (EPI ISL 413015)  2697049 Severe acute respiratory syndrome coronavirus 2 WGS     GENOMIC RT-PCR  SRS7233795      MinION  96202  79690689 SRR12486810     96202   86575096
SRP276671       SRX8909137      hCoV-19/Canada/ON-VIDO-01/2020 (EPI_ISL_425177) hCoV-19/Canada/ON-VIDO-01/2020 (EPI_ISL_425177) 2697049 Severe acute respiratory syndrome coronavirus 2 WGS     GENOMIC RT-PCR  SRS7166526      Illumina MiSeq 866225   173474986       SRR12412952     866225  338457239

|

::: note ::: title Note :::

[pysradb]{.title-ref}, when used in python, returns the retrieved metadata as a [pandas]{.title-ref} DataFrame, with all regular select/query operations available through [pandas]{.title-ref}. :::

|

For more detailed metadata (including download URLs), we can include the [detailed]{.title-ref} flag:

::: tabbed Console

$ pysradb metadata SRP276671 --detailed

:::

::: tabbed Python

from pysradb.sraweb import SRAweb

db = SRAweb()
df = db.sra_metadata('SRP016501', detailed=True)
df

:::

Output: :

study_accession experiment_accession    experiment_title        experiment_desc organism_taxid  organism_name   library_strategy        library_source  library_selection       sample_accession        sample_title    instrument      total_spots     total_size      run_accession   run_total_spots run_total_bases run_alias       sra_url_alt     sra_url experiment_alias        isolate collected_by    collection_date geo_loc_name    host    host_disease    isolation_source       lat_lon  host_sex        host_subject_id passage_history BioSampleModel  sra_url_alt1    sra_url_alt2    sra_url_alt3   ena_fastq_http   ena_fastq_ftp
SRP276671       SRX8978626      hCov-19/Canada/ON/VIDO01/2020 (EPI ISL 413015)  hCov-19/Canada/ON/VIDO01/2020 (EPI ISL 413015)  2697049 Severe acute respiratory syndrome coronavirus 2 WGS     GENOMIC RT-PCR  SRS7233795      N/A     MinION 96202    79690689        SRR12486810     96202   86575096        VIDO-01.tar.gz  https://sra-download.ncbi.nlm.nih.gov/traces/sra1/SRZ/012486/SRR12486810/VIDO-01.tar.gz https://sra-download.ncbi.nlm.nih.gov/traces/sra78/SRR/012194/SRR12486810       N/A     ON-VIDO-01-P3   Public Health Ontario   2020-01-23      Canada: Ontario Homo sapiens    COVID-19       missing  missing male    VIDO-01 Vero E6 P3      Pathogen.cl     N/A     N/A     N/A     http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/010/SRR12486810/SRR12486810_1.fastq.gz       era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR124/010/SRR12486810/SRR12486810_1.fastq.gz
SRP276671       SRX8909137      hCoV-19/Canada/ON-VIDO-01/2020 (EPI_ISL_425177) hCoV-19/Canada/ON-VIDO-01/2020 (EPI_ISL_425177) 2697049 Severe acute respiratory syndrome coronavirus 2 WGS     GENOMIC RT-PCR  SRS7166526      N/A     Illumina MiSeq  866225  173474986       SRR12412952     866225  338457239       SP-2_R1.fastq.gz        N/A     https://sra-download.ncbi.nlm.nih.gov/traces/sra48/SRR/012122/SRR12412952       N/A     ON-VIDO-01-P2   Public Health Ontario   2020-01-23      Canada: Ontario Homo sapiens    COVID-19        missing missing male    VIDO-01 Vero E6 P2      Pathogen.cl    gs://sra-pub-src-10/SRR12412952/SP-2_R2.fastq.1  s3://sra-pub-src-10/SRR12412952/SP-2_R2.fastq.1 https://sra-pub-sars-cov2.s3.amazonaws.com/sra-src/SRR12412952/SP-2_R2.fastq.1  http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR124/052/SRR12412952/SRR12412952.fastq.gz era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR124/052/SRR12412952/SRR12412952.fastq.gz

---

|

Searching SRA/ENA databases and retrieving metadata

Let’s take for example we are interested in coronavirus sequences published on Short Reads Archive (SRA) in the first week of August 2020.

