Changelogs » Pysradb

Pysradb

0.10.3

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* 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

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0.10.2

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

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0.10.1

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

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0.10.0

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* 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

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0.9.9

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* 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-

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0.9.7

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* 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.

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0.9.6

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* Introduced `SRAweb` to perform queries over the web if the SQLite is missing or does not contain the relevant record.

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0.9.0

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Others
======

* This release completely changes the command line interface replacing click with argparse (https://github.com/saketkc/pysradb/pull/3)
* Removed Python 2 comptaible stale code

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0.8.0

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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`


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0.7.1

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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


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0.7.0

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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`.



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0.6.0

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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




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0.5.0

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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


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0.4.2

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Bugfix
======

* Fixed unicode error in tests for Python2


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0.4.0

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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

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0.3.0

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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


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0.2.2

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New methods/functionality
=========================

* `search_sra()` allows full text search on SRA metadata.


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0.2.0

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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.


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0.1.0

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* First release on PyPI.