pysradb 2.2.0

# A Python package for retrieving metadata from SRA/ENA/GEO

[](https://pypi.python.org/pypi/pysradb) [](https://anaconda.org/bioconda/pysradb/badges/version.svg) [](http://bioconda.github.io/recipes/pysradb/README.html) [](https://pepy.tech/project/pysradb) [](https://anaconda.org/bioconda/pysradb) [](https://zenodo.org/badge/latestdoi/159590788) [](https://github.com/saketkc/pysradb/actions)

## Documentation

<https://saketkc.github.io/pysradb>

## CLI Usage

pysradb supports command line usage. See [CLI](https://saket-choudhary.me/pysradb/cmdline.html) instructions or [quickstart guide](https://www.saket-choudhary.me/pysradb/quickstart.html).

$ pysradb

usage: pysradb [-h] [–version] [–citation]

{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: 2.0.1 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:

{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}

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 requires only an active internet connection (no additional downloads are made).

The following notebooks document all the possible features of `pysradb`:

1. [Python API](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/01.Python-API_demo.ipynb)

2. [Downloading datasets from SRA - command line](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/02.Commandline_download.ipynb)

3. [Parallely download multiple datasets - Python API](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/03.ParallelDownload.ipynb)

4. [Converting SRA-to-fastq - command line (requires conda)](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/04.SRA_to_fastq_conda.ipynb)

5. [Downloading subsets of a project - Python API](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/05.Downloading_subsets_of_a_project.ipynb)

6. [Download BAMs](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/06.Download_BAMs.ipynb)

7. [Metadata for multiple SRPs](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/07.Multiple_SRPs.ipynb)

8. [Multithreaded fastq downloads using Aspera Client](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/08.pysradb_ascp_multithreaded.ipynb)

9. [Searching SRA/GEO/ENA](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/09.Query_Search.ipynb)

## Installation

To install stable version using `pip`:

` bash pip install pysradb `

Alternatively, if you use conda:

` 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:

` bash conda create -c bioconda -n pysradb PYTHON=3.10 pysradb `

### Dependencies

pandas requests tqdm xmltodict

### Installing pysradb in development mode

git clone https://github.com/saketkc/pysradb.git cd pysradb && pip install -r requirements.txt pip install -e .

## Using pysradb

### Obtaining SRA metadata

$ pysradb metadata SRP000941 | head

study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_strategy library_source library_selection sample_accession sample_title instrument total_spots total_size run_accession run_total_spots run_total_bases SRP000941 SRX056722 Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H1 Cells Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC ChIP SRS184466 Illumina HiSeq 2000 26900401 531654480 SRR179707 26900401 807012030 SRP000941 SRX027889 Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC Cells Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC Cells 9606 Homo sapiens ChIP-Seq GENOMIC ChIP SRS116481 Illumina Genome Analyzer II 37528590 779578968 SRR067978 37528590 1351029240 SRP000941 SRX027888 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS116483 Illumina Genome Analyzer II 13603127 3232309537 SRR067977 13603127 489712572 SRP000941 SRX027887 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS116562 Illumina Genome Analyzer II 22430523 506327844 SRR067976 22430523 807498828 SRP000941 SRX027886 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS116560 Illumina Genome Analyzer II 15342951 301720436 SRR067975 15342951 552346236 SRP000941 SRX027885 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS116482 Illumina Genome Analyzer II 39725232 851429082 SRR067974 39725232 1430108352 SRP000941 SRX027884 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS116481 Illumina Genome Analyzer II 32633277 544478483 SRR067973 32633277 1174797972 SRP000941 SRX027883 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS004118 Illumina Genome Analyzer II 22150965 3262293717 SRR067972 9357767 336879612 SRP000941 SRX027883 Reference Epigenome: ChIP-Seq Input from hESC H1 Cells Reference Epigenome: ChIP-Seq Input from hESC H1 Cells 9606 Homo sapiens ChIP-Seq GENOMIC RANDOM SRS004118 Illumina Genome Analyzer II 22150965 3262293717 SRR067971 12793198 460555128

