pysradb package

Submodules

pysradb.basedb module

class pysradb.basedb.BASEdb(sqlite_file)

Bases: object

all_row_counts()

Get row counts of all tables in the db file.

Returns

row_counts: DataFrame

A dataframe with table names and corresponding row count.

close()

Close sqlite connection.

desc_table(table)

Describe all fields in a table.

Parameters

table: string

Table name. See list_tables for getting all table names

Returns

table_desc: DataFrame

A DataFrame with field name and its schema description

get_row_count(table)

Get row counts for a table.

Parameters

table: string

Table name. See list_tables for getting all table names

Returns

row_count: int

Number of rows in table

list_fields(table)

List all fields in a given table.

Parameters

table: string

Table name. See list_tables for getting all table names

Returns

field_list: list

A list of field names for the table

list_tables()

List all tables in the sqlite file.

Returns

table_list: list

List of all table names

open()

Open sqlite connection.

query(sql_query)

Run SQL query.

Parameters

sql_query: string

SQL query string

Returns

results: DataFrame

Query results formatted as dataframe

pysradb.cli module

Command line interface for pysradb

class pysradb.cli.ArgParser(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=<class 'argparse.HelpFormatter'>, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True)

Bases: argparse.ArgumentParser

error(message: string)

Prints a usage message incorporating the message to stderr and exits.

If you override this in a subclass, it should not return – it should either exit or raise an exception.

class pysradb.cli.CustomFormatterArgP(prog, indent_increment=2, max_help_position=24, width=None)

Bases: argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescriptionHelpFormatter

pysradb.cli.download(out_dir, srx, srp, geo, skip_confirmation, col='sra_url', use_ascp=False, threads=1)

pysradb.cli.get_geo_search_info()

pysradb.cli.gse_to_gsm(gse_ids, saveto, detailed, desc, expand)

pysradb.cli.gse_to_srp(gse_ids, saveto, detailed, desc, expand)

pysradb.cli.gsm_to_gse(gsm_ids, saveto, detailed, desc, expand)

pysradb.cli.gsm_to_srp(gsm_ids, saveto, detailed, desc, expand)

pysradb.cli.gsm_to_srr(gsm_ids, saveto, detailed, desc, expand)

pysradb.cli.gsm_to_srs(gsm_ids, saveto, detailed, desc, expand)

pysradb.cli.gsm_to_srx(gsm_ids, saveto, detailed, desc, expand)

pysradb.cli.metadata(srp_id, assay, desc, detailed, expand, saveto)

pysradb.cli.parse_args(args=None)

Argument parser

pysradb.cli.search(saveto, db, verbosity, return_max, fields)

pysradb.cli.srp_to_gse(srp_id, saveto, detailed, desc, expand)

pysradb.cli.srp_to_srr(srp_id, saveto, detailed, desc, expand)

pysradb.cli.srp_to_srs(srp_id, saveto, detailed, desc, expand)

pysradb.cli.srp_to_srx(srp_id, saveto, detailed, desc, expand)

pysradb.cli.srr_to_gsm(srr_ids, saveto, detailed, desc, expand)

pysradb.cli.srr_to_srp(srr_ids, saveto, detailed, desc, expand)

pysradb.cli.srr_to_srs(srr_ids, saveto, detailed, desc, expand)

pysradb.cli.srr_to_srx(srr_ids, saveto, detailed, desc, expand)

pysradb.cli.srs_to_gsm(srs_ids, saveto, detailed, desc, expand)

pysradb.cli.srs_to_srx(srs_ids, saveto, detailed, desc, expand)

pysradb.cli.srx_to_srp(srx_ids, saveto, detailed, desc, expand)

pysradb.cli.srx_to_srr(srx_ids, saveto, detailed, desc, expand)

pysradb.cli.srx_to_srs(srx_ids, saveto, detailed, desc, expand)

pysradb.download module

Utility function to download data

pysradb.download.download_file(url, file_path, md5_hash=None, timeout=10, block_size=1048576, show_progress=False)

Resumable download. Expect the server to support byte ranges.

Parameters

url: string

URL

file_path: string

Local file path to store the downloaded file

md5_hash: string

Expected MD5 string of downloaded file

timeout: int

Seconds to wait before terminating request

block_size: int

Chunkx of bytes to read (default: 1024 * 1024 = 1MB)

show_progress: bool

Show progress bar

pysradb.download.get_file_size(row, url_col)

Get size of file to be downloaded.

