Fixed bug, where description was not populated in PEP
[0.12.4] -- 2023-08-01
Fixed SRA convert
Added how to convert SRA
[0.12.3] -- 2023-06-21
Fixed preserving order of project keys (#119)
[0.12.2] -- 2023-04-25
Added max-prefetch-size argument. #113
Improved code and logger structure.
[0.12.0] -- 2023-03-27
Added functionality that saves gse metadata to config file
Fixed description in initialization of pepy object
[0.11.2] -- 2022-12-25
Changed sample_name of PEP of processed files to file oriented
Added --max-soft-size argument, that sets size limit of soft files
Added functionality that skips downloading GEO tables that are in soft files
Fixed bug of creating unwanted empty folders
Fixed problem with missing data
[0.11.1] -- 2022-11-28
Fixed requirements file
Fixed bug in expanding metadata list
Fixed bug in metadata links
[0.11.0] -- 2022-10-26
Added initialization of peppy Project without saving any files (from within Python using an API)
Added Finder (searching GSE tool)
Added progress bar
Switched way of saving soft files to request library
Improved documentation
Refactored code
Added --add-convert-modifier flag
fixed looper amendments in the config file
Fixed special character bug in the config file
Fixed None issue in config file
Fixed saving raw peps bug
[0.10.1] -- 2022-08-04
Updated metadata fetching requests from SRA database
[0.10.0] -- 2022-07-07
Fixed subprocesses continuing to run during program interrupt.
Fixed issues with compatibility with NCBI API
[0.9.0] -- 2022-06-20
Updated --pipeline-interface argument that adds it in for looper. --pipeline-interface argument was divided into:
--pipeline-samples and --pipeline-project.
Fixed empty sample_name error while creating PEP.
Added --discard-soft argument.
Added --const-limit-project argument.
Added --const-limit-discard argument.
Added --attr-limit-truncate argument.
Added "--add-dotfile" argument.
Disabled creating combined pep when flag --acc-anno is set.
Improved finding and separating metadata keys and genome assembly information.
Added standardization of column names by replacing characters to lowercase and spaces by underscore.
[0.8.0] -- 2022-03-10
Added --filter-size argument.
Added --data-source argument.
Removed --tar_re argument.
Added PEP for processed data.
Updated regex filter (case-insensitive update).
Changed way of downloading processed data (downloading each file separately).
Fixed code errors.
Separated sample and experiment processed data.
[0.7.0] -- 2020-05-21
Fixed user interface for bam conversions
Added regex filter for processed data filenames, which will also auto-extract from tar archives
Updated output to PEP 2.0
Added --skip argument
Added more control over where to store results.
Integrate sraconvert into geofetch package.
[0.6.0] -- 2019-06-20
Fixed a bug with specifying a processed data output folder
Added a pre-check and warning message for prefetch command
[0.5.0] -- 2019-05-09
geofetch will now re-try a failed prefetch 3 times and warn if unsuccessful.
Fixed a bug that prevented writing metadata in python3.