::: tabbed Console

$ pysradb search -q coronavirus --publication-date 01-08-2020:07-08-2020 --max 10000

:::

::: tabbed Python

from pysradb.search import SraSearch

instance = SraSearch(return_max=10000, query="coronavirus", publication_date="01-08-2020:07-08-2020")
instance.search()
instance.get_df()

:::

Output (showing only the first 10 entries): :

study_accession  experiment_accession    experiment_title        sample_taxon_id sample_scientific_name  experiment_library_strategy     experiment_library_source       experiment_library_selection    sample_accession        sample_alias    experiment_instrument_model     pool_member_spots       run_1_size     run_1_accession  run_1_total_spots       run_1_total_bases       pmid
SRP270658       SRX8679965      GSM4658808: SARS-CoV-2-infected 24h 3; Chlorocebus sabaeus; Severe acute respiratory syndrome coronavirus 2; RNA-Seq    60711   Chlorocebus sabaeus     RNA-Seq TRANSCRIPTOMIC  cDNA    SRS6959042      GSM4658808      NextSeq 500     104223040       9743267247      SRR12164500     104223040       31475358080     11295714
SRP270658       SRX8679964      GSM4658807: SARS-CoV-2-infected 24h 2; Chlorocebus sabaeus; Severe acute respiratory syndrome coronavirus 2; RNA-Seq    60711   Chlorocebus sabaeus     RNA-Seq TRANSCRIPTOMIC  cDNA    SRS6959041      GSM4658807      NextSeq 500     92813819        8703506222      SRR12164499     92813819        28029773338     11295713
SRP253798       SRX8677889      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956975      hCoV-19/Australia/VIC1898/2020  NextSeq 500    456828   51422072        SRR12162149     456828  130280958       11292876
SRP253798       SRX8677888      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956974      hCoV-19/Australia/VIC1886/2020  NextSeq 500    268832   29923966        SRR12162150     268832  75885223        11292875
SRP253798       SRX8677887      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956973      hCoV-19/Australia/VIC1890/2020  NextSeq 500    483526   54629557        SRR12162151     483526  139019404       11292874
SRP253798       SRX8677886      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956971      hCoV-19/Australia/VIC1888/2020  NextSeq 500    473895   53675126        SRR12162152     473895  136058655       11292873
SRP253798       SRX8677885      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956972      hCoV-19/Australia/VIC1891/2020  NextSeq 500    482373   53331905        SRR12162153     482373  135769259       11292872
SRP253798       SRX8677884      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956970      hCoV-19/Australia/VIC1816/2020  NextSeq 550    357052   41111134        SRR12162154     357052  103693201       11292871
SRP253798       SRX8677883      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956969      hCoV-19/Australia/VIC1815/2020  NextSeq 550    307106   35306959        SRR12162155     307106  89866234        11292870
SRP253798       SRX8677882      Severe acute respiratory syndrome coronavirus 2 2697049 Severe acute respiratory syndrome coronavirus 2 AMPLICON        VIRAL RNA       PCR     SRS6956968      hCoV-19/Australia/VIC1814/2020  NextSeq 550    353704   40652239        SRR12162156     353704  103366580       11292869

|

To query European Nucleotide Archive (ENA) instead:

::: tabbed Console

$ pysradb search --db ena -q coronavirus --publication-date 01-08-2020:07-08-2020 --max 10000

:::

::: tabbed Python

from pysradb.search import EnaSearch

instance = EnaSearch(return_max=10000, query="coronavirus", publication_date="01-08-2020:07-08-2020")
instance.search()
instance.get_df()

:::

Output (showing only the first 10 entries): :

study_accession experiment_accession    experiment_title        description     tax_id  scientific_name library_strategylibrary_source  library_selection       sample_accession        sample_title    instrument_model        run_accession  read_count       base_count
PRJEB12126      ERX1264364      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    OTHER   TRANSCRIPTOMIC  other   SAMEA3708907    Sample 1        Illumina HiSeq 2000     ERR1190989      38883498        1161289538
PRJEB12126      ERX1264365      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    OTHER   TRANSCRIPTOMIC  other   SAMEA3708908    Sample 10       Illumina HiSeq 2000     ERR1190990      55544297        1779600908
PRJEB12126      ERX1264366      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    OTHER   TRANSCRIPTOMIC  other   SAMEA3708909    Sample 11       Illumina HiSeq 2000     ERR1190991      54474851        1713994365
PRJEB12126      ERX1264367      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    OTHER   TRANSCRIPTOMIC  other   SAMEA3708910    Sample 12       Illumina HiSeq 2000     ERR1190992      78497711        2489092061
PRJEB12126      ERX1264368      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    RNA-Seq TRANSCRIPTOMIC  RANDOM  SAMEA3708911    Sample 13       Illumina HiSeq 2000     ERR1190993      84955423        2627276298
PRJEB12126      ERX1264369      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    RNA-Seq TRANSCRIPTOMIC  RANDOM  SAMEA3708912    Sample 14       Illumina HiSeq 2000     ERR1190994      75097651        2293097872
PRJEB12126      ERX1264370      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    RNA-Seq TRANSCRIPTOMIC  RANDOM  SAMEA3708913    Sample 15       Illumina HiSeq 2000     ERR1190995      67177553        2060926619
PRJEB12126      ERX1264371      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    RNA-Seq TRANSCRIPTOMIC  RANDOM  SAMEA3708914    Sample 16       Illumina HiSeq 2000     ERR1190996      62940694        2061757111
PRJEB12126      ERX1264372      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    RNA-Seq TRANSCRIPTOMIC  RANDOM  SAMEA3708915    Sample 17       Illumina HiSeq 2000     ERR1190997      80591061        2475034240
PRJEB12126      ERX1264373      Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    Illumina HiSeq 2000 sequencing; Analysis of coronavirus and infected host-cell gene expression through RNA sequencing and ribosome profiling    10090   Mus musculus    RNA-Seq TRANSCRIPTOMIC  RANDOM  SAMEA3708916    Sample 18       Illumina HiSeq 2000     ERR1190998      68575621        2149386138

