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Recent Releases of pysradb

pysradb - v2.3.0

What's Changed

  • Handle missing VALUE in value_x dict by @andrewdavidsmith in https://github.com/saketkc/pysradb/pull/223
  • Merge develop to master by @saketkc in https://github.com/saketkc/pysradb/pull/236

New Contributors

  • @andrewdavidsmith made their first contribution in https://github.com/saketkc/pysradb/pull/223

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.2.2...2.3.0

- Python
Published by saketkc 7 months ago

pysradb - v2.2.2

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.2.1...v2.2.2

- Python
Published by saketkc over 1 year ago

pysradb - v2.2.1

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.2.0...v2.2.1

- Python
Published by saketkc over 1 year ago

pysradb - v2.2.0

What's Changed

  • Fix GeoSearch elink using retmode xml by @jggatter in https://github.com/saketkc/pysradb/pull/200
  • Capture Biosample and Bioproject by @jggatter in https://github.com/saketkc/pysradb/pull/199
  • Fix typos SRAWeb -> SRAweb by @jggatter in https://github.com/saketkc/pysradb/pull/198

New Contributors

  • @jggatter made their first contribution in https://github.com/saketkc/pysradb/pull/200

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.1.0...v2.2.0

- Python
Published by saketkc over 2 years ago

pysradb - v2.1.0

  • Fix for gse-to-srp returning unrequested GSEs #186
  • Fix for download using public_urls
  • Fix for gsm-to-srx returning false positives #165
  • Fix for delimiter not being consistent when metadata is printed on terminal #147
  • ENA search is currently broken because of an API change

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.0.2...v2.1.0

- Python
Published by saketkc almost 3 years ago

pysradb - v2.0.2

What's Changed

  • Handle all links by @saketkc in https://github.com/saketkc/pysradb/pull/177

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.0.1...v2.0.2

- Python
Published by saketkc almost 3 years ago

pysradb - v2.0.1

What's Changed

  • Fix SRX -> SRR conversion by @tfehlmann in https://github.com/saketkc/pysradb/pull/183

New Contributors

  • @tfehlmann made their first contribution in https://github.com/saketkc/pysradb/pull/183

Full Changelog: https://github.com/saketkc/pysradb/compare/v2.0.0...v2.0.1

- Python
Published by saketkc almost 3 years ago

pysradb - v2.0

  • BREAKING change: Overhaul of how urls and associated metadata are returned (not backward compatible); all column names are lower cased by default
  • Fix extra space in "organism_taxid" column
  • Added support for Experiment attributes (#89 <https://github.com/saketkc/pysradb/issues/89#issuecomment-1439319532>)

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.4.2...v2.0.0

- Python
Published by saketkc about 3 years ago

pysradb - v1.4.2

  • Fix ENA fastq fetching #163

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.4.1...v1.4.2

- Python
Published by saketkc over 3 years ago

pysradb - v1.4.1

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.4.0...v1.4.1

  • Fix for fetching alternative URLs in metadata --detailed

- Python
Published by saketkc almost 4 years ago

pysradb - v1.4.0

What's Changed

  • Added ability to fetch alternative URLs (GCP/AWS) for metadata #161
  • Fix for xmldict 0.13.0 no longer defaulting to OrderedDict #159 by @zhoulytwinyu
  • Fix for missing experiment model and description in metadata #160

New Contributors

  • @zhoulytwinyu made their first contribution in https://github.com/saketkc/pysradb/pull/159

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.3.0...v1.4.0

- Python
Published by saketkc almost 4 years ago

pysradb - v1.3.0

1.3.0 (02-18-2022)

  • Add study_title to --detailed flag (#152 <https://github.com/saketkc/pysradb/issues/152>_)
  • Fix KeyError in metadata where some new IDs do not have any metadata (#151 <https://github.com/saketkc/pysradb/issues/151>_)

What's Changed

  • Do not exit on no search hits by @saketkc in https://github.com/saketkc/pysradb/pull/149
  • Fix typos in README by @mphschmitt in https://github.com/saketkc/pysradb/pull/150

New Contributors

  • @mphschmitt made their first contribution in https://github.com/saketkc/pysradb/pull/150

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.1.0...v1.3.0

- Python
Published by saketkc about 4 years ago

pysradb - v1.2.0

  • Do not exit if a qeury returns no hits (#149)

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.1.0...v1.2.0

- Python
Published by saketkc about 4 years ago

pysradb - v1.1.0

What's Changed

  • Gsm to gse fix by @DevangThakkar in https://github.com/saketkc/pysradb/pull/128
  • Add support for downloading GEO files by @DevangThakkar in https://github.com/saketkc/pysradb/pull/129
  • Ena bug by @bscrow in https://github.com/saketkc/pysradb/pull/144
  • Pub date by @bscrow in https://github.com/saketkc/pysradb/pull/146

New Contributors

  • @DevangThakkar made their first contribution in https://github.com/saketkc/pysradb/pull/128

Full Changelog: https://github.com/saketkc/pysradb/compare/v1.0.1...v1.1.0

- Python
Published by saketkc about 4 years ago

pysradb -

  • Dropped Python 3.6 since pandas 1.2 is not supported

- Python
Published by saketkc about 5 years ago

pysradb -

1.0.0 (01-09-2021)

  • Retired metadb and SRAdb based search through CLI - everything defaults to SRAweb
  • SRAweb now supports search <https://saket-choudhary.me/pysradb/quickstart.html#search>_
  • N/A is now replcaced with pd.NA
  • Two new fields in --detailed: instrument_model and instrument_model_desc #75
  • Updated documentation

- Python
Published by saketkc about 5 years ago

pysradb -

  • library_layout is now outputted in metadata #56
  • detailed unifies columns for ENA fastq links instead of appending x/y #59
  • bugfix for parsing namespace in xml outputs #65
  • XML errors from NCBI are now handled more gracefully #69
  • Documentation and dependency updates

- Python
Published by saketkc over 5 years ago

pysradb -

  • pysradb download now supports multiple threads for paralle downloads
  • pysradb download also supports ultra fast downloads of FASTQs from ENA using aspera-client

- Python
Published by saketkc over 5 years ago

pysradb -

  • Fixed a bug in detailed mode with multiple SRPs
  • Added requirements to MANIFEST

- Python
Published by saketkc almost 6 years ago

pysradb -

  • Added test cases for SRAweb
  • API limit exceeding errors are automagically handled
  • Bug fixes for GSE <=> SRR
  • Bug fix for metadata - supports multiple SRPs

- Python
Published by saketkc almost 6 years ago

pysradb -

  • Bug fix: Handle API-rate limit exceeding => Retries
  • Enhancement: 'Alternatives' URLs are now part of --detailed

- Python
Published by saketkc about 6 years ago

pysradb -

  • Bug fix: Handle Python3.6 for capture_output in subprocess.run

- Python
Published by saketkc about 6 years ago

pysradb -

  • All the subcommands (srx-to-srr, srx-to-srs) will now print additional columns where the first two columns represent the relevant conversion
  • Fixed a bug where for fetching entries with single efetch record

- Python
Published by saketkc about 6 years ago

pysradb -

  • Major fix: some SRRs would go missing as the experiment dict was being created only once per SRR (See #15)
  • Features: More detailed metadata by default in the SRAweb mode

See notebook: https://colab.research.google.com/drive/1C60V-jkcNZiaCra_V5iEyFs318jgVoUR

- Python
Published by saketkc about 6 years ago

pysradb -

  • Metadata: instrument, run size and total spots are now printed in the metadata by default (SRAweb mode only)
  • Issue: Fixed an issue with srapath failing on SRP. srapath is now run on individual SRRs.

- Python
Published by saketkc about 6 years ago

pysradb - ISMB/ECCB 2019 release

This version of pysradb introduces `SRAweb to perform queries over the web if the SQLite is missing or does not contain the relevant record.

- Python
Published by saketkc over 6 years ago

pysradb -

0.9.0 (02-27-2019)

Others

  • This release completely changes the command line interface replacing click with argparse (https://github.com/saketkc/pysradb/pull/3)
  • Removed Python 2 comptaible stale code

- Python
Published by saketkc about 7 years ago

pysradb -

0.8.0 (02-26-2019)

New methods/functionality

  • srr-to-gsm: convert SRR to GSM
  • SRAmetadb.sqlite.gz file is deleted by default after extraction
  • When SRAmetadb is not found a confirmation is seeked before downloading
  • Confirmation option before SRA downloads

- Python
Published by saketkc about 7 years ago

pysradb -

0.7.1 (02-18-2019)

Important: Python2 is no longer supported. Please consider moving to Python3.

Bugfix

  • Included docs in the index whihch were missed out in the previous release

- Python
Published by saketkc about 7 years ago

pysradb -

0.7.0 (02-08-2019)

New methods/functionality

  • gsm-to-srr: convert GSM to SRR
  • gsm-to-srx: convert GSM to SRX
  • gsm-to-gse: convert GSM to GSE

Renamed methods

The following commad line options have been renamed and the changes are not compatible with 0.6.0 release:

  • sra-metadata -> metadata.
  • sra-search -> search.
  • srametadb -> metadb.

- Python
Published by saketkc about 7 years ago

pysradb -

0.6.0 (12-25-2018)

Bugfix

  • Fixed bugs introduced in 0.5.0 with API changes where multiple redundant columns were output in sra-metadata

New methods/functionality

  • download now allows piped inputs

- Python
Published by saketkc about 7 years ago

pysradb -

0.5.0 (12-24-2018)

New methods/functionality

  • Support for filtering by SRX Id for SRA downloads.
  • srr_to_srx: Convert SRR to SRX/SRP
  • srp_to_srx: Convert SRP to SRX
  • Stripped down sra-metadata to give minimal information
  • Added --assay, --desc, --detailed flag for sra-metadata
  • Improved table printing on terminal

- Python
Published by saketkc about 7 years ago

pysradb -

0.4.2 (12-16-2018)

Bugfix

  • Fixed unicode error in tests for Python2

- Python
Published by saketkc about 7 years ago

pysradb - Zenodo release

Archiving on Zenodo.

New methods/functionality

  • New command line utility srp-to-srx to convert SRP to SRX/SRR

- Python
Published by saketkc about 7 years ago

pysradb -

0.4.0 (12-12-2018)

New methods/functionality

  • Added a new BASEdb class to handle common database connections
  • Initial support for GEOmetadb through GEOdb class
  • Initial support or a command line interface:
    • download Download SRA project (SRPnnnn)
    • gse-metadata Fetch metadata for GEO ID (GSEnnnn)
    • gse-to-gsm Get GSM(s) for GSE
    • gsm-metadata Fetch metadata for GSM ID (GSMnnnn)
    • sra-metadata Fetch metadata for SRA project (SRPnnnn)
  • Added three separate notebooks for SRAdb, GEOdb, CLI usage

- Python
Published by saketkc about 7 years ago

pysradb -

0.3.0 (12-05-2018)

New methods/functionality

  • sample_attribute and experiment_attribute are now included by default in the df returned by sra_metadata()
  • expand_sample_attribute_columns: expand metadata dataframe based on attributes insample_attribute` column
  • New methods to guess cell/tissue/strain: guess_cell_type()/guess_tissue_type()/guess_strain_type()
  • Improved README and usage instructions

- Python
Published by saketkc over 7 years ago

pysradb - Implemented full text search

New methods/functionality

  • search_sra() allows full text search on SRA metadata.

- Python
Published by saketkc over 7 years ago

pysradb - v0.2.0

0.2.0 (12-03-2018)

Renamed methods

The following methods have been renamed and the changes are not compatible with 0.1.0 release:

  • get_query() -> query().
  • sra_convert() -> sra_metadata().
  • get_table_counts() -> all_row_counts().

New methods/functionality

  • download_sradb_file() makes fetching SRAmetadb.sqlite file easy; wget is no longer required.
  • ftp protocol is now supported besides fsp and hence aspera-client is now optional. We however, strongly recommend aspera-client for faster downloads.

Bug fixes

  • Silenced SettingWithCopyWarning by excplicitly doing operations on a copy of the dataframe instead of the original.

Besides these, all methods now follow a numpydoc compatible documentation.

- Python
Published by saketkc over 7 years ago