Parameters

row: pd.DataFrame row

url_col: str

url_column

Returns

content_length: int

pysradb.download.md5_validate_file(file_path, md5_hash)

Check file containt against an MD5.

Parameters

file_path: string

Path to file

md5_hash: string

Expected md5 hash

Returns

valid: bool

True if expected and observed md5 match

pysradb.download.millify(n)

Convert integer to human readable format.

Parameters

nint

Returns

millidxstr

Formatted integer

pysradb.exceptions module

This file contains custom Exceptions for pysradb

exception pysradb.exceptions.IncorrectFieldException

Bases: Exception

Exception raised when the user enters incorrect inputs for a flag.

exception pysradb.exceptions.MissingQueryException

Bases: Exception

Exception raised when the user did not supply any query fields.

Attributes:

message: string

Error message for this Exception

pysradb.filter_attrs module

pysradb.filter_attrs.expand_sample_attribute_columns(metadata_df)

Expand sample attribute columns to individual columns.

Since the sample_attribute column content can be different for differnt rows even if coming from the same project (SRP), we explicitly iterate through the rows to first determine what additional columns need to be created.

Parameters

metadata_df: DataFrame

Dataframe as obtained from sra_metadata or equivalent

Returns

expanded_df: DataFrame

Dataframe with additionals columns pertaining to sample_attribute appended

pysradb.filter_attrs.guess_cell_type(sample_attribute)

Guess possible cell line from sample_attribute data.

Parameters

sample_attribute: string

sample_attribute string as in the metadata column

Returns

cell_type: string

Possible cell type of sample. Returns None if no match found.

pysradb.filter_attrs.guess_strain_type(sample_attribute)

Guess strain type from sample_attribute data.

Parameters

sample_attribute: string

sample_attribute string as in the metadata column

Returns

strain_type: string

Possible cell type of sample. Returns None if no match found.

pysradb.filter_attrs.guess_tissue_type(sample_attribute)

Guess tissue type from sample_attribute data.

Parameters

sample_attribute: string

sample_attribute string as in the metadata column

Returns

tissue_type: string

Possible cell type of sample. Returns None if no match found.

pysradb.geodb module

Methods to interact with SRA

class pysradb.geodb.GEOdb(sqlite_file)

Bases: pysradb.basedb.BASEdb

geo_convert(from_acc)

Convert one GEO accession to other.

Parameters

from_acc: string

GPL/GSE/GSM accession ID

Returns

mapping_df: DataFrame

A dataframe with relevant mappings

gse_metadata(gse)

Get metadata for GSE ID.

Parameters

gse: string

GSE ID

Returns

metadata_df: DataFrame

A dataframe with relevant fields

gse_to_gsm(gse)

Fetch GSMs for a GSE.

Parameters

gse: string

GSE ID

Returns

mapping_df: DataFrame

A dataframe with relevant mappings

gsm_metadata(gsm)

Get metadata for GSM ID.

Parameters

gsm: string

GSM ID

Returns

metadata_df: DataFrame

A dataframe with relevant fields

gsm_to_gse(gsm)

Fetch GSE for a GSM.

Parameters

gsm: string

GSM ID

Returns

mapping_df: DataFrame

A dataframe with relevant mappings

guess_srp_from_gse(gse)

Convert GSE to SRP id.

Parameters

gse: string

GSE ID

Returns

srp: string

SRP ID

pysradb.geodb.download_geodb_file(download_dir='/github/workspace/docs', overwrite=True)

Download GEOmetadb.sqlite file.

Parameters

download_dir: string

Directory to download SRAmetadb.sqlite

overwrite: bool

overwrite existing file(s). Set to True by default.

pysradb.search module

This file contains the search classes for the search feature.

class pysradb.search.EnaSearch(verbosity=2, return_max=20, query=None, accession=None, organism=None, layout=None, mbases=None, publication_date=None, platform=None, selection=None, source=None, strategy=None, title=None, suppress_validation=False)

Bases: pysradb.search.QuerySearch

Subclass of QuerySearch that implements search via querying ENA API

See also

QuerySearch

Superclass of EnaSearch

Methods

search()	sends the user query via requests to ENA API and stores search result as an instance attribute in the form of a pandas dataframe
show_result_statistics()	Shows summary information about search results.
visualise_results()	Generate graphs that visualise the search results.
get_plot_objects():	Get the plot objects for plots generated.
_format_query_string()	formats the input user query into a string
_format_request()	formats the request payload
_format_result(content)	formats the search query output and converts it into a pandas dataframe

search()

class pysradb.search.GeoSearch(verbosity=2, return_max=20, query=None, accession=None, organism=None, layout=None, mbases=None, publication_date=None, platform=None, selection=None, source=None, strategy=None, title=None, geo_query=None, geo_dataset_type=None, geo_entry_type=None, suppress_validation=False)

Bases: pysradb.search.SraSearch

Subclass of SraSearch that can query both GEO DataSets and SRA API.

