louiejtaylor grabseqs issues

louiejtaylor / grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

MIT License

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issues

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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