|

If the number of returned entries is large, it might be troublesome to filter through the metadata to find any information of interest. As a starting point, we can use the search feature to generate summary statistics and graphs for the search result:

|

Statistics

::: tabbed Console

$ pysradb search --db ena --organism "Severe acute respiratory syndrome coronavirus 2" --max 10000 -s

:::

::: tabbed Python

from pysradb.search import EnaSearch
instance = EnaSearch(return_max=10000, organism="Severe acute respiratory syndrome coronavirus 2")
instance.search()
instance.show_result_statistics()

:::

Output: :

Statistics for the search query:
=================================
Number of unique studies: 7
Number of unique experiments: 10000
Number of unique runs: 10000
Number of unique samples: 9797
Mean base count of samples: 238380171.626
Median base count of samples: 164470138.000
Sample base count standard deviation: 261654776.053
Date range:
    2020-04:  1299
    2020-05:  2518
    2020-06:  6181
    2020-07:  2

Organisms:
    Severe acute respiratory syndrome coronavirus 2:  10000

Platform:
    ILLUMINA:  5175
    OXFORD_NANOPORE:  4825

Library strategy:
    AMPLICON:  9789
    RNA-Seq:  1
    Targeted-Capture:  202
    WGS:  8

Library source:
    GENOMIC:  8
    METATRANSCRIPTOMIC:  1
    TRANSCRIPTOMIC:  1
    VIRAL RNA:  9990

Library selection:
    PCR:  9789
    RANDOM:  9
    other:  202

Library layout:
    PAIRED:  5059
    SINGLE:  4941

|

Plotting

::: tabbed Console

$ pysradb search --db ena -q e --max 500000 -g

:::

::: tabbed Python

from pysradb.search import EnaSearch

instance = EnaSearch(return_max=500000, "e")
instance.search()
instance.visualise_results()

:::

Output: Graphs generated will automatically be saved under [./search_plots/]{.title-ref}. Optionally, graphs can be shown in python by including the argument [show=True]{.title-ref} Here are some of the available graphs that will be generated:

{width=”600px”}

{width=”600px”}

{width=”600px”}

---

|

List of possible [pysradb]{.title-ref} operations

$ pysradb
usage: pysradb [-h] [--version] [--citation]
               {metadb,metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
               ...

pysradb: Query NGS metadata and data from NCBI Sequence Read Archive.
Citation: 10.12688/f1000research.18676.1

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --citation            how to cite

subcommands:
  {metadb,metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
    metadata            Fetch metadata for SRA project (SRPnnnn)
    download            Download SRA project (SRPnnnn)
    search              Search SRA/ENA for matching text
    gse-to-gsm          Get GSM for a GSE
    gse-to-srp          Get SRP for a GSE
    gsm-to-gse          Get GSE for a GSM
    gsm-to-srp          Get SRP for a GSM
    gsm-to-srr          Get SRR for a GSM
    gsm-to-srs          Get SRS for a GSM
    gsm-to-srx          Get SRX for a GSM
    srp-to-gse          Get GSE for a SRP
    srp-to-srr          Get SRR for a SRP
    srp-to-srs          Get SRS for a SRP
    srp-to-srx          Get SRX for a SRP
    srr-to-gsm          Get GSM for a SRR
    srr-to-srp          Get SRP for a SRR
    srr-to-srs          Get SRS for a SRR
    srr-to-srx          Get SRX for a SRR
    srs-to-gsm          Get GSM for a SRS
    srs-to-srx          Get SRX for a SRS
    srx-to-srp          Get SRP for a SRX
    srx-to-srr          Get SRR for a SRX
    srx-to-srs          Get SRS for a SRX

::: {.toctree maxdepth=”1”} commands/download commands/metadata commands/search commands/gse-to-gsm commands/gse-to-srp commands/srp-to-gse commands/srp-to-srr commands/srp-to-srs commands/srp-to-srx commands/srr-to-srs commands/srr-to-srx commands/srs-to-srx commands/srx-to-srr commands/srx-to-srs :::