### Obtaining detailed SRA metadata

$ pysradb metadata SRP075720 –detailed | head

study_accession experiment_accession experiment_title experiment_desc organism_taxid organism_name library_strategy library_source library_selection sample_accession sample_title instrument total_spots total_size run_accession run_total_spots run_total_bases SRP075720 SRX1800476 GSM2177569: Kcng4_2la_H9; Mus musculus; RNA-Seq GSM2177569: Kcng4_2la_H9; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467643 Illumina HiSeq 2500 2547148 97658407 SRR3587912 2547148 127357400 SRP075720 SRX1800475 GSM2177568: Kcng4_2la_H8; Mus musculus; RNA-Seq GSM2177568: Kcng4_2la_H8; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467642 Illumina HiSeq 2500 2676053 101904264 SRR3587911 2676053 133802650 SRP075720 SRX1800474 GSM2177567: Kcng4_2la_H7; Mus musculus; RNA-Seq GSM2177567: Kcng4_2la_H7; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467641 Illumina HiSeq 2500 1603567 61729014 SRR3587910 1603567 80178350 SRP075720 SRX1800473 GSM2177566: Kcng4_2la_H6; Mus musculus; RNA-Seq GSM2177566: Kcng4_2la_H6; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467640 Illumina HiSeq 2500 2498920 94977329 SRR3587909 2498920 124946000 SRP075720 SRX1800472 GSM2177565: Kcng4_2la_H5; Mus musculus; RNA-Seq GSM2177565: Kcng4_2la_H5; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467639 Illumina HiSeq 2500 2226670 83473957 SRR3587908 2226670 111333500 SRP075720 SRX1800471 GSM2177564: Kcng4_2la_H4; Mus musculus; RNA-Seq GSM2177564: Kcng4_2la_H4; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467638 Illumina HiSeq 2500 2269546 87486278 SRR3587907 2269546 113477300 SRP075720 SRX1800470 GSM2177563: Kcng4_2la_H3; Mus musculus; RNA-Seq GSM2177563: Kcng4_2la_H3; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467636 Illumina HiSeq 2500 2333284 88669838 SRR3587906 2333284 116664200 SRP075720 SRX1800469 GSM2177562: Kcng4_2la_H2; Mus musculus; RNA-Seq GSM2177562: Kcng4_2la_H2; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467637 Illumina HiSeq 2500 2071159 79689296 SRR3587905 2071159 103557950 SRP075720 SRX1800468 GSM2177561: Kcng4_2la_H1; Mus musculus; RNA-Seq GSM2177561: Kcng4_2la_H1; Mus musculus; RNA-Seq 10090 Mus musculus RNA-Seq TRANSCRIPTOMIC cDNA SRS1467635 Illumina HiSeq 2500 2321657 89307894 SRR3587904 2321657 116082850

### 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

### Downloading supplementary files from GEO

$ pysradb download -g GSE161707

### Downloading an entire SRA/ENA project (multithreaded)

pysradb makes it super easy to download datasets from SRA parallely: Using 8 threads to download:

$ pysradb download -y -t 8 –out-dir ./pysradb_downloads -p SRP063852

Downloads are organized by SRP/SRX/SRR mimicking the hierarchy of SRA projects.

### Downloading only certain samples of interest

$ pysradb metadata SRP000941 –detailed | grep ‘study|RNA-Seq’ | pysradb download

This will download all RNA-seq samples coming from this project.

### Ultrafast fastq downloads

With [aspera-client](https://downloads.asperasoft.com/en/downloads/8?list) installed, [pysradb]{.title-ref} can perform ultra fast downloads:

To download all original fastqs with [aspera-client]{.title-ref} installed utilizing 8 threads:

$ pysradb download -t 8 –use_ascp -p SRP002605

Refer to the notebook for [(shallow) time benchmarks](https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/08.pysradb_ascp_multithreaded.ipynb).

## 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>

## 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

## Questions?

Open an [issue](https://github.com/saketkc/pysradb/issues) or join our [Slack Channel](https://join.slack.com/t/pysradb/shared_invite/zt-f01jndpy-KflPu3Be5Aq3FzRh5wj1Ug).

# History

# 2.2.0 (2023-09-17)

• Add support for Biosamples and bioproject [#199](https://github.com/saketkc/pysradb/pull/198)

• Use retmode xml for Geo search [#200](https://github.com/saketkc/pysradb/pull/200)

• Documentation fixes

## 2.1.0 (2023-05-16)

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

• Fix for [download]{.title-ref} using [public_urls]{.title-ref}

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

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

• ENA search is currently broken because of an API change

## 2.0.2 (2023-04-09)

• Fix for [gse-to-srp]{.title-ref} to handle cases where a project is missing but SRXs are returned ([#186 <https://github.com/saketkc/pysradb/issues/186>]{.title-ref})

• Fix gse-to-gsm ([#187 <https://github.com/saketkc/pysradb/issues/187>]{.title-ref})

