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louiejtaylor
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grabseqs
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
MIT License
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grabseqs sra -l PRJDB5400 pigz not found, using gzip Traceback (most recent call last): File "/home/tools/anaconda3/bin/grabseqs", line 8, in <module> sys.exit(main()) File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/__init__.py", line 58, in main metadata_agg = process_sra(args, zip_func) File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/sra.py", line 27, in process_sra acclist, metadata_agg = get_sra_acc_metadata(sra_identifier, File "/home/tools/anaconda3/lib/python3.8/site-packages/grabseqslib/sra.py", line 97, in get_sra_acc_metadata run_col = lines[0].index("Run") ValueError: 'Run' is not in list
#57
Damianyangyang
opened
1 year ago
1
Grabseqs error
#56
xsq2022
opened
1 year ago
9
All grabseqs SRA downloads failing
#55
cdiener
opened
2 years ago
10
Add support to download data from National Genomics Data Center
#54
sejsong
opened
4 years ago
0
Add support to download data from EBI
#53
ElDeveloper
opened
4 years ago
3
Properly handle accession numbers which aren't associated with samples
#52
louiejtaylor
closed
4 years ago
0
error handling when sra accession doesn't exist / doesn't return runs
#51
a-h-b
closed
4 years ago
1
add citation info
#50
louiejtaylor
closed
4 years ago
0
Add a tutorial for adding a new repository using the repo template
#49
louiejtaylor
closed
4 years ago
0
v0.7.0
#48
louiejtaylor
closed
4 years ago
0
Allow custom fast(er)qdump args
#47
louiejtaylor
closed
4 years ago
0
Abstract sample and project parsing logic from __init__.py
#46
louiejtaylor
closed
4 years ago
0
grabseqs and geofetch
#45
nsheff
opened
4 years ago
0
Allow users to pass custom args to fast(er)q-dump
#44
louiejtaylor
closed
4 years ago
0
Fix pigz attempting to zip files that don't exist
#43
louiejtaylor
closed
4 years ago
0
grabseqs v0.6.0
#42
louiejtaylor
closed
4 years ago
0
Reorganize and improve tests
#41
louiejtaylor
closed
4 years ago
0
Gracefully handle missing dependencies
#40
louiejtaylor
closed
4 years ago
0
Ensure compatibility with multiple Python versions
#39
louiejtaylor
closed
4 years ago
0
Not compatible with Python 3.7?
#38
dutchscientist
closed
4 years ago
4
handle users not having fasterq-dump installed
#37
louiejtaylor
closed
4 years ago
0
Dependency check
#36
louiejtaylor
closed
4 years ago
0
Check to see whether user has fasterq-dump installed
#35
louiejtaylor
closed
4 years ago
1
pigz attempting to zip files that don't exist
#34
louiejtaylor
closed
4 years ago
1
fix #32, use conda activate in test script
#33
louiejtaylor
closed
5 years ago
0
Use "conda deactivate" instead of "source deactivate"
#32
louiejtaylor
closed
5 years ago
0
Refactor code
#31
louiejtaylor
closed
4 years ago
0
SRA metadata not including BioSample attributes
#30
ressy
opened
5 years ago
4
Version 0.5.0 breaks numpy
#29
louiejtaylor
closed
5 years ago
3
Add callout to FAQ in main README
#28
louiejtaylor
closed
5 years ago
0
Fix iMicrobe tests
#27
louiejtaylor
closed
5 years ago
0
Format metadata
#26
louiejtaylor
closed
5 years ago
0
fasterq-dump error:
#25
EisenRa
closed
5 years ago
3
Figure out why iMicrobe breaks on circleCI
#24
louiejtaylor
closed
5 years ago
0
Make --no_SRR_parsing default
#23
louiejtaylor
closed
5 years ago
0
Nicely format SRA, MG-RAST, and iMicrobe metadata
#22
ArwaAbbas
closed
5 years ago
3
Add imicrobe
#21
ArwaAbbas
closed
5 years ago
0
Add tests for iMicrobe
#20
louiejtaylor
closed
5 years ago
0
Add template, abstract some functions
#19
louiejtaylor
closed
5 years ago
0
Filter output from `-l` to conform with expected result from `--no_parsing` flag
#18
louiejtaylor
closed
5 years ago
0
Look into downloading from iMicrobe
#17
louiejtaylor
closed
5 years ago
0
Migrate tests to be platform-independent
#16
louiejtaylor
closed
5 years ago
0
Add tests for not clobbering already-downloaded samples
#15
louiejtaylor
closed
5 years ago
1
Running with previously downloaded file prints hundreds of thousands of "helpful" messages
#14
louiejtaylor
closed
5 years ago
0
Add a -l option for MG-RAST
#13
louiejtaylor
closed
5 years ago
0
For SRA downloading, make sure pigz zips only the correct sequence files
#12
louiejtaylor
closed
5 years ago
1
Add documentation/FAQs for all subparsers
#11
louiejtaylor
closed
5 years ago
0
Add integration tests for a few (very small) .fastq files
#10
louiejtaylor
closed
5 years ago
0
Allow the user to use `fastq-dump` instead of `fasterq-dump` if they want
#9
louiejtaylor
closed
5 years ago
0
Warn the user if the SRA metadata "paired/unpaired" information does not match which reads come down
#8
louiejtaylor
closed
4 years ago
1
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