dgenies.config_reader module¶
dgenies.database module¶
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class
dgenies.database.
BaseModel
(*args, **kwargs)[source]¶ Bases:
peewee.Model
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DoesNotExist
¶ alias of
BaseModelDoesNotExist
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_data
= None¶
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_meta
= <ModelOptions: basemodel>¶
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id
= <peewee.PrimaryKeyField object>¶
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class
dgenies.database.
Gallery
(*args, **kwargs)[source]¶ Bases:
dgenies.database.BaseModel
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DoesNotExist
¶ alias of
GalleryDoesNotExist
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_data
= None¶
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_meta
= <ModelOptions: gallery>¶
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id
= <peewee.PrimaryKeyField object>¶
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job
= <peewee.ForeignKeyField object>¶
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job_id
= <peewee.ForeignKeyField object>¶
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name
= <peewee.CharField object>¶
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picture
= <peewee.CharField object>¶
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query
= <peewee.CharField object>¶
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target
= <peewee.CharField object>¶
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class
dgenies.database.
Job
(*args, **kwargs)[source]¶ Bases:
dgenies.database.BaseModel
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DoesNotExist
¶ alias of
JobDoesNotExist
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_data
= None¶
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_meta
= <ModelOptions: job>¶
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batch_type
= <peewee.CharField object>¶
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date_created
= <peewee.DateTimeField object>¶
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email
= <peewee.CharField object>¶
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error
= <peewee.CharField object>¶
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gallery_set
¶ Back-reference to expose related objects as a SelectQuery.
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id
= <peewee.PrimaryKeyField object>¶
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id_job
= <peewee.CharField object>¶
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id_process
= <peewee.IntegerField object>¶
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mem_peak
= <peewee.IntegerField object>¶
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status
= <peewee.CharField object>¶
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time_elapsed
= <peewee.IntegerField object>¶
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tool
= <peewee.CharField object>¶
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class
dgenies.database.
MyRetryDB
(database, threadlocals=True, autocommit=True, fields=None, ops=None, autorollback=False, use_speedups=True, **connect_kwargs)[source]¶ Bases:
playhouse.shortcuts.RetryOperationalError
,peewee.MySQLDatabase
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class
dgenies.database.
Session
(*args, **kwargs)[source]¶ Bases:
dgenies.database.BaseModel
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DