Skip to content

Latest commit

 

History

History
298 lines (201 loc) · 8.94 KB

HISTORY.md

File metadata and controls

298 lines (201 loc) · 8.94 KB
Raw

History

2.2.0 (2023-09-17)

  • Add support for Biosamples and bioproject #199
  • Use retmode xml for Geo search #200
  • Documentation fixes

2.1.0 (2023-05-16)

  • 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

2.0.2 (2023-04-09)

  • Fix for [gse-to-srp] to handle cases where a project is missing but SRXs are returned #186
  • Fix gse-to-gsm #187

2.0.1 (2023-03-18)

  • Fix for [pysradb download] - using [public_url]
  • Fix for SRX -> SRR and related conversions #183

2.0.0 (2023-02-23)

  • 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

1.4.2 (06-17-2022)

  • Fix ENA fastq fetching #163

1.4.1 (06-04-2022)

  • Fix for fetching alternative URLs

1.4.0 (06-04-2022)

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

1.3.0 (02-18-2022)

  • Add [study_title] to [--detailed] flag (#152)
  • Fix [KeyError] in [metadata] where some new IDs do not have any metadata (#151)

1.2.0 (01-10-2022)

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

1.1.0 (12-12-2021)

  • Fixed [gsm-to-gse] failure (#128)
  • Fixed case sensitivity bug for ENA search (#144)
  • Fixed publication date bug for search (#146)
  • Added support for downloading data from GEO [pysradb dowload -g GSE] (#129)

1.0.1 (01-10-2021)

  • Dropped Python 3.6 since pandas 1.2 is not supported

1.0.0 (01-09-2021)

  • Retired metadb and SRAdb based search through CLI - everything defaults to SRAweb
  • SRAweb now supports search
  • [N/A] is now replaced with [pd.NA]
  • Two new fields in `--detailed`: [instrument_model] and [instrument_model_desc] #75
  • Updated documentation

0.11.1 (09-18-2020)

  • [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

0.11.0 (09-04-2020)

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

0.10.3 (03-26-2020)

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

Contributors

  • Dibya Gautam
  • Marius van den Beek

0.10.2 (02-05-2020)

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

0.10.1 (02-04-2020)

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

0.10.0 (01-31-2020)

  • 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

0.9.9 (01-15-2020)

  • 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-

0.9.7 (01-20-2020)

  • Feature: 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.

0.9.6 (07-20-2019)

  • Introduced [SRAweb] to perform queries over the web if the SQLite is missing or does not contain the relevant record.

0.9.0 (02-27-2019)

Others

  • This release completely changes the command line interface replacing click with argparse (#3)
  • Removed Python 2 comptaible stale code

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

Bugfix

  • download() works with wget

Others

  • [--out_dir] is now [out-dir]

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

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].

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

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

0.4.2 (12-16-2018)

Bugfix

  • Fixed unicode error in tests for Python2

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

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 in `sample_attribute] column
  • New methods to guess cell/tissue/strain: [guess_cell_type()]/[guess_tissue_type()]/[guess_strain_type()]
  • Improved README and usage instructions

0.2.2 (12-03-2018)

New methods/functionality

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

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.

0.1.0 (12-01-2018)

  • First release on PyPI.