Metadata-Version: 1.2
Name: pysradb
Version: 0.10.2
Summary: Python package for interacting with SRAdb and downloading datasets from SRA
Home-page: https://github.com/saketkc/pysradb
Author: Saket Choudhary
Author-email: saketkc@gmail.com
License: BSD license
Description: .. image:: https://raw.githubusercontent.com/saketkc/pysradb/master/docs/_static/pysradb_v3.png
            :target: https://raw.githubusercontent.com/saketkc/pysradb/master/docs/_static/pysradb_v3.png
        
        #####################################################################################
        pysradb: Python package for interacting with SRAdb and downloading datasets from SRA.
        #####################################################################################
        
        
        
        
        
        
        .. image:: https://img.shields.io/pypi/v/pysradb.svg?style=flat-square
            :target: https://pypi.python.org/pypi/pysradb
        
        .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
            :target: http://bioconda.github.io/recipes/pysradb/README.html
        
        .. image:: https://zenodo.org/badge/159590788.svg
            :target: https://zenodo.org/badge/latestdoi/159590788
        
        .. image:: https://img.shields.io/travis/saketkc/pysradb.svg?style=flat-square
            :target: https://travis-ci.com/saketkc/pysradb
        
        
        .. image:: https://asciinema.org/a/0C3SjYmPTkkemldprUpdVhiKx.svg
            :target: https://asciinema.org/a/0C3SjYmPTkkemldprUpdVhiKx?speed=5&autoplay=1
            
        ***********
        Publication
        ***********
        
         `pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive <https://f1000research.com/articles/8-532/v1>`_ 
         
         
         Presentation slides from BOSC (ISMB-ECCB) 2019: https://f1000research.com/slides/8-1183
        
        *********
        CLI Usage
        *********
        
        ``pysradb`` supports command line ussage. The documentation
        is in progress. See  `cmdline <https://github.com/saketkc/pysradb/blob/master/docs/cmdline.rst>`_ for
        some quick usage instructions. See `quickstart <https://www.saket-choudhary.me/pysradb/quickstart.html#the-full-list-of-possible-pysradb-operations>`_ for
        a list of instructions for each sub-command.
        
        
        ::
        
           $ pysradb
            usage: pysradb [-h] [--version] [--citation]
                           {metadb,metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
                           ...
        
            pysradb: Query NGS metadata and data from NCBI Sequence Read Archive.
            version: 0.9.0.
            Citation: 10.12688/f1000research.18676.1
        
            optional arguments:
              -h, --help            show this help message and exit
              --version             show program's version number and exit
              --citation            how to cite
        
            subcommands:
              {metadb,metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
                metadb              Download SRAmetadb.sqlite
                metadata            Fetch metadata for SRA project (SRPnnnn)
                download            Download SRA project (SRPnnnn)
                search              Search SRA for matching text
                gse-to-gsm          Get GSM for a GSE
                gse-to-srp          Get SRP for a GSE
                gsm-to-gse          Get GSE for a GSM
                gsm-to-srp          Get SRP for a GSM
                gsm-to-srr          Get SRR for a GSM
                gsm-to-srs          Get SRS for a GSM
                gsm-to-srx          Get SRX for a GSM
                srp-to-gse          Get GSE for a SRP
                srp-to-srr          Get SRR for a SRP
                srp-to-srs          Get SRS for a SRP
                srp-to-srx          Get SRX for a SRP
                srr-to-gsm          Get GSM for a SRR
                srr-to-srp          Get SRP for a SRR
                srr-to-srs          Get SRS for a SRR
                srr-to-srx          Get SRX for a SRR
                srs-to-gsm          Get GSM for a SRS
                srs-to-srx          Get SRX for a SRS
                srx-to-srp          Get SRP for a SRX
                srx-to-srr          Get SRR for a SRX
                srx-to-srs          Get SRS for a SRX
        
        
        **********
        Quickstart
        **********
        
        A Google Colaboratory version of most used commands are available in this `Colab Notebook <https://colab.research.google.com/drive/1C60V-jkcNZiaCra_V5iEyFs318jgVoUR>`_ . Note that this does not require you to download the heavy SQLite file and uses the `SRAWeb` mode (explained below).
        
