{ "info": { "author": "Saket Choudhary", "author_email": "saketkc@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Healthcare Industry", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "#######\npysradb\n#######\n\nPython package for interacting with SRAdb and downloading datasets from SRA.\n(python3 only!)\n\n.. image:: https://raw.githubusercontent.com/saketkc/pysradb/master/docs/_static/pysradb_v3.png\n :target: https://raw.githubusercontent.com/saketkc/pysradb/master/docs/_static/pysradb_v3.png\n\n\n.. image:: https://img.shields.io/pypi/v/pysradb.svg?style=flat-square\n :target: https://pypi.python.org/pypi/pysradb\n\n.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square\n :target: http://bioconda.github.io/recipes/pysradb/README.html\n\n.. image:: https://zenodo.org/badge/159590788.svg\n :target: https://zenodo.org/badge/latestdoi/159590788\n\n.. image:: https://img.shields.io/travis/saketkc/pysradb.svg?style=flat-square\n :target: https://travis-ci.com/saketkc/pysradb\n\n\n.. image:: https://asciinema.org/a/0C3SjYmPTkkemldprUpdVhiKx.svg\n :target: https://asciinema.org/a/0C3SjYmPTkkemldprUpdVhiKx?speed=5&autoplay=1\n\n\n*********\nCLI Usage\n*********\n\n``pysradb`` supports command line ussage. The documentation\nis in progress. See `cmdline `_ for\nsome quick usage instructions. See `quickstart `_ for\na list of instructions for each sub-command.\n\n\n::\n\n $ pysradb\n usage: pysradb [-h] [--version] [--citation]\n {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}\n ...\n\n pysradb: Query NGS metadata and data from NCBI Sequence Read Archive.\n version: 0.9.0.\n Citation: 10.12688/f1000research.18676.1\n\n optional arguments:\n -h, --help show this help message and exit\n --version show program's version number and exit\n --citation how to cite\n\n subcommands:\n {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}\n metadb Download SRAmetadb.sqlite\n metadata Fetch metadata for SRA project (SRPnnnn)\n download Download SRA project (SRPnnnn)\n search Search SRA for matching text\n gse-to-gsm Get GSM for a GSE\n gse-to-srp Get SRP for a GSE\n gsm-to-gse Get GSE for a GSM\n gsm-to-srp Get SRP for a GSM\n gsm-to-srr Get SRR for a GSM\n gsm-to-srs Get SRS for a GSM\n gsm-to-srx Get SRX for a GSM\n srp-to-gse Get GSE for a SRP\n srp-to-srr Get SRR for a SRP\n srp-to-srs Get SRS for a SRP\n srp-to-srx Get SRX for a SRP\n srr-to-gsm Get GSM for a SRR\n srr-to-srp Get SRP for a SRR\n srr-to-srs Get SRS for a SRR\n srr-to-srx Get SRX for a SRR\n srs-to-gsm Get GSM for a SRS\n srs-to-srx Get SRX for a SRS\n srx-to-srp Get SRP for a SRX\n srx-to-srr Get SRR for a SRX\n srx-to-srs Get SRS for a SRX\n\n\n\n************\nInstallation\n************\n\n\nTo install stable version using `pip`:\n\n.. code-block:: bash\n\n pip install pysradb\n\nAlternatively, if you use conda:\n\n.. code-block:: bash\n\n conda install -c bioconda pysradb\n\nThis step will install all the dependencies.\nIf you have an existing environment with a lot of pre-installed packages, conda might be `slow `_.\nPlease consider creating a new enviroment for ``pysradb``:\n\n.. code-block:: bash\n\n conda create -c bioconda -n pysradb PYTHON=3 pysradb\n\nDependecies\n===========\n\n.. code-block:: bash\n\n pandas>=0.23.4\n tqdm>=4.28\n requests>=2.22.0\n xmltodict>-0.12.0i\n sra-tools\n SRAmetadb.sqlite (optional)\n\n\nInstalling sratools\n===================\n\nNCBI has slowly transitioned towards using Google cloud for storing SRA files. As such\nthe ftp links are slowly getting obsolete. With release ``0.9.5``, ``pysradb`` has\nmoved to utilizing ``srapath`` available through NCBI's ``sra-tools`` for getting\nthe SRA location. Thus ``aspera-client`` is no longer required. But, ``sra-tools``\nis now a requirement and can be installed through bioconda.