Parallel Download¶
This notebook demonstrates how to download multiple SRA datasets in parallel using joblib.
[ ]:
# 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!")
[1]:
# pip install git+https://github.com/saketkc/pysradb
[2]:
pip install joblib
Requirement already satisfied: joblib in /home/saket/miniforge3/lib/python3.12/site-packages (1.5.2)
Note: you may need to restart the kernel to use updated packages.
[3]:
from joblib import Parallel, delayed
[4]:
from pysradb.sraweb import SRAweb
db = SRAweb()
/home/saket/miniforge3/lib/python3.12/site-packages/pysradb/utils.py:14: 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
[5]:
df = db.sra_metadata("SRP098789", detailed=True)
df
[5]:
| run_accession | study_accession | study_title | experiment_accession | experiment_title | experiment_desc | organism_taxid | organism_name | library_name | library_strategy | ... | source_name | cell line | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_Veh_60 min_Ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_vehcile_60 min_Ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_PF-06446846_60 min_mRNA-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_vehicle_60 min_RNA-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_PF-06446846_60 min_mRNA-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_vehicle_60 min_RNA-seq | Huh7 | 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> |
26 rows × 54 columns
[6]:
# randomply split into two dataframes
df1, df2 = df.iloc[:5, :], df.iloc[5:, :]
df2
[6]:
| run_accession | study_accession | study_title | experiment_accession | experiment_title | experiment_desc | organism_taxid | organism_name | library_name | library_strategy | ... | source_name | cell line | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_10 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_0.3 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_vehicle_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_Veh_60 min_Ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_1.5 µM PF-067446846_60 min_ribo-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_vehcile_60 min_Ribo-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_PF-06446846_60 min_mRNA-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_vehicle_60 min_RNA-seq | Huh7 | 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> |
| 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 | <NA> | OTHER | ... | Huh7_PF-06446846_60 min_mRNA-seq | Huh7 | 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> |
| 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 | <NA> | RNA-Seq | ... | Huh7_vehicle_60 min_RNA-seq | Huh7 | 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> |
21 rows × 54 columns
[7]:
def single_download(df_single):
db.download(df=df_single, skip_confirmation=True)
[8]:
Parallel(n_jobs=2)(delayed(single_download)(df_x) for df_x in [df1, df2])
Checking download URLs
Checking download URLs
The following files will be downloaded:
run_accession study_accession experiment_accession public_url download_url out_dir filesize
SRR5227288 SRP098789 SRX2536403 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227288/SRR5227288.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227288/SRR5227288.sra /data/github/pysradb/notebooks/pysradb_downloads 533.5 MB
SRR5227289 SRP098789 SRX2536404 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227289/SRR5227289.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227289/SRR5227289.sra /data/github/pysradb/notebooks/pysradb_downloads 603.2 MB
SRR5227290 SRP098789 SRX2536405 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227290/SRR5227290.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227290/SRR5227290.sra /data/github/pysradb/notebooks/pysradb_downloads 586.1 MB
SRR5227291 SRP098789 SRX2536406 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227291.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227291/SRR5227291.sra /data/github/pysradb/notebooks/pysradb_downloads 521.5 MB
SRR5227292 SRP098789 SRX2536407 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227292.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227292/SRR5227292.sra /data/github/pysradb/notebooks/pysradb_downloads 871.3 MB
Total size: 3.1 GB
0%| | 0/5 [00:00<?, ?it/s]
The following files will be downloaded:
run_accession study_accession experiment_accession public_url download_url out_dir filesize
SRR5227293 SRP098789 SRX2536408 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227293.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227293/SRR5227293.sra /data/github/pysradb/notebooks/pysradb_downloads 616.6 MB
SRR5227294 SRP098789 SRX2536409 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227294.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227294/SRR5227294.sra /data/github/pysradb/notebooks/pysradb_downloads 962.4 MB
SRR5227295 SRP098789 SRX2536410 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227295.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227295/SRR5227295.sra /data/github/pysradb/notebooks/pysradb_downloads 668.3 MB
SRR5227296 SRP098789 SRX2536411 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227296.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227296/SRR5227296.sra /data/github/pysradb/notebooks/pysradb_downloads 755.3 MB
SRR5227297 SRP098789 SRX2536412 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227297.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227297/SRR5227297.sra /data/github/pysradb/notebooks/pysradb_downloads 869.8 MB
SRR5227298 SRP098789 SRX2536413 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227298.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227298/SRR5227298.sra /data/github/pysradb/notebooks/pysradb_downloads 681.0 MB
SRR5227299 SRP098789 SRX2536414 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227299.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227299/SRR5227299.sra /data/github/pysradb/notebooks/pysradb_downloads 702.4 MB
SRR5227300 SRP098789 SRX2536415 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227300.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227300/SRR5227300.sra /data/github/pysradb/notebooks/pysradb_downloads 438.7 MB
SRR5227301 SRP098789 SRX2536416 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227301.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227301/SRR5227301.sra /data/github/pysradb/notebooks/pysradb_downloads 707.4 MB
SRR5227302 SRP098789 SRX2536417 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227302.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227302/SRR5227302.sra /data/github/pysradb/notebooks/pysradb_downloads 642.3 MB
SRR5227303 SRP098789 SRX2536418 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227303.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227303/SRR5227303.sra /data/github/pysradb/notebooks/pysradb_downloads 733.0 MB
SRR5227304 SRP098789 SRX2536419 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227304.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227304/SRR5227304.sra /data/github/pysradb/notebooks/pysradb_downloads 682.1 MB
SRR5227305 SRP098789 SRX2536420 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227305.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227305/SRR5227305.sra /data/github/pysradb/notebooks/pysradb_downloads 698.4 MB
SRR5227306 SRP098789 SRX2536421 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227306.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227306/SRR5227306.sra /data/github/pysradb/notebooks/pysradb_downloads 838.8 MB
SRR5227307 SRP098789 SRX2536422 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227307.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227307/SRR5227307.sra /data/github/pysradb/notebooks/pysradb_downloads 965.8 MB
SRR5227308 SRP098789 SRX2536423 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR005/227/SRR5227308/SRR5227308.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227308/SRR5227308.sra /data/github/pysradb/notebooks/pysradb_downloads 953.1 MB
SRR5227309 SRP098789 SRX2536424 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227309.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227309/SRR5227309.sra /data/github/pysradb/notebooks/pysradb_downloads 586.8 MB
SRR5227310 SRP098789 SRX2536425 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227310.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227310/SRR5227310.sra /data/github/pysradb/notebooks/pysradb_downloads 965.6 MB
SRR5227311 SRP098789 SRX2536426 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227311.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227311/SRR5227311.sra /data/github/pysradb/notebooks/pysradb_downloads 926.0 MB
SRR5227312 SRP098789 SRX2536427 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227312.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227312/SRR5227312.sra /data/github/pysradb/notebooks/pysradb_downloads 846.2 MB
SRR5227313 SRP098789 SRX2536428 https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/227/SRR5227313.sralite.1 ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR522/SRR5227313/SRR5227313.sra /data/github/pysradb/notebooks/pysradb_downloads 1.0 GB
Total size: 16.2 GB
100%|██████████| 5/5 [06:17<00:00, 75.54s/it]]
100%|██████████| 21/21 [25:17<00:00, 72.24s/it]
[8]:
[None, None]