        ************
        Installation
        ************
        
        
        To install stable version using `pip`:
        
        .. code-block:: bash
        
           pip install pysradb
        
        Alternatively, if you use conda:
        
        .. code-block:: bash
        
           conda install -c bioconda pysradb
        
        This step will install all the dependencies.
        If you have an existing environment with a lot of pre-installed packages, conda might be `slow <https://github.com/bioconda/bioconda-recipes/issues/13774>`_.
        Please consider creating a new enviroment for ``pysradb``:
        
        .. code-block:: bash
        
           conda create -c bioconda -n pysradb PYTHON=3 pysradb
        
        Dependecies
        ===========
        
        .. code-block:: bash
        
           pandas==0.25.3
           tqdm==4.41.1
           requests==2.22.0
           xmltodict=0.12.0
           sra-tools (required only if you want to also download)
        
        Installing sratools
        ===================
        
        NCBI has slowly transitioned towards using Google cloud for storing SRA files. As such
        the ftp links are slowly getting obsolete. With release ``0.9.5``, ``pysradb`` has
        moved to utilizing ``srapath``  available through NCBI's ``sra-tools`` for getting
        the SRA location. Thus ``aspera-client`` is no longer required. But, ``sra-tools``
        is now a requirement and can be installed through bioconda. We are in the process of
        doing away with this requirement completely soon.
        
        Downloading SRAmetadb (optional)
        =================================
        
        ``pysradb`` can utilize a SQLite database file that has preprocessed metadata made available by the
        `SRAdb <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-19>`_ project.
        Though, with the release ``0.9.5``, this database file is not a hard requirement for any of the operations.
        
        
        
        SRAmetadb can be downloaded using:
        
        .. code-block:: bash
        
           wget -c https://starbuck1.s3.amazonaws.com/sradb/SRAmetadb.sqlite.gz && gunzip SRAmetadb.sqlite.gz
        
        Alternatively, you can also download it using ``pysradb``, which by default downloads it into your
        current working directory:
        
        
        ::
        
            $ pysradb metadb
        
        You can also specify an alternate directory for download by supplying the ``--out-dir <OUT_DIR>`` argument.
        
        
        Installing pysradb in development mode
        ======================================
        
        .. code-block:: bash
        
           pip install -U pandas tqdm requests xmltodict
           git clone https://github.com/saketkc/pysradb.git
           cd pysradb
           pip install -e .
        
        
        
        *************
        Using pysradb
        *************
        
        Please see `usage_scenarios <https://saket-choudhary.me/pysradb/usage_scenarios.html>`_ for a few usage scenarios.
        Here are few hand-picked examples.
        
        
        Mode: SRAmetadb or SRAWeb
        =========================
        
        ``pysradb``'s initial versions were completely dependent on the ``SRAmnetadb.sqlite`` file made available by the ``SRAdb`` project, we refer to this as the ``SRAmetadb`` mode. However, with ```pysradb 0.9.5``, the depedence on the SQLite file has been made optional. In the abseence of the SQLite file, the operations are performed usiNCBi's ``esrarch`` and ``esummary`` interface, a mode which we refer to as the ``SRAweb`` mode.  All the operations
        with the exception of ``search`` can be performed withoudownloading the SQLite file.
        NOTE: The additional flags such as ``--desc``, ``-detailed`` and ``-expand`` are currently not fully supported in the ``SRAweb`` mode and will be supported in a future release. However, all the basic funcuionality of interconverting one ID to another is available in both ``SRAweb`` and ``SRAmetadb`` mode.
        
        
        
        Search
        ======
        
        Search for all projects containing "ribosome profiling":
        
        ::
        
           $  pysradb search "ribosome profiling" | head
        
            study_accession experiment_accession sample_accession run_accession
            DRP000927       DRX002899            DRS002983        DRR003575
            DRP000927       DRX002900            DRS002992        DRR003576
            DRP000927       DRX002901            DRS003001        DRR003577
            DRP000927       DRX002902            DRS003010        DRR003578
            DRP000927       DRX002903            DRS003019        DRR003579
            DRP000927       DRX002904            DRS003028        DRR003580
            DRP000927       DRX002905            DRS003037        DRR003581
            DRP000927       DRX002906            DRS003038        DRR003582
            DRP003075       DRX019536            DRS026974        DRR021383
        
        
        
        Getting SRA metadata
        ====================
        
        ::
        
            $ pysradb metadata --db ./SRAmetadb.sqlite SRP000941 --assay --desc --expand | head
        