## 2.0.1 (2023-03-18)

• Fix for [pysradb download]{.title-ref} - using [public_url]{.title-ref}

• Fix for SRX -> SRR and related conversions ([#183 <https://github.com/saketkc/pysradb/pull/183>]{.title-ref})

## 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>]{.title-ref})

## 1.4.2 (06-17-2022)

• Fix ENA fastq fetching ([#163 <https://github.com/saketkc/pysradb/issues/163>]{.title-ref})

## 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>]{.title-ref})

• Fix for xmldict 0.13.0 no longer defaulting to OrderedDict ([#159 <https://github.com/saketkc/pysradb/pull/159>]{.title-ref})

• Fix for missing experiment model and description in metadata ([#160 <https://github.com/saketkc/pysradb/issues/160>]{.title-ref})

## 1.3.0 (02-18-2022)

• Add [study_title]{.title-ref} to [--detailed]{.title-ref} flag ([#152](https://github.com/saketkc/pysradb/issues/152))

• Fix [KeyError]{.title-ref} in [metadata]{.title-ref} where some new IDs do not have any metadata ([#151](https://github.com/saketkc/pysradb/issues/151))

## 1.2.0 (01-10-2022)

• Do not exit if a qeury returns no hits ([#149 <https://github.com/saketkc/pysradb/pull/149>]{.title-ref})

## 1.1.0 (12-12-2021)

• Fixed [gsm-to-gse]{.title-ref} failure ([#128](https://github.com/saketkc/pysradb/pull/128))

• Fixed case sensitivity bug for ENA search ([#144](https://github.com/saketkc/pysradb/pull/144))

• Fixed publication date bug for search ([#146](https://github.com/saketkc/pysradb/pull/146))

• Added support for downloading data from GEO [pysradb dowload -g <GSE>]{.title-ref} ([#129](https://github.com/saketkc/pysradb/pull/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](https://saket-choudhary.me/pysradb/quickstart.html#search)

• [N/A]{.title-ref} is now replaced with [pd.NA]{.title-ref}

• Two new fields in `--detailed`: [instrument_model]{.title-ref} and [instrument_model_desc]{.title-ref} [#75](https://github.com/saketkc/pysradb/issues/75)

• Updated documentation

## 0.11.1 (09-18-2020)

• [library_layout]{.title-ref} is now outputted in metadata #56

• [-detailed]{.title-ref} 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]{.title-ref} now supports multiple threads for paralle downloads

• [pysradb download]{.title-ref} 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]{.title-ref}

## 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]{.title-ref} 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]{.title-ref} is now [out-dir]{.title-ref}

## 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]{.title-ref} -> [metadata]{.title-ref}.

• [sra-search]{.title-ref} -> [search]{.title-ref}.

• [srametadb]{.title-ref} -> [metadb]{.title-ref}.

## 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]{.title-ref}

### New methods/functionality

• [download]{.title-ref} 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]{.title-ref} to give minimal information

• Added [--assay]{.title-ref}, [--desc]{.title-ref}, [--detailed]{.title-ref} flag for [sra-metadata]{.title-ref}

• 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]{.title-ref} 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]{.title-ref} and [experiment_attribute]{.title-ref} are now included by default in the df returned by [sra_metadata()]{.title-ref}

• [expand_sample_attribute_columns: expand metadata dataframe based on attributes in `sample_attribute]{.title-ref} column

• New methods to guess cell/tissue/strain: [guess_cell_type()]{.title-ref}/[guess_tissue_type()]{.title-ref}/[guess_strain_type()]{.title-ref}

• Improved README and usage instructions

## 0.2.2 (12-03-2018)

### New methods/functionality

• [search_sra()]{.title-ref} 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()]{.title-ref} -> [query()]{.title-ref}.

• [sra_convert()]{.title-ref} -> [sra_metadata()]{.title-ref}.

• [get_table_counts()]{.title-ref} -> [all_row_counts()]{.title-ref}.

### New methods/functionality

• [download_sradb_file()]{.title-ref} makes fetching [SRAmetadb.sqlite]{.title-ref} file easy; wget is no longer required.

• [ftp]{.title-ref} protocol is now supported besides [fsp]{.title-ref} and hence [aspera-client]{.title-ref} is now optional. We however, strongly recommend [aspera-client]{.title-ref} for faster downloads.

### Bug fixes

• Silenced [SettingWithCopyWarning]{.title-ref} by excplicitly doing operations on a copy of the dataframe instead of the original.

Besides these, all methods now follow a [numpydoc]{.title-ref} compatible documentation.

## 0.1.0 (12-01-2018)

• First release on PyPI.