\n\nDownloading SRAmetadb (optional)\n=================================\n\n``pysradb`` can utilize a SQLite database file that has preprocessed metadata made available by the\n`SRAdb `_ project.\nThough, with the release ``0.9.5``, this database file is not a hard requirement for any of the operations.\n\n\n\nSRAmetadb can be downloaded using:\n\n.. code-block:: bash\n\n wget -c https://starbuck1.s3.amazonaws.com/sradb/SRAmetadb.sqlite.gz && gunzip SRAmetadb.sqlite.gz\n\nAlternatively, you can also download it using ``pysradb``, which by default downloads it into your\ncurrent working directory:\n\n\n::\n\n $ pysradb metadb\n\nYou can also specify an alternate directory for download by supplying the ``--out-dir `` argument.\n\n\nInstalling pysradb in development mode\n======================================\n\n.. code-block:: bash\n\n pip install -U pandas tqdm requests xmltodict\n git clone https://github.com/saketkc/pysradb.git\n cd pysradb\n pip install -e .\n\n\n\n*************\nUsing pysradb\n*************\n\nPlease see `usage_scenarios `_ for a few usage scenarios.\nHere are few hand-picked examples.\n\n\nMode: SRAmetadb or SRAWeb\n=========================\n\n``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\nwith the exception of ``search`` can be performed withoudownloading the SQLite file.\nNOTE: 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.\n\n\nSearch\n======\n\nSearch for all projects containing \"ribosome profiling\":\n\n::\n\n $ pysradb search \"ribosome profiling\" | head\n\n study_accession experiment_accession sample_accession run_accession\n DRP000927 DRX002899 DRS002983 DRR003575\n DRP000927 DRX002900 DRS002992 DRR003576\n DRP000927 DRX002901 DRS003001 DRR003577\n DRP000927 DRX002902 DRS003010 DRR003578\n DRP000927 DRX002903 DRS003019 DRR003579\n DRP000927 DRX002904 DRS003028 DRR003580\n DRP000927 DRX002905 DRS003037 DRR003581\n DRP000927 DRX002906 DRS003038 DRR003582\n DRP003075 DRX019536 DRS026974 DRR021383\n\n\n\nGetting SRA metadata\n====================\n\n::\n\n $ pysradb metadata --db ./SRAmetadb.sqlite SRP000941 --assay --desc --expand | head\n\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n\n\nGetting detailed SRA metadata\n=============================\n\n::\n\n $ pysradb metadata --db ./SRAmetadb.sqlite SRP075720 --detailed --expand | head\n\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n 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\n\n\nConverting SRP to GSE\n=====================\n\n::\n\n $ pysradb srp-to-gse --db ./SRAmetadb.sqlite SRP075720\n\n study_accession study_alias\n SRP075720 GSE81903\n\n\nConverting GSM to SRP\n=====================\n\n::\n\n $ pysradb gsm-to-srp --db ./SRAmetadb.sqlite GSM2177186\n\n experiment_alias study_accession\n GSM2177186 SRP075720\n\n\nConverting GSM to GSE\n=====================\n\n::\n\n $ pysradb gsm-to-gse --db ./SRAmetadb.sqlite GSM2177186\n\n experiment_alias study_alias\n GSM2177186 GSE81903\n\n\nConverting GSM to SRX\n=====================\n\n::\n\n $ pysradb gsm-to-srx --db ./SRAmetadb.sqlite GSM2177186\n\n experiment_alias experiment_accession\n GSM2177186 SRX1800089\n\n\nConverting GSM to SRR\n=====================\n\n::\n\n $ pysradb gsm-to-srr --db ./SRAmetadb.sqlite GSM2177186\n\n experiment_alias run_accession\n GSM2177186 SRR3587529\n\n\nComplete Metadata for any