            study_accession experiment_accession sample_accession run_accession library_strategy batch         biomaterial_provider             biomaterial_type cell_type    collection_method differentiation_method                                                                                                                     differentiation_stage                                                                disease                                                          donor_age donor_ethnicity                 donor_health_status                                                                                 donor_id donor_sex line          lineage                                                               medium                                                                                                                                                                                                   molecule     passage                             sample_term_id  sex     source_name              tissue                   tissue_depot tissue_type
            SRP000941       SRX006235            SRS004118        SRR018454     ChIP-Seq         NaN           cellular dynamics international  cell line        NaN          NaN               none                                                                                                                                       none                                                                                 none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            embryonic stem cell                                                   mteser                                                                                                                                                                                                   genomic dna  between 30 and 50                   efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006236            SRS004118        SRR018456     ChIP-Seq         NaN           cellular dynamics international  cell line        NaN          NaN               none                                                                                                                                       none                                                                                 none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            embryonic stem cell                                                   mteser                                                                                                                                                                                                   genomic dna  between 30 and 50                   efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006237            SRS004118        SRR018455     ChIP-Seq         NaN           cellular dynamics international  cell line        NaN          NaN               none                                                                                                                                       none                                                                                 none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            embryonic stem cell                                                   mteser                                                                                                                                                                                                   genomic dna  between 30 and 50                   efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006239            SRS004213        SRR019072     Bisulfite-Seq    #2            thomson laboratory               cell line        NaN          NaN               na                                                                                                                                         embryonic stem cell                                                                  none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            na                                                                    tesr                                                                                                                                                                                                     genomic dna  27                                  efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006239            SRS004213        SRR019080     Bisulfite-Seq    #2            thomson laboratory               cell line        NaN          NaN               na                                                                                                                                         embryonic stem cell                                                                  none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            na                                                                    tesr                                                                                                                                                                                                     genomic dna  27                                  efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006239            SRS004213        SRR019081     Bisulfite-Seq    #2            thomson laboratory               cell line        NaN          NaN               na                                                                                                                                         embryonic stem cell                                                                  none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            na                                                                    tesr                                                                                                                                                                                                     genomic dna  27                                  efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006239            SRS004213        SRR019082     Bisulfite-Seq    #2            thomson laboratory               cell line        NaN          NaN               na                                                                                                                                         embryonic stem cell                                                                  none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            na                                                                    tesr                                                                                                                                                                                                     genomic dna  27                                  efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006239            SRS004213        SRR019083     Bisulfite-Seq    #2            thomson laboratory               cell line        NaN          NaN               na                                                                                                                                         embryonic stem cell                                                                  none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            na                                                                    tesr                                                                                                                                                                                                     genomic dna  27                                  efo_0003042     male    NaN                      NaN                      NaN          NaN
            SRP000941       SRX006239            SRS004213        SRR019084     Bisulfite-Seq    #2            thomson laboratory               cell line        NaN          NaN               na                                                                                                                                         embryonic stem cell                                                                  none                                                             NaN       NaN                             NaN                                                                                                 NaN      NaN       h1            na                                                                    tesr                                                                                                                                                                                                     genomic dna  27                                  efo_0003042     male    NaN                      NaN                      NaN          NaN
        
        
        Getting detailed SRA metadata
        =============================
        
        ::
        
            $ pysradb metadata --db ./SRAmetadb.sqlite SRP075720 --detailed --expand | head
        
            study_accession experiment_accession sample_accession run_accession experiment_title                                  experiment_attribute        taxon_id library_selection library_layout library_strategy library_source  library_name  bases      spots   adapter_spec  avg_read_length developmental_stage retina_id source_name                tissue
            SRP075720       SRX1800089           SRS1467259       SRR3587529    GSM2177186: Kcng4_1Ra_A10; Mus musculus; RNA-Seq  GEO Accession: GSM2177186  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         79101650   1582033  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800090           SRS1467260       SRR3587530    GSM2177187: Kcng4_1Ra_A11; Mus musculus; RNA-Seq  GEO Accession: GSM2177187  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         84573650   1691473  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800091           SRS1467261       SRR3587531    GSM2177188: Kcng4_1Ra_A12; Mus musculus; RNA-Seq  GEO Accession: GSM2177188  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         77835550   1556711  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800092           SRS1467262       SRR3587532    GSM2177189: Kcng4_1Ra_A1; Mus musculus; RNA-Seq   GEO Accession: GSM2177189  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         73905150   1478103  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800093           SRS1467263       SRR3587533    GSM2177190: Kcng4_1Ra_A2; Mus musculus; RNA-Seq   GEO Accession: GSM2177190  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         77193150   1543863  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800094           SRS1467264       SRR3587534    GSM2177191: Kcng4_1Ra_A3; Mus musculus; RNA-Seq   GEO Accession: GSM2177191  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         59205550   1184111  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800095           SRS1467265       SRR3587535    GSM2177192: Kcng4_1Ra_A4; Mus musculus; RNA-Seq   GEO Accession: GSM2177192  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         61794700   1235894  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800096           SRS1467266       SRR3587536    GSM2177193: Kcng4_1Ra_A5; Mus musculus; RNA-Seq   GEO Accession: GSM2177193  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         78437650   1568753  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
            SRP075720       SRX1800097           SRS1467267       SRR3587537    GSM2177194: Kcng4_1Ra_A6; Mus musculus; RNA-Seq   GEO Accession: GSM2177194  10090     cDNA              SINGLE -       RNA-Seq          TRANSCRIPTOMIC  None         77392700   1547854  None         50.0             p17                 1ra       mus musculus retina__ p17  retina
        
        
        Converting SRP to GSE
        =====================
        
        ::
        