See also

GeoSearch.info

GeoSearch usage details

SraSearch

Superclass of GeoSearch

QuerySearch

Superclass of SraSearch

Methods

search()	sends the user query via requests to SRA, GEO DataSets, or both depending on the search query. If query is sent to both APIs, the intersection of the two sets of query results are returned.
show_result_statistics()	Shows summary information about search results.
visualise_results()	Generate graphs that visualise the search results.
get_plot_objects():	Get the plot objects for plots generated.
_format_geo_query_string()	formats the GEO DataSets portion of the input user query into a string.
_format_geo_request()	formats the GEO DataSets request payload
_format_result(content)	formats the search query output and converts it into a pandas dataframe

classmethod info()

Information on how to use GeoSearch.

Displays information on how to query GEO DataSets / SRA via GeoSearch, including accepted inputs for geo_query, geo_dataset_type and geo_entry_type.

Returns

info: str

Information on how to use GeoSearch.

search()

class pysradb.search.QuerySearch(verbosity=2, return_max=20, query=None, accession=None, organism=None, layout=None, mbases=None, publication_date=None, platform=None, selection=None, source=None, strategy=None, title=None, suppress_validation=False)

Bases: object

This is the base class for the search feature.

This class takes as input the user’s search query, which has been tokenized by the ArgParser. The query will be sent to either SRA or ENA depending on the user’s input, and the results will be returned as a pandas dataframe.

Parameters

verbosityinteger

The level of details of the search result.

return_maxint

The maximum number of entries to be returned.

querystr

The main query string.

accessionstr

A relevant study / experiment / sample / run accession number.

organismstr

Scientific name of the sample organism

layoutstr

Library layout. Possible inputs: single, paired

mbasesint

Size of the sample of interest rounded to the nearest megabase.

publication_datestr

The publication date of the run in the format dd-mm-yyyy. If a date range is desired, input should be in the format of dd-mm-yyyy:dd-mm-yyyy

platformstr

Sequencing platform used for the run. Some possible inputs include: illumina, ion torrent, oxford nanopore

selectionstr

Library selection. Some possible inputs: cdna, chip, dnase, pcr

sourcestr

Library source. Some possible inputs: genomic, metagenomic, transcriptomic

strategystr

Library Preparation strategy. Some possible inputs: wgs, amplicon, rna seq

titlestr

Title of the experiment associated with the run

suppress_validation: bool

Defaults to False. If this is set to True, the user input format checks will be skipped. Setting this to True may cause the program to behave in unexpected ways, but allows the user to search queries that does not pass the format check.

Attributes

self.df: Pandas DataFrame

The search result belonging to this search instance

Methods

get_df()	Returns the dataframe storing this search result.
search()	Executes the search.
show_result_statistics()	Shows summary information about search results.
visualise_results()	Generate graphs that visualise the search results.
get_plot_objects():	Get the plot objects for plots generated.

get_df()

Getter for the search result dataframe.

get_plot_objects()

Get the plot objects for plots generated.

search()

show_result_statistics()

Shows search result statistics.

visualise_results(graph_types=('all',), show=False, saveto='./search_plots/')

Generate graphs that visualise the search results.

This method will only work if the optional dependency, matplotlib, is installed in the system.

Parameters

graph_typestuple

tuple containing strings representing types of graphs to generate. Possible strings: all, daterange, organism, source, selection, platform, basecount

savetostr

directory name where the generated graphs are saved.

showbool

Whether plotted graphs are immediately shown.

class pysradb.search.SraSearch(verbosity=2, return_max=20, query=None, accession=None, organism=None, layout=None, mbases=None, publication_date=None, platform=None, selection=None, source=None, strategy=None, title=None, suppress_validation=False)

Bases: pysradb.search.QuerySearch

Subclass of QuerySearch that implements search by querying NCBI Entrez API

See also

QuerySearch

Superclass of SraSearch

Methods

search()	sends the user query via requests to NCBI Entrez API and returns search results as a pandas dataframe.
show_result_statistics()	Shows summary information about search results.
visualise_results()	Generate graphs that visualise the search results.
get_plot_objects():	Get the plot objects for plots generated.
get_uids():	Get NCBI uids retrieved during this search query.
_format_query_string()	formats the input user query into a string
_format_request()	formats the request payload
_format_result(content)	formats the search query output.

get_uids()

Get NCBI uids retrieved during this search query.