record\n================================\n\nUse the ``--detailed`` flag:\n\n::\n\n $ pysradb gsm-to-srr --db ./SRAmetadb.sqlite GSM2177186 --detailed --desc --expand\n\n experiment_alias run_accession experiment_accession sample_accession study_accession run_alias sample_alias study_alias developmental_stage retina_id source_name tissue\n GSM2177186 SRR3587529 SRX1800089 SRS1467259 SRP075720 GSM2177186_r1 GSM2177186 GSE81903 p17 1ra mus musculus retina__ p17 retina\n\n\nGetting only the assay type\n===========================\n\n::\n\n $ pysradb metadata SRP000941 --db ./SRAmetadb.sqlite --assay | tr -s ' ' | cut -f5 -d ' ' | sort | uniq -c\n\n 999 Bisulfite-Seq\n 768 ChIP-Seq\n 1 library_strategy\n 121 OTHER\n 353 RNA-Seq\n 28 WGS\n\n\nDownloading entire project\n==========================\n\n``pysradb`` makes it super easy to download datasets from SRA.\n\n::\n\n $ pysradb download --db ./SRAmetadb.sqlite --out-dir ./pysradb_downloads -p SRP063852\n\nDownloads are organized by ``SRP/SRX/SRR`` mimicking the hiererachy of SRA projects.\n\n\nDownloading only certain samples of interest\n============================================\n\n::\n\n $ pysradb metadata SRP000941 --assay | grep 'study\\|RNA-Seq' | pysradb download\n\nThis will download all ``RNA-seq`` samples coming from this project using ``aspera-client``, if available.\nAlternatively, it can also use ``wget``.\n\n**************\nDemo Notebooks\n**************\n\nThese notebooks document all the possible features of `pysradb`:\n\n1. `Python API usage `_\n2. `Command line usage `_\n\n\n\n********\nCitation\n********\n\nChoudhary, 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)\n\n::\n\n @article{Choudhary2019,\n doi = {10.12688/f1000research.18676.1},\n url = {https://doi.org/10.12688/f1000research.18676.1},\n year = {2019},\n month = apr,\n publisher = {F1000 (Faculty of 1000 Ltd)},\n volume = {8},\n pages = {532},\n author = {Saket Choudhary},\n title = {pysradb: A Python package to query next-generation sequencing metadata and data from {NCBI} Sequence Read Archive},\n journal = {F1000Research}\n }\n\n\nZenodo archive: https://zenodo.org/badge/latestdoi/159590788\n\nZenodo DOI: 10.5281/zenodo.2306881\n\nA lot of functionality in ``pysradb`` is based on ideas from the original `SRAdb package `_. Please cite the original SRAdb publication:\n\n 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.\n\n\n* Free software: BSD license\n* Documentation: https://saketkc.github.io/pysradb\n\n\n#######\nHistory\n#######\n\n******************\n0.9.0 (02-27-2019)\n******************\n\nOthers\n======\n\n* This release completely changes the command line interface replacing click with argparse (https://github.com/saketkc/pysradb/pull/3)\n* Removed Python 2 comptaible stale code\n\n*******************\n0.8.0 (02-26-2019)\n*******************\n\nNew methods/functionality\n=========================\n* `srr-to-gsm`: convert SRR to GSM\n* SRAmetadb.sqlite.gz file is deleted by default after extraction\n* When SRAmetadb is not found a confirmation is seeked before downloading\n* Confirmation option before SRA downloads\n\nBugfix\n======\n* download() works with wget\n\nOthers\n======\n\n* `--out_dir` is now `out-dir`\n\n\n*******************\n0.7.1 (02-18-2019)\n*******************\n\nImportant: Python2 is no longer supported.\nPlease consider moving to Python3.