v0.5.0

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0.5.0 (12-24-2018)

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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

v0.4.2

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0.4.2 (12-16-2018)

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Bugfix

• Fixed unicode error in tests for Python2

Zenodo release

Archiving on Zenodo.

New methods/functionality

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

v0.4.0

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0.4.0 (12-12-2018)

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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

v0.3.0

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0.3.0 (12-05-2018)

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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

Implemented full text search

New methods/functionality

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

v0.2.0

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0.2.0 (12-03-2018)

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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.