Note: There is a chance that some uids retrieved do not appear in the search result output (Refer to #88)

search()

pysradb.sradb module

Methods to interact with SRA

class pysradb.sradb.SRAdb(sqlite_file)

Bases: pysradb.basedb.BASEdb

download(srp=None, df=None, url_col=None, out_dir=None, filter_by_srx=[], use_ascp=False, ascp_dir=None, ascp_bin=None, skip_confirmation=False, threads=1)

Download SRA files.

Parameters

srp: string

SRP ID (optional)

df: Dataframe

A dataframe as obtained from sra_metadata

url_col: string

Column of df to use for downloading

out_dir: string

Directory location for download

filter_by_srx: list

List of SRX ids to filter

protocol: string

[‘fasp’/’ftp’] fasp => faster download, ftp => slower

ascp_dir: string

Location of ascp directory

gse_to_gsm(gses, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert GSE to GSM

Parameters

gses: string or list

List of GSE ID

Returns

gse_to_gsm_df: DataFrame

gse_to_srp(gses, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRP to GSE

Parameters

gses: string or list

List of GSE ID

Returns

gse_to_srp_df: DataFrame

gsm_to_gse(gsms, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert GSM to GSE

Parameters

gsms: string or list

List of GSM ID

Returns

gsm_to_gse_df: DataFrame

gsm_to_srp(gsms, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert GSM to SRP.

Parameters

gsms: string or list

List of GSM ID

Returns

gsm_to_srp_df: DataFrame

gsm_to_srr(gsms, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert GSMs to SRR.

Parameters

gsms: string or list

List of GSM id

sample_attribute: bool

Include sample_attribute column

Returns

gsm_to_srr_df: DataFrame

DataFrame with two columns for GSM/SRR

gsm_to_srs(gsms, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert GSM to SRS.

Parameters

gsms: list or string

List of gsms

Returns

gsm_to_srs_df: DataFrame

gsm_to_srx(gsms, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert GSM to SRX.

Parameters

srx: string

SRX ID

Returns

srs_to_srx_df: DataFrame

search_by_expt_id(srx)

Search for a SRX/GSM id in the experiments.

Parameters

srx: string

SRX (experiment_accession) ID

Returns

results: dict

Dictionary with relevant hits

search_sra(search_str, out_type=['study_accession', 'experiment_accession', 'sample_accession', 'run_accession'], assay=False, sample_attribute=False, detailed=False, expand_sample_attributes=False, output_read_lengths=False)

Search SRA for any search term.

Parameters

search_str: string

SQL like text string to search. SQL like text => For example, terms in quotes “” enforce an exact search.

Returns

query_df: DataFrame

Dataframe with relevant query results

sra_metadata(acc, out_type=['study_accession', 'experiment_accession', 'sample_accession', 'run_accession'], assay=False, sample_attribute=False, detailed=False, expand_sample_attributes=False, output_read_lengths=False, acc_is_searchstr=False)

Get metadata for the provided SRA accession.

Parameters

acc: string or list

SRA accession ID

out_type: list

List of columns to output

assay: bool

True if assay should be outputted

sample_attribute: bool

True if sample_attribute should be outputted

detailed: bool

True if full metadata tables should be outputted

expand_sample_attributes: bool

Should sample_attribute column be expanded?

output_read_lengths: bool

True if read lengths should be calculated

acc_is_searchstr: bool

True if acc is a search string

Returns

metadata_df: DataFrame

A dataframe with all relevant columns

srp_to_gse(srp, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRP to GSE

Parameters

srp: string

SRP ID

Returns

srp_to_srr_df: DataFrame

srp_to_srr(srp, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRP to SRR.

Parameters

srp: string

SRP ID

Returns

srp_to_srr_df: DataFrame

srp_to_srs(srp, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRP to SRS.

Parameters

srp: string

SRP ID

Returns

srp_to_srs_df: DataFrame

DataFrame with two columns for SRS

srp_to_srx(srp, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRP to SRX/SRR.

