ensimpl_snps package¶

Submodules¶

ensimpl_snps.app module¶

ensimpl_snps.app.create_app(settings_override=None)¶

Create a Flask application using the app factory pattern.

Parameters:	settings_override (dict) – A `dict` which will override the default settings.
Returns:	The Flask application object.
Return type:	flask.Flask

ensimpl_snps.app.error_templates(app)¶

Register 0 or more custom error pages (mutates the app passed in).

Parameters:	app (flask.Flask) – The Flask application object.

ensimpl_snps.app.extensions(app)¶

Register 0 or more extensions (mutates the app passed in).

Parameters:	app (flask.Flask) – The Flask application object.

ensimpl_snps.app.middleware(app)¶

Register 0 or more middleware (mutates app that is passed in).

Parameters:	app (flask.Flask) – The Flask application object.

ensimpl_snps.db_config module¶

ensimpl_snps.db_config.get_all_ensimpl_snps_dbs(top_dir)¶

Configure the list of ensimpl snp db files in directory. This will set values for ENSIMPL_SNPS_DBS and ENSIMPL_SNPS_DBS_DICT.

Parameters:	top_dir (str) – The directory path.

ensimpl_snps.db_config.get_ensimpl_snp_db(version, species)¶

Get the database based upon the version and species values which should represent the Ensembl reference number and species identifier.

Parameters:	version (int) – The Ensembl version number. species (str) – The short identifier of a species.
Returns:	The database file.
Return type:	str
Raises:	`ValueError` – If unable to find the version and species combination or if version is not a number.

Examples

>>> get_ensimpl_snps_db(91, 'Mm')
'ensimpl_snps.91.Mm.db3'

ensimpl_snps.db_config.init(directory=None)¶

Initialize the configuration of the Ensimpl SNPs databases.

NOTE: This method is referenced from the __init__.py in this module.

Parameters:	directory (str, optional) – A directory that specifies where the ensimpl databases live. If None the environment variable `ENSIMPL_SNPS_DIR` will be used.

ensimpl_snps.extensions module¶

ensimpl_snps.utils module¶

Useful generic utilities for the package.

class ensimpl_snps.utils.ReverseProxied(app)¶

Bases: object

Wrap the application in this middleware and configure the front-end server to add these headers, to let you quietly bind this to a URL other than / and to an HTTP scheme that is different than what is used locally.

Taken from: http://flask.pocoo.org/snippets/35/

Example

In Apache:

<Proxy http://server:port>
    Header add X_FORWADED_PATH "/myprefix"
    RequestHeader set X_FORWARDED_PATH "/myprefix"
</Proxy>

ProxyPass /myprefix http://server:port disablereuse=On
ProxyPassReverse /myprefix http://server:port

In nginx:

location /myprefix {
    proxy_pass http://192.168.0.1:5001;
    proxy_set_header Host $host;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header X-Scheme $scheme;
    proxy_set_header X-Script-Name /myprefix;
}

ensimpl_snps.utils.bins(start, stop, fmt='gff', one=True)¶

Uses the definition of a “genomic bin” described in Fig 7 of http://genome.cshlp.org/content/12/6/996.abstract.

Parameters:	start (int) – start position stop (int) – fmt (str, optional) – Either `'gff'` or `'bed'`. This specifies 1-based start coords (gff) or 0-based start coords (bed). one (bool) – If `one=True` (default), then only return the smallest bin that completely contains these coordinates (useful for assigning a single bin). If `one=False`, then return the set of all bins that overlap these coordinates (useful for looking for features that could intersect)
Returns:	The calculated bin.
Return type:	int

ensimpl_snps.utils.cmp(value_1, value_2)¶

Compare two values. The return value will be -1 if value_1 is less than value_2, 0 if value_1 is equal to value_2, or 1 if value_1 is greater than value_2.

Parameters:	value_1 – The first value. value_2 – The second value.
Returns:	`-1`, `0`, or `1`
Return type:	int

ensimpl_snps.utils.configure_logging(level=0)¶

Configure the logger with the specified level. Valid level values are:

level	logging value
0	logging.WARNING is informational
1	logging.INFO is user debug
2+	logging.DEBUG is developer debug

Anything greater than 2 is treated as 2.

Parameters:	level (int, optional) – The logging level; defaults to `0`.

ensimpl_snps.utils.create_random_string(size=6, chars='ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789')¶

Generate a random string of length size using the characters specified by chars.