            $ pysradb srp-to-gse SRP075720
        
            study_accession study_alias
            SRP075720       GSE81903
        
        
        Converting GSM to SRP
        =====================
        
        ::
        
            $ pysradb gsm-to-srp GSM2177186
        
            experiment_alias study_accession
            GSM2177186       SRP075720
        
        
        Converting GSM to GSE
        =====================
        
        ::
        
            $ pysradb gsm-to-gse GSM2177186
        
            experiment_alias study_alias
            GSM2177186       GSE81903
        
        
        Converting GSM to SRX
        =====================
        
        ::
        
            $ pysradb gsm-to-srx GSM2177186
        
            experiment_alias experiment_accession
            GSM2177186       SRX1800089
        
        
        Converting GSM to SRR
        =====================
        
        ::
        
            $ pysradb gsm-to-srr GSM2177186
        
            experiment_alias run_accession
            GSM2177186       SRR3587529
        
        
        Complete Metadata for any record
        ================================
        
        Use the ``--detailed`` flag:
        
        ::
        
            $ pysradb gsm-to-srr --db ./SRAmetadb.sqlite GSM2177186 --detailed --desc --expand
        
            experiment_alias run_accession experiment_accession sample_accession study_accession run_alias      sample_alias study_alias developmental_stage retina_id source_name                tissue
            GSM2177186       SRR3587529    SRX1800089           SRS1467259       SRP075720       GSM2177186_r1  GSM2177186   GSE81903    p17                 1ra       mus musculus retina__ p17  retina
        
        
        Getting only the assay type
        ===========================
        
        ::
        
            $ pysradb metadata SRP000941 --db ./SRAmetadb.sqlite --assay  | tr -s '  ' | cut -f5 -d ' ' | sort | uniq -c
        
            999 Bisulfite-Seq
            768 ChIP-Seq
              1 library_strategy
            121 OTHER
            353 RNA-Seq
             28 WGS
        
        
        Downloading entire project
        ==========================
        
        ``pysradb`` makes it super easy to download datasets from SRA.
        
        ::
        
            $ pysradb download --out-dir ./pysradb_downloads -p SRP063852
        
        Downloads are organized by ``SRP/SRX/SRR`` mimicking the hiererachy of SRA projects.
        
        
        Downloading only certain samples of interest
        ============================================
        
        ::
        
            $ pysradb metadata SRP000941 --assay | grep 'study\|RNA-Seq' | pysradb download
        
        This will download all ``RNA-seq`` samples coming from this project using ``aspera-client``, if available.
        Alternatively, it can also use ``wget``.
        
        **************
        Demo Notebooks
        **************
        
        These notebooks document all the possible features of `pysradb`:
        
        1. `Python API usage <https://nbviewer.jupyter.org/github/saketkc/pysradb/blob/master/notebooks/01.SRAdb-demo.ipynb>`_
        2. `Command line usage <https://nbviewer.jupyter.org/github/saketkc/pysradb/blob/master/notebooks/03.CommandLine-demo.ipynb>`_
        
        
        
        ********
        Citation
        ********
        
        Choudhary, Saket. "pysradb: A Python Package to Query next-Generation Sequencing Metadata and Data from NCBI Sequence Read Archive." F1000Research, vol. 8, F1000 (Faculty of 1000 Ltd), Apr. 2019, p. 532 (https://f1000research.com/articles/8-532/v1)
        
        ::
        
            @article{Choudhary2019,
            doi = {10.12688/f1000research.18676.1},
            url = {https://doi.org/10.12688/f1000research.18676.1},
            year = {2019},
            month = apr,
            publisher = {F1000 (Faculty of 1000 Ltd)},
            volume = {8},
            pages = {532},
            author = {Saket Choudhary},
            title = {pysradb: A {P}ython package to query next-generation sequencing metadata and data from {NCBI} {S}equence {R}ead {A}rchive},
            journal = {F1000Research}
            }
        
        
        Zenodo archive: https://zenodo.org/badge/latestdoi/159590788
        
        Zenodo DOI: 10.5281/zenodo.2306881
        
        A lot of functionality in ``pysradb`` is based on ideas from the original `SRAdb package <https://bioconductor.org/packages/release/bioc/html/SRAdb.html>`_. Please cite the original SRAdb publication:
        
            Zhu, Yuelin, Robert M. Stephens, Paul S. Meltzer, and Sean R. Davis. "SRAdb: query and use public next-generation sequencing data from within R." BMC bioinformatics 14, no. 1 (2013): 19.
        
        
        * Free software: BSD license
        * Documentation: https://saketkc.github.io/pysradb
        
        
        #######
        History
        #######
        
        
        *******************
        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 (https://github.com/saketkc/pysradb/pull/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.
        
Keywords: pysradb
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3