Parameters

srp: string

SRP ID

Returns

srp_to_srx_df: DataFrame

DataFrame with two columns for SRX/SRR

srr_to_gsm(srrs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRR to GSM

Parameters

gses: string or list

List of SRR

Returns

srr_to_gsm_df: DataFrame

srr_to_srp(srrs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRR to SRP.

Parameters

srr: list of string

List of SRR IDs

Returns

srr_to_srp_df: DataFrame

srr_to_srs(srrs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRR to SRS.

Parameters

srr: list of string

List of SRR IDs

Returns

srp_to_srs_df: DataFrame

srr_to_srx(srrs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRR to SRX.

Parameters

srrs: string or list

List of SRR id

sample_attribute: bool

Include sample_attribute column

Returns

srr_to_srx_df: DataFrame

DataFrame with two columns for SRX/SRR

srs_to_gsm(srss, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRS to GSM.

Parameters

srss: list or string

List of SRS ID

Returns

srs_to_gsm_df: DataFrame

srs_to_srx(srss, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRS to SRX.

Parameters

srx: string

SRX ID

Returns

srs_to_srx_df: DataFrame

srx_to_srp(srxs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRXs to SRP.

Parameters

srxs: string or list

List of SRX id

sample_attribute: bool

Include sample_attribute column

Returns

srx_to_srp_df: DataFrame

DataFrame with two columns for SRX

srx_to_srr(srxs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRXs to SRR/SRP.

Parameters

srxs: string or list

List of SRX id

sample_attribute: bool

Include sample_attribute column

Returns

srx_to_srp_df: DataFrame

DataFrame with two columns for SRX/SRR

srx_to_srs(srxs, sample_attribute=False, detailed=False, expand_sample_attributes=False)

Convert SRX to SRS.

Parameters

srx: string

SRX ID

Returns

srp_to_srs_df: DataFrame

pysradb.sradb.download_sradb_file(download_dir='/github/workspace/docs', overwrite=True, keep_gz=False)

Download SRAdb.sqlite file.

Parameters

download_dir: string

Directory to download SRAmetadb.sqlite

overwrite: bool

overwrite existing file(s). Set to True by default.

keep_gz: bool

Delete .gz file after extraction is complete

pysradb.sraweb module

Utilities to interact with SRA online

class pysradb.sraweb.SRAweb(api_key=None)

Bases: pysradb.sradb.SRAdb

close()

Close sqlite connection.

create_esummary_params(esearchresult, db='sra')

fetch_ena_fastq(srp)

Fetch FASTQ records from ENA (EXPERIMENTAL)

Parameters

srp: string

Srudy accession

Returns

srr_url: list

List of SRR fastq urls

fetch_gds_results(gse, **kwargs)

static format_xml(string)

Create a fake root to make ‘string’ a valid xml

Parameters

string: str

Returns

xml: str

get_efetch_response(db, term, usehistory='y')

get_esummary_response(db, term, usehistory='y')

gse_to_gsm(gse, **kwargs)

Convert GSE to GSM

Parameters

gses: string or list

List of GSE ID

Returns

gse_to_gsm_df: DataFrame

gse_to_srp(gse, **kwargs)

Convert SRP to GSE

Parameters

gses: string or list

List of GSE ID

Returns

gse_to_srp_df: DataFrame

gsm_to_gse(gsm, **kwargs)

Convert GSM to GSE

Parameters

gsms: string or list

List of GSM ID

Returns

gsm_to_gse_df: DataFrame

gsm_to_srp(gsm, **kwargs)

Convert GSM to SRP.

Parameters

gsms: string or list

List of GSM ID

Returns

gsm_to_srp_df: DataFrame

gsm_to_srr(gsm, **kwargs)

Convert GSMs to SRR.

Parameters

gsms: string or list

List of GSM id

sample_attribute: bool

Include sample_attribute column

Returns

gsm_to_srr_df: DataFrame

DataFrame with two columns for GSM/SRR

gsm_to_srs(gsm, **kwargs)

Get SRS for a GSM

gsm_to_srx(gsm, **kwargs)

Get SRX for a GSM

search(*args, **kwargs)

sra_metadata(srp, sample_attribute=False, detailed=False, expand_sample_attributes=False, output_read_lengths=False, **kwargs)

Get metadata for the provided SRA accession.

