Pysradb

Bugfix

- Fixed unicode error in tests for Python2

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

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

New methods/functionality

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

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.

- First release on PyPI.