History#

2.1.0 (2023-05-16)#

  • Fix for gse-to-srp returning unrequested GSEs (#186 <https://github.com/saketkc/pysradb/issues/190>)

  • Fix for download using public_urls

  • Fix for gsm-to-srx returning false positives (#165 <https://github.com/saketkc/pysradb/issues/165>)

  • Fix for delimiter not being consistent when metadata is printed on terminal (#147 <https://github.com/saketkc/pysradb/issues/147>)

  • NOTE: ENA search is currently broken because of an API change

2.0.2 (2023-04-09)#

<<<<<<< HEAD * Fix for gse-to-srp to handle cases where a project is missing but SRXs

are returned (#186 <https://github.com/saketkc/pysradb/issues/186>)

  • Fix gse-to-gsm (#187 <https://github.com/saketkc/pysradb/issues/187>)

2.0.1 (2023-03-18)#

  • Fix for pysradb download - using public_url

  • Fix for SRX -> SRR and related conversions (#183 <https://github.com/saketkc/pysradb/pull/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 <https://github.com/saketkc/pysradb/issues/89#issuecomment-1439319532>)

1.4.2 (06-17-2022)#

  • Fix ENA fastq fetching (#163 <https://github.com/saketkc/pysradb/issues/163>)

1.4.1 (06-04-2022)#

  • Fix for fetchin alternative URLs

1.4.0 (06-04-2022)#

  • Added ability to fetch alternative URLs (GCP/AWS) for metadata (#161 <https://github.com/saketkc/pysradb/issues/161>)

  • Fix for xmldict 0.13.0 no longer defaulting to OrderedDict (#159 <https://github.com/saketkc/pysradb/pull/159>)

  • Fix for missing experiment model and description in metadata (#160 <https://github.com/saketkc/pysradb/issues/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 <https://github.com/saketkc/pysradb/pull/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 (saketkc/pysradb#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.