Parameters

acc: string or list

SRA accession ID

out_type: list

List of columns to output

assay: bool

True if assay should be outputted

sample_attribute: bool

True if sample_attribute should be outputted

detailed: bool

True if full metadata tables should be outputted

expand_sample_attributes: bool

Should sample_attribute column be expanded?

output_read_lengths: bool

True if read lengths should be calculated

acc_is_searchstr: bool

True if acc is a search string

Returns

metadata_df: DataFrame

A dataframe with all relevant columns

srp_to_gse(srp, **kwargs)

Get GSE for a SRP

srp_to_srr(srp, **kwargs)

Get SRR for a SRP

srp_to_srs(srp, **kwargs)

Get SRS for a SRP

srp_to_srx(srp, **kwargs)

Get SRX for a SRP

srr_to_gsm(srr, **kwargs)

Get GSM for a SRR

srr_to_srp(srr, **kwargs)

Get SRP for a SRR

srr_to_srs(srr, **kwargs)

Get SRS for a SRR

srr_to_srx(srr, **kwargs)

Get SRX for a SRR

srs_to_gsm(srs, **kwargs)

Get GSM for a SRS

srs_to_srx(srs, **kwargs)

Get SRX for a SRS

srx_to_gsm(srx, **kwargs)

srx_to_srp(srx, **kwargs)

Get SRP for a SRX

srx_to_srr(srx, **kwargs)

Get SRR for a SRX

srx_to_srs(srx, **kwargs)

Get SRS for a SRX

static xml_to_json(xml)

Convert xml to json.

Parameters

xml: str

Input XML

Returns

xml_dict: dict

Parsed xml as dict

pysradb.sraweb.get_retmax(n_records, retmax=500)

Get retstart and retmax till n_records are exhausted

pysradb.sraweb.xmlescape(data)

pysradb.taxid2name module

pysradb.utils module

class pysradb.utils.TqdmUpTo(*_, **__)

Bases: tqdm.std.tqdm

Alternative Class-based version of the above. Provides update_to(n) which uses tqdm.update(delta_n). Inspired by [twine#242](https://github.com/pypa/twine/pull/242), [here](https://github.com/pypa/twine/commit/42e55e06).

Credits: https://github.com/tqdm/tqdm/blob/69326b718905816bb827e0e66c5508c9c04bc06c/examples/tqdm_wget.py

update_to(b=1, bsize=1, tsize=None)

bint, optional

Number of blocks transferred so far [default: 1].

bsizeint, optional

Size of each block (in tqdm units) [default: 1].

tsizeint, optional

Total size (in tqdm units). If [default: None] remains unchanged.

pysradb.utils.confirm(preceeding_text)

Confirm user input.

Parameters

preceeding_text: str

Text to print

Returns

response: bool

pysradb.utils.copyfileobj(fsrc, fdst, bufsize=16384, filesize=None, desc='')

Copy file object with a progress bar.

Parameters

fsrc: filehandle

Input file handle

fdst: filehandle

Output file handle

bufsize: int

Length of output buffer

filesize: int

Input file file size

desc: string

Description for tqdm status

pysradb.utils.get_gzip_uncompressed_size(filepath)

Get uncompressed size of a .gz file

Parameters

filepath: string

Path to input file

Returns

filesize: int

Uncompressed file size

pysradb.utils.mkdir_p(path)

Python version mkdir -p

Parameters

pathstring

Path to directory to create

pysradb.utils.order_dataframe(df, columns)

Order a dataframe

Order a dataframe by moving the columns in the front

Parameters

df: Dataframe

Dataframe

columns: list

List of columns that need to be put in front

pysradb.utils.path_leaf(path)

Get path’s tail from a filepath.

Parameters

path: string

Filepath

Returns

tail: string

Filename

pysradb.utils.requests_3_retries()

Generates a requests session object that allows 3 retries.

Returns

session: requests.Session

requests session object that allows 3 retries for server-side errors.

pysradb.utils.run_command(command, verbose=False)

Run a shell command

pysradb.utils.scientific_name_to_taxid(name)

Converts a scientific name to its corresponding taxonomy ID.

Parameters

name: str

Scientific name of interest.

Returns

taxid: str

Taxonomy Id of the Scientific name.

Raises

IncorrectFieldException

If the scientific name cannot be found.

pysradb.utils.unique(sequence)

Get unique elements from a list maintaining the order.

Parameters

input_list: list

Returns

unique_list: list

List with unique elements maintaining the order

Module contents

Top-level package for pysradb.

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