\n\nBugfix\n======\n\n* Included docs in the index whihch were missed\n out in the previous release\n\n\n*******************\n0.7.0 (02-08-2019)\n*******************\n\nNew methods/functionality\n=========================\n* `gsm-to-srr`: convert GSM to SRR\n* `gsm-to-srx`: convert GSM to SRX\n* `gsm-to-gse`: convert GSM to GSE\n\n\nRenamed methods\n===============\n\nThe following commad line options have been renamed\nand the changes are not compatible with 0.6.0\nrelease:\n\n* `sra-metadata` -> `metadata`.\n* `sra-search` -> `search`.\n* `srametadb` -> `metadb`.\n\n\n\n*******************\n0.6.0 (12-25-2018)\n*******************\n\nBugfix\n======\n\n* Fixed bugs introduced in 0.5.0 with API changes where\n multiple redundant columns were output in `sra-metadata`\n\n\nNew methods/functionality\n=========================\n* `download` now allows piped inputs\n\n\n\n\n*******************\n0.5.0 (12-24-2018)\n*******************\n\nNew methods/functionality\n=========================\n* Support for filtering by SRX Id for SRA downloads.\n* `srr_to_srx`: Convert SRR to SRX/SRP\n* `srp_to_srx`: Convert SRP to SRX\n* Stripped down `sra-metadata` to give minimal information\n* Added `--assay`, `--desc`, `--detailed` flag for `sra-metadata`\n* Improved table printing on terminal\n\n\n*******************\n0.4.2 (12-16-2018)\n*******************\n\nBugfix\n======\n\n* Fixed unicode error in tests for Python2\n\n\n*******************\n0.4.0 (12-12-2018)\n*******************\n\nNew methods/functionality\n=========================\n\n* Added a new `BASEdb` class to handle common database connections\n* Initial support for GEOmetadb through GEOdb class\n* Initial support or a command line interface:\n - download Download SRA project (SRPnnnn)\n - gse-metadata Fetch metadata for GEO ID (GSEnnnn)\n - gse-to-gsm Get GSM(s) for GSE\n - gsm-metadata Fetch metadata for GSM ID (GSMnnnn)\n - sra-metadata Fetch metadata for SRA project (SRPnnnn)\n* Added three separate notebooks for SRAdb, GEOdb, CLI usage\n\n*******************\n0.3.0 (12-05-2018)\n*******************\n\nNew methods/functionality\n=========================\n\n* `sample_attribute` and `experiment_attribute` are now included by default in the df returned by `sra_metadata()`\n* `expand_sample_attribute_columns: expand metadata dataframe based on attributes in `sample_attribute` column\n* New methods to guess cell/tissue/strain: `guess_cell_type()`/`guess_tissue_type()`/`guess_strain_type()`\n* Improved README and usage instructions\n\n\n*******************\n0.2.2 (12-03-2018)\n*******************\n\nNew methods/functionality\n=========================\n\n* `search_sra()` allows full text search on SRA metadata.\n\n\n*******************\n0.2.0 (12-03-2018)\n*******************\n\nRenamed methods\n===============\n\nThe following methods have been renamed\nand the changes are not compatible with 0.1.0\nrelease:\n\n* `get_query()` -> `query()`.\n* `sra_convert()` -> `sra_metadata()`.\n* `get_table_counts()` -> `all_row_counts()`.\n\n\nNew methods/functionality\n=========================\n\n* `download_sradb_file()` makes fetching `SRAmetadb.sqlite` file easy; wget is no longer\n required.\n* `ftp` protocol is now supported besides `fsp` and hence `aspera-client` is now optional.\n We however, strongly recommend `aspera-client` for faster downloads.\n\nBug fixes\n=========\n* Silenced `SettingWithCopyWarning` by excplicitly doing operations on a copy of\n the dataframe instead of the original.\n\nBesides these, all methods now follow a `numpydoc` compatible documentation.\n\n\n******************\n0.1.0 (12-01-2018)\n******************\n\n* First release on PyPI.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/saketkc/pysradb", 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