Parameters:	size (int, optional) – The length of the string. 6 is the default. chars (list, optional) – The characters to use.
Returns:	A random generated string.
Return type:	str

ensimpl_snps.utils.delete_file(file_name)¶

Delete specified file_name. This will fail silently.

Parameters:	file_name (str) – The name of file to delete.

ensimpl_snps.utils.dictify_cursor(cursor)¶

All rows are converted into a collections.OrderedDict where keys are the column names.

Parameters:	cursor (sqlite3.Cursor) – The database cursor.
Returns:	A `list` of `dicts` where each `dict's` key is a column name.
Return type:	list

ensimpl_snps.utils.dictify_row(cursor, row)¶

Turns the given row into a dictionary where the keys are the column names.

Parameters:	cursor (sqlite3.Cursor) – The database cursor. row (sqlite3.Row) – The current row.
Returns:	A `dict` with keys as column names.
Return type:	collections.OrderedDict

ensimpl_snps.utils.format_time(start, end)¶

Format length of time between start and end into a readable string.

Parameters:	start (float) – The start time. end (float) – The end time.
Returns:	A formatted string of hours, minutes, and seconds.
Return type:	str

ensimpl_snps.utils.get_file_name(url, directory=None)¶

Get the file name of url. If directory has a value, return the name of the file with directory prepended.

Examples

>>> get_file_name('http://www.google.com/a/b/c/file.html', '/tmp')
'/tmp/file.html

Parameters:	url (str) – The url of a file. directory (str, optional) – The name of a directory.
Returns:	The full path of file.
Return type:	str

ensimpl_snps.utils.get_logger()¶

Get the logger.

Returns:	The logging object.
Return type:	logging.Logger

ensimpl_snps.utils.is_url(url)¶

Check if this is a URL or not by just checking the protocol.

Parameters:	url (str) – A string in the form of a url.
Returns:	`True` if url has a valid protocol, `False` otherwise.
Return type:	bool

ensimpl_snps.utils.merge_two_dicts(x, y)¶

Given two dicts, merge them into a new dict as a shallow copy.

Parameters:	x (dict) – Dictionary 1. y (dict) – Dictionary 2.
Returns:	The merged dictionary.
Return type:	dict

ensimpl_snps.utils.multikeysort(items, columns)¶

Sort a list of dicts by multiple keys in ascending or descending order. To sort in descending order, prepend a ‘-‘ (minus sign) on the column name.

Pulled from: https://stackoverflow.com/questions/1143671/python-sorting-list-of-dictionaries-by-multiple-keys

Examples

>>> my_list = [
    {'name': 'apple', 'count': 10, 'price': 1.00},
    {'name': 'banana', 'count': 5, 'price': 1.00},
    {'name': 'orange', 'count': 20, 'price': 2.00},
]

>>> multikeysort(my_list, ['-name', 'count'])
[{'count': 20, 'name': 'orange', 'price': 2.0},
 {'count': 5, 'name': 'banana', 'price': 1.0},
 {'count': 10, 'name': 'apple', 'price': 1.0}]

>>> multikeysort(my_list, ['-price', 'count'])
[{'count': 20, 'name': 'orange', 'price': 2.0},
 {'count': 5, 'name': 'banana', 'price': 1.0},
 {'count': 10, 'name': 'apple', 'price': 1.0}]

Parameters:	items (list) – The `list` of `dict` objects. columns (list) – A `list` of columns names to sort items.
Returns:	The sorted `list`.
Return type:	list

ensimpl_snps.utils.open_resource(resource, mode='rb')¶

Open different types of files and return a handle to that resource. Valid types of resources are gzipped and bzipped files along with URLs.

Parameters:	resource (str) – A string representing a file or url. mode (str, optional) – Mode to open the file.
Returns:	A handle to the opened `resource`.

ensimpl_snps.utils.str2bool(val)¶

Convert a string into a boolean. Valid strings that return True are: true, 1, t, y, yes

Canse-sensitivity does NOT matter. yes is the same as YeS.

Parameters:	val (str) – A string representing the boolean value of `True`.
Returns:	`True` if val represents a boolean `True`.
Return type:	bool

Module contents¶

Top-level package for Ensimpl SNPS.

ensimpl_snps package¶

Subpackages¶

Submodules¶

ensimpl_snps.app module¶

ensimpl_snps.db_config module¶

ensimpl_snps.extensions module¶

ensimpl_snps.utils module¶

Module contents¶

Related Topics