Open In Colab

Parallel Download

This notebook demonstrates how to download multiple SRA datasets in parallel using joblib.

[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]:

# joblib is included in the documentation environment

[4]:

from joblib import Parallel, delayed

[5]:

from pysradb.sraweb import SRAweb

db = SRAweb()

[6]:

df = db.sra_metadata("SRP098789", detailed=True)
df

[6]:
run_accession study_accession study_title experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy ... treatment time library type 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 SRR5227288 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 NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2475997
1 SRR5227289 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 NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2475998
2 SRR5227290 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 NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2475999
3 SRR5227291 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 NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476000
4 SRR5227292 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 NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476001
5 SRR5227293 SRP098789 Selective stalling of human translation throug... SRX2536408 GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476002
6 SRR5227294 SRP098789 Selective stalling of human translation throug... SRX2536409 GSM2476003: vehicle, 10 min rep 1; Homo sapien... GSM2476003: vehicle, 10 min rep 1; Homo sapien... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476003
7 SRR5227295 SRP098789 Selective stalling of human translation throug... SRX2536410 GSM2476004: vehicle, 10 min rep 2; Homo sapien... GSM2476004: vehicle, 10 min rep 2; Homo sapien... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476004
8 SRR5227296 SRP098789 Selective stalling of human translation throug... SRX2536411 GSM2476005: vehicle, 10 min rep 3; Homo sapien... GSM2476005: vehicle, 10 min rep 3; Homo sapien... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476005
9 SRR5227297 SRP098789 Selective stalling of human translation throug... SRX2536412 GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476006
10 SRR5227298 SRP098789 Selective stalling of human translation throug... SRX2536413 GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476007
11 SRR5227299 SRP098789 Selective stalling of human translation throug... SRX2536414 GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476008
12 SRR5227300 SRP098789 Selective stalling of human translation throug... SRX2536415 GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476009
13 SRR5227301 SRP098789 Selective stalling of human translation throug... SRX2536416 GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476010
14 SRR5227302 SRP098789 Selective stalling of human translation throug... SRX2536417 GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476011
15 SRR5227303 SRP098789 Selective stalling of human translation throug... SRX2536418 GSM2476012: vehicle, 60 min rep 1; Homo sapien... GSM2476012: vehicle, 60 min rep 1; Homo sapien... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476012
16 SRR5227304 SRP098789 Selective stalling of human translation throug... SRX2536419 GSM2476013: vehicle, 60 min rep 2; Homo sapien... GSM2476013: vehicle, 60 min rep 2; Homo sapien... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476013
17 SRR5227305 SRP098789 Selective stalling of human translation throug... SRX2536420 GSM2476014: vehicle, 60 min rep 3; Homo sapien... GSM2476014: vehicle, 60 min rep 3; Homo sapien... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476014
18 SRR5227306 SRP098789 Selective stalling of human translation throug... SRX2536421 GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476015
19 SRR5227307 SRP098789 Selective stalling of human translation throug... SRX2536422 GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... 9606 Homo sapiens NaN RNA-Seq ... 60 min Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476016
20 SRR5227308 SRP098789 Selective stalling of human translation throug... SRX2536423 GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476017
21 SRR5227309 SRP098789 Selective stalling of human translation throug... SRX2536424 GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... 9606 Homo sapiens NaN RNA-Seq ... 60 min Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476018
22 SRR5227310 SRP098789 Selective stalling of human translation throug... SRX2536425 GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... 9606 Homo sapiens NaN OTHER ... 60 min mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476019
23 SRR5227311 SRP098789 Selective stalling of human translation throug... SRX2536426 GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... 9606 Homo sapiens NaN RNA-Seq ... 60 min polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476020
24 SRR5227312 SRP098789 Selective stalling of human translation throug... SRX2536427 GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... 9606 Homo sapiens NaN OTHER ... 60 min mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476021
25 SRR5227313 SRP098789 Selective stalling of human translation throug... SRX2536428 GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... 9606 Homo sapiens NaN RNA-Seq ... 60 min polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476022

26 rows × 56 columns

[7]:

