Python API Demo¶

This notebook demonstrates the core functionality of pysradb Python API for querying SRA metadata.

[1]:

# Install pysradb if not already installed
try:
    import pysradb

    print(f"pysradb {pysradb.__version__} is already installed")
except ImportError:
    print("Installing pysradb from GitHub...")
    import sys

    !{sys.executable} -m pip install -q git+https://github.com/saketkc/pysradb
    print("pysradb installed successfully!")

pysradb 3.0.0.dev0 is already installed

/home/runner/work/pysradb/pysradb/pysradb/download.py:15: TqdmExperimentalWarning: Using `tqdm.autonotebook.tqdm` in notebook mode. Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console)
  from tqdm.autonotebook import tqdm

[2]:

# pip install git+https://github.com/saketkc/pysradb

[3]:

!pysradb --version

pysradb 3.0.0.dev0

[4]:

from pysradb.sraweb import SRAweb

[5]:

db = SRAweb()

Get metadata of one project¶

[6]:

df = db.sra_metadata("SRP016501")
df

[6]:

	study_accession	study_title	experiment_accession	experiment_title	experiment_desc	organism_taxid	organism_name	library_name	library_strategy	library_source	...	biosample	bioproject	instrument	instrument_model	instrument_model_desc	total_spots	total_size	run_accession	run_total_spots	run_total_bases
133	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196264	GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq	GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq	10090	Mus musculus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766814	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	87264604	5927043102	SRR594393	87264604	8726460400
132	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196265	GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq	GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq	10090	Mus musculus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766815	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	101816491	6835402318	SRR594394	101816491	10181649100
131	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196266	GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq	GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq	10090	Mus musculus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766816	PRJNA177791	Illumina Genome Analyzer IIx	Illumina Genome Analyzer IIx	ILLUMINA	35175982	1502674440	SRR594395	35175982	2532670704
130	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196267	GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq	GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq	10090	Mus musculus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766817	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	119274786	7555854784	SRR594396	119274786	11927478600
129	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196268	GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq	GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq	10090	Mus musculus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766818	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	116292478	7481554926	SRR594397	116292478	11629247800
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
4	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196393	GSM1020769: chicken_c_liver; Gallus gallus; RN...	GSM1020769: chicken_c_liver; Gallus gallus; RN...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766943	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	18978066	562367072	SRR594522	18978066	1366420752
3	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196394	GSM1020770: chicken_c_lung; Gallus gallus; RNA...	GSM1020770: chicken_c_lung; Gallus gallus; RNA...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766944	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	26604280	931417024	SRR594523	26604280	1862299600
2	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196395	GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq	GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766945	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	25606436	986287075	SRR594524	25606436	1792450520
1	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196396	GSM1020772: chicken_c_spleen; Gallus gallus; R...	GSM1020772: chicken_c_spleen; Gallus gallus; R...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766946	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	24401708	1201671888	SRR594525	24401708	1756922976
0	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196397	GSM1020773: chicken_c_testes; Gallus gallus; R...	GSM1020773: chicken_c_testes; Gallus gallus; R...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766947	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	37423394	1980545796	SRR594526	37423394	2993871520

134 rows × 24 columns

Get detailed metadata¶

[7]:

df = db.sra_metadata("SRP016501", detailed=True)
df

[7]:

	run_accession	study_accession	study_title	experiment_accession	experiment_title	experiment_desc	organism_taxid	organism_name	library_name	library_strategy	...	tissue	strain	ena_fastq_http	ena_fastq_http_1	ena_fastq_http_2	ena_fastq_ftp	ena_fastq_ftp_1	ena_fastq_ftp_2	study_geo_accession	experiment_geo_accession
0	SRR594393	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196264	GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq	GSM1020640: mouse_a_brain; Mus musculus; RNA-Seq	10090	Mus musculus	NaN	RNA-Seq	...	brain	DBA/2J	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020640
1	SRR594394	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196265	GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq	GSM1020641: mouse_a_colon; Mus musculus; RNA-Seq	10090	Mus musculus	NaN	RNA-Seq	...	colon	DBA/2J	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020641
2	SRR594395	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196266	GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq	GSM1020642: mouse_a_heart; Mus musculus; RNA-Seq	10090	Mus musculus	NaN	RNA-Seq	...	heart	DBA/2J	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020642
3	SRR594396	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196267	GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq	GSM1020643: mouse_a_kidney; Mus musculus; RNA-Seq	10090	Mus musculus	NaN	RNA-Seq	...	kidney	DBA/2J	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020643
4	SRR594397	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196268	GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq	GSM1020644: mouse_a_liver; Mus musculus; RNA-Seq	10090	Mus musculus	NaN	RNA-Seq	...	liver	DBA/2J	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020644
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
129	SRR594522	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196393	GSM1020769: chicken_c_liver; Gallus gallus; RN...	GSM1020769: chicken_c_liver; Gallus gallus; RN...	9031	Gallus gallus	NaN	RNA-Seq	...	liver	NaN	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020769
130	SRR594523	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196394	GSM1020770: chicken_c_lung; Gallus gallus; RNA...	GSM1020770: chicken_c_lung; Gallus gallus; RNA...	9031	Gallus gallus	NaN	RNA-Seq	...	lung	NaN	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020770
131	SRR594524	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196395	GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq	GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq	9031	Gallus gallus	NaN	RNA-Seq	...	skeletal muscle	NaN	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020771
132	SRR594525	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196396	GSM1020772: chicken_c_spleen; Gallus gallus; R...	GSM1020772: chicken_c_spleen; Gallus gallus; R...	9031	Gallus gallus	NaN	RNA-Seq	...	spleen	NaN	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020772
133	SRR594526	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196397	GSM1020773: chicken_c_testes; Gallus gallus; R...	GSM1020773: chicken_c_testes; Gallus gallus; R...	9031	Gallus gallus	NaN	RNA-Seq	...	testes	NaN	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR594/SRR...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR594/...	GSE41637	GSM1020773

134 rows × 55 columns

Get metadata of multiple projects¶

[8]:

df = db.sra_metadata(["SRP016501", "SRP098789"])
df

[8]:

	study_accession	study_title	experiment_accession	experiment_title	experiment_desc	organism_taxid	organism_name	library_name	library_strategy	library_source	...	biosample	bioproject	instrument	instrument_model	instrument_model_desc	total_spots	total_size	run_accession	run_total_spots	run_total_bases
25	SRP098789	Selective stalling of human translation throug...	SRX2536403	GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...	GSM2475997: 1.5 µM PF-067446846, 10 min, rep 1...	9606	Homo sapiens		OTHER	TRANSCRIPTOMIC	...	SAMN06293487	PRJNA369742	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	42082855	916745706	SRR5227288	42082855	2104142750
24	SRP098789	Selective stalling of human translation throug...	SRX2536404	GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...	GSM2475998: 1.5 µM PF-067446846, 10 min, rep 2...	9606	Homo sapiens		OTHER	TRANSCRIPTOMIC	...	SAMN06293486	PRJNA369742	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	41657461	1360366732	SRR5227289	41657461	2082873050
23	SRP098789	Selective stalling of human translation throug...	SRX2536405	GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...	GSM2475999: 1.5 µM PF-067446846, 10 min, rep 3...	9606	Homo sapiens		OTHER	TRANSCRIPTOMIC	...	SAMN06293485	PRJNA369742	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	40462973	1287284933	SRR5227290	40462973	2023148650
22	SRP098789	Selective stalling of human translation throug...	SRX2536406	GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...	GSM2476000: 0.3 µM PF-067446846, 10 min, rep 1...	9606	Homo sapiens		OTHER	TRANSCRIPTOMIC	...	SAMN06293484	PRJNA369742	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	41143319	843881081	SRR5227291	41143319	2057165950
21	SRP098789	Selective stalling of human translation throug...	SRX2536407	GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...	GSM2476001: 0.3 µM PF-067446846, 10 min, rep 2...	9606	Homo sapiens		OTHER	TRANSCRIPTOMIC	...	SAMN06293483	PRJNA369742	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	60552437	1875910244	SRR5227292	60552437	3027621850
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
30	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196393	GSM1020769: chicken_c_liver; Gallus gallus; RN...	GSM1020769: chicken_c_liver; Gallus gallus; RN...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766943	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	18978066	562367072	SRR594522	18978066	1366420752
29	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196394	GSM1020770: chicken_c_lung; Gallus gallus; RNA...	GSM1020770: chicken_c_lung; Gallus gallus; RNA...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766944	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	26604280	931417024	SRR594523	26604280	1862299600
28	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196395	GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq	GSM1020771: chicken_c_skm; Gallus gallus; RNA-Seq	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766945	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	25606436	986287075	SRR594524	25606436	1792450520
27	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196396	GSM1020772: chicken_c_spleen; Gallus gallus; R...	GSM1020772: chicken_c_spleen; Gallus gallus; R...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766946	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	24401708	1201671888	SRR594525	24401708	1756922976
26	SRP016501	Evolutionary dynamics of gene and isoform regu...	SRX196397	GSM1020773: chicken_c_testes; Gallus gallus; R...	GSM1020773: chicken_c_testes; Gallus gallus; R...	9031	Gallus gallus		RNA-Seq	TRANSCRIPTOMIC	...	SAMN01766947	PRJNA177791	Illumina HiSeq 2000	Illumina HiSeq 2000	ILLUMINA	37423394	1980545796	SRR594526	37423394	2993871520

160 rows × 24 columns

Get metadata of a Run¶

[9]:

df = db.sra_metadata("SRR11085797", detailed=True)
df

No results found for ['SRP249482'] | Obtained result: {}
No results found for ['SRX7724752'] | Obtained result: {}

[9]:

	run_accession	study_accession	study_title	experiment_accession	experiment_title	experiment_desc	organism_taxid	organism_name	library_name	library_strategy	...	lat_lon	biosamplemodel	ena_fastq_http	ena_fastq_http_1	ena_fastq_http_2	ena_fastq_ftp	ena_fastq_ftp_1	ena_fastq_ftp_2	study_geo_accession	experiment_geo_accession
0	SRR11085797	SRP249482	Bat coronavirus RaTG13 Genome sequencing	SRX7724752	RNA-Seq of Rhinolophus affinis:Fecal swab	RNA-Seq of Rhinolophus affinis:Fecal swab	694135	unidentified coronavirus	RaTG13	RNA-Seq	...	not collected	Pathogen.cl	<NA>	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR110/097...	http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR110/097...	<NA>	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR110/...	era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR110/...	<NA>	<NA>

1 rows × 62 columns

SRX to GSM¶

[10]:

df = db.srx_to_gsm("SRX1254413")
df

[10]:

	experiment_accession	experiment_alias
0	SRX1254413	GSM1887643