History

1.0.2 (Unreleased)

  • Fixed gsm-to-gse failure (#128)

  • 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

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.

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