# randomply split into two dataframes
df1, df2 = df.iloc[:5, :], df.iloc[5:, :]

df2

[7]:
run_accession study_accession study_title experiment_accession experiment_title experiment_desc organism_taxid organism_name library_name library_strategy ... treatment time library type 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
5 SRR5227293 SRP098789 Selective stalling of human translation throug... SRX2536408 GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... GSM2476002: 0.3 µM PF-067446846, 10 min, rep 3... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476002
6 SRR5227294 SRP098789 Selective stalling of human translation throug... SRX2536409 GSM2476003: vehicle, 10 min rep 1; Homo sapien... GSM2476003: vehicle, 10 min rep 1; Homo sapien... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476003
7 SRR5227295 SRP098789 Selective stalling of human translation throug... SRX2536410 GSM2476004: vehicle, 10 min rep 2; Homo sapien... GSM2476004: vehicle, 10 min rep 2; Homo sapien... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476004
8 SRR5227296 SRP098789 Selective stalling of human translation throug... SRX2536411 GSM2476005: vehicle, 10 min rep 3; Homo sapien... GSM2476005: vehicle, 10 min rep 3; Homo sapien... 9606 Homo sapiens NaN OTHER ... 10 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476005
9 SRR5227297 SRP098789 Selective stalling of human translation throug... SRX2536412 GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... GSM2476006: 1.5 µM PF-067446846, 60 min, rep 1... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476006
10 SRR5227298 SRP098789 Selective stalling of human translation throug... SRX2536413 GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... GSM2476007: 1.5 µM PF-067446846, 60 min, rep 2... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476007
11 SRR5227299 SRP098789 Selective stalling of human translation throug... SRX2536414 GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... GSM2476008: 1.5 µM PF-067446846, 60 min, rep 3... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476008
12 SRR5227300 SRP098789 Selective stalling of human translation throug... SRX2536415 GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... GSM2476009: 0.3 µM PF-067446846, 60 min, rep 1... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476009
13 SRR5227301 SRP098789 Selective stalling of human translation throug... SRX2536416 GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... GSM2476010: 0.3 µM PF-067446846, 60 min, rep 2... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476010
14 SRR5227302 SRP098789 Selective stalling of human translation throug... SRX2536417 GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... GSM2476011: 0.3 µM PF-067446846, 60 min, rep 3... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476011
15 SRR5227303 SRP098789 Selective stalling of human translation throug... SRX2536418 GSM2476012: vehicle, 60 min rep 1; Homo sapien... GSM2476012: vehicle, 60 min rep 1; Homo sapien... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476012
16 SRR5227304 SRP098789 Selective stalling of human translation throug... SRX2536419 GSM2476013: vehicle, 60 min rep 2; Homo sapien... GSM2476013: vehicle, 60 min rep 2; Homo sapien... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/004... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476013
17 SRR5227305 SRP098789 Selective stalling of human translation throug... SRX2536420 GSM2476014: vehicle, 60 min rep 3; Homo sapien... GSM2476014: vehicle, 60 min rep 3; Homo sapien... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/005... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476014
18 SRR5227306 SRP098789 Selective stalling of human translation throug... SRX2536421 GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... GSM2476015: 1.5 µM PF-067446846, 60 min, rep 4... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/006... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476015
19 SRR5227307 SRP098789 Selective stalling of human translation throug... SRX2536422 GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... GSM2476016: Vehicle, 60 min, rep 4-ribo-seq; H... 9606 Homo sapiens NaN RNA-Seq ... 60 min Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/007... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476016
20 SRR5227308 SRP098789 Selective stalling of human translation throug... SRX2536423 GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... GSM2476017: 1.5 µM PF-067446846, 60 min, rep 5... 9606 Homo sapiens NaN OTHER ... 60 min ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/008... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476017
21 SRR5227309 SRP098789 Selective stalling of human translation throug... SRX2536424 GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... GSM2476018: vehicle, 60 min, rep 5-Ribo-seq; H... 9606 Homo sapiens NaN RNA-Seq ... 60 min Ribo-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/009... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476018
22 SRR5227310 SRP098789 Selective stalling of human translation throug... SRX2536425 GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... GSM2476019: PF-06446846, 60 min, rep 4 -mRNA-s... 9606 Homo sapiens NaN OTHER ... 60 min mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/000... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476019
23 SRR5227311 SRP098789 Selective stalling of human translation throug... SRX2536426 GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... GSM2476020: vehicle, 60 min, rep 4-mRNAseq; Ho... 9606 Homo sapiens NaN RNA-Seq ... 60 min polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/001... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476020
24 SRR5227312 SRP098789 Selective stalling of human translation throug... SRX2536427 GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... GSM2476021: PF-06446846, 60 min, rep 5 -mRNA-s... 9606 Homo sapiens NaN OTHER ... 60 min mRNA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/002... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476021
25 SRR5227313 SRP098789 Selective stalling of human translation throug... SRX2536428 GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... GSM2476022: vehicle, 60 min, rep 5-mRNAseq; Ho... 9606 Homo sapiens NaN RNA-Seq ... 60 min polyA-seq http://ftp.sra.ebi.ac.uk/vol1/fastq/SRR522/003... <NA> <NA> era-fasp@fasp.sra.ebi.ac.uk:vol1/fastq/SRR522/... <NA> <NA> GSE94454 GSM2476022

21 rows × 56 columns

[8]:

def single_download(df_single):
    """Dry-run one download batch for executable documentation."""
    columns = ["run_accession", "study_accession", "experiment_accession"]
    return df_single[columns].assign(status="ready")

[9]:

Parallel(n_jobs=2)(delayed(single_download)(df_x) for df_x in [df1, df2])

[9]:

[  run_accession study_accession experiment_accession status
 0    SRR5227288       SRP098789           SRX2536403  ready
 1    SRR5227289       SRP098789           SRX2536404  ready
 2    SRR5227290       SRP098789           SRX2536405  ready
 3    SRR5227291       SRP098789           SRX2536406  ready
 4    SRR5227292       SRP098789           SRX2536407  ready,
    run_accession study_accession experiment_accession status
 5     SRR5227293       SRP098789           SRX2536408  ready
 6     SRR5227294       SRP098789           SRX2536409  ready
 7     SRR5227295       SRP098789           SRX2536410  ready
 8     SRR5227296       SRP098789           SRX2536411  ready
 9     SRR5227297       SRP098789           SRX2536412  ready
 10    SRR5227298       SRP098789           SRX2536413  ready
 11    SRR5227299       SRP098789           SRX2536414  ready
 12    SRR5227300       SRP098789           SRX2536415  ready
 13    SRR5227301       SRP098789           SRX2536416  ready
 14    SRR5227302       SRP098789           SRX2536417  ready
 15    SRR5227303       SRP098789           SRX2536418  ready
 16    SRR5227304       SRP098789           SRX2536419  ready
 17    SRR5227305       SRP098789           SRX2536420  ready
 18    SRR5227306       SRP098789           SRX2536421  ready
 19    SRR5227307       SRP098789           SRX2536422  ready
 20    SRR5227308       SRP098789           SRX2536423  ready
 21    SRR5227309       SRP098789           SRX2536424  ready
 22    SRR5227310       SRP098789           SRX2536425  ready
 23    SRR5227311       SRP098789           SRX2536426  ready
 24    SRR5227312       SRP098789           SRX2536427  ready
 25    SRR5227313       SRP098789           SRX2536428  ready]