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GitHub / louiejtaylor/grabseqs issues and pull requests

#57 - 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

Issue - State: open - Opened by Damianyangyang about 1 year ago - 1 comment

#56 - Grabseqs error

Issue - State: open - Opened by xsq2022 about 2 years ago - 9 comments

#55 - All grabseqs SRA downloads failing

Issue - State: open - Opened by cdiener over 2 years ago - 9 comments

#54 - Add support to download data from National Genomics Data Center

Issue - State: open - Opened by sejsong over 4 years ago

#53 - Add support to download data from EBI

Issue - State: open - Opened by ElDeveloper over 4 years ago - 3 comments

#52 - Properly handle accession numbers which aren't associated with samples

Pull Request - State: closed - Opened by louiejtaylor over 4 years ago

#51 - error handling when sra accession doesn't exist / doesn't return runs

Issue - State: closed - Opened by a-h-b over 4 years ago - 1 comment

#50 - add citation info

Pull Request - State: closed - Opened by louiejtaylor over 4 years ago

#49 - Add a tutorial for adding a new repository using the repo template

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#48 - v0.7.0

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#47 - Allow custom fast(er)qdump args

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#46 - Abstract sample and project parsing logic from init.py

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#45 - grabseqs and geofetch

Issue - State: open - Opened by nsheff almost 5 years ago

#44 - Allow users to pass custom args to fast(er)q-dump

Issue - State: closed - Opened by louiejtaylor almost 5 years ago

#43 - Fix pigz attempting to zip files that don't exist

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#42 - grabseqs v0.6.0

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#41 - Reorganize and improve tests

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#40 - Gracefully handle missing dependencies

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#39 - Ensure compatibility with multiple Python versions

Pull Request - State: closed - Opened by louiejtaylor almost 5 years ago

#38 - Not compatible with Python 3.7?

Issue - State: closed - Opened by dutchscientist almost 5 years ago - 4 comments

#37 - handle users not having fasterq-dump installed

Pull Request - State: closed - Opened by louiejtaylor about 5 years ago

#36 - Dependency check

Issue - State: closed - Opened by louiejtaylor about 5 years ago

#35 - Check to see whether user has fasterq-dump installed

Issue - State: closed - Opened by louiejtaylor about 5 years ago - 1 comment

#34 - pigz attempting to zip files that don't exist

Issue - State: closed - Opened by louiejtaylor about 5 years ago - 1 comment

#33 - fix #32, use conda activate in test script

Pull Request - State: closed - Opened by louiejtaylor over 5 years ago

#32 - Use "conda deactivate" instead of "source deactivate"

Issue - State: closed - Opened by louiejtaylor over 5 years ago

#31 - Refactor code

Issue - State: closed - Opened by louiejtaylor over 5 years ago
Labels: enhancement

#30 - SRA metadata not including BioSample attributes

Issue - State: open - Opened by ressy over 5 years ago - 4 comments
Labels: enhancement

#29 - Version 0.5.0 breaks numpy

Issue - State: closed - Opened by louiejtaylor over 5 years ago - 3 comments

#28 - Add callout to FAQ in main README

Issue - State: closed - Opened by louiejtaylor over 5 years ago

#27 - Fix iMicrobe tests

Pull Request - State: closed - Opened by louiejtaylor over 5 years ago

#26 - Format metadata

Pull Request - State: closed - Opened by louiejtaylor over 5 years ago

#25 - fasterq-dump error:

Issue - State: closed - Opened by EisenRa over 5 years ago - 3 comments

#24 - Figure out why iMicrobe breaks on circleCI

Issue - State: closed - Opened by louiejtaylor over 5 years ago

#23 - Make --no_SRR_parsing default

Issue - State: closed - Opened by louiejtaylor over 5 years ago

#22 - Nicely format SRA, MG-RAST, and iMicrobe metadata

Issue - State: closed - Opened by ArwaAbbas almost 6 years ago - 3 comments

#21 - Add imicrobe

Pull Request - State: closed - Opened by ArwaAbbas almost 6 years ago

#20 - Add tests for iMicrobe

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#19 - Add template, abstract some functions

Pull Request - State: closed - Opened by louiejtaylor almost 6 years ago

#18 - Filter output from `-l` to conform with expected result from `--no_parsing` flag

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#17 - Look into downloading from iMicrobe

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#16 - Migrate tests to be platform-independent

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#15 - Add tests for not clobbering already-downloaded samples

Issue - State: closed - Opened by louiejtaylor almost 6 years ago - 1 comment

#14 - Running with previously downloaded file prints hundreds of thousands of "helpful" messages

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#13 - Add a -l option for MG-RAST

Issue - State: closed - Opened by louiejtaylor almost 6 years ago
Labels: enhancement

#12 - For SRA downloading, make sure pigz zips only the correct sequence files

Issue - State: closed - Opened by louiejtaylor almost 6 years ago - 1 comment
Labels: bug

#11 - Add documentation/FAQs for all subparsers

Issue - State: closed - Opened by louiejtaylor almost 6 years ago
Labels: enhancement

#10 - Add integration tests for a few (very small) .fastq files

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#9 - Allow the user to use `fastq-dump` instead of `fasterq-dump` if they want

Issue - State: closed - Opened by louiejtaylor almost 6 years ago
Labels: enhancement

#8 - Warn the user if the SRA metadata "paired/unpaired" information does not match which reads come down

Issue - State: closed - Opened by louiejtaylor almost 6 years ago - 1 comment

#7 - More intelligently handle HTTP errors in downloading MG-RAST files

Issue - State: open - Opened by louiejtaylor almost 6 years ago - 1 comment
Labels: bug

#6 - Abstract metadata-parsing and downloading functions to separate modules

Issue - State: closed - Opened by louiejtaylor almost 6 years ago
Labels: enhancement

#5 - add circleci test

Pull Request - State: closed - Opened by louiejtaylor almost 6 years ago

#4 - Retries parameter should be improved

Issue - State: closed - Opened by louiejtaylor almost 6 years ago

#3 - download a list of SRR

Issue - State: closed - Opened by guanxiangliang about 6 years ago - 4 comments

#2 - allow restarting if download fails

Issue - State: closed - Opened by louiejtaylor about 6 years ago

#1 - gzip fasterq-dump output

Issue - State: closed - Opened by louiejtaylor about 6 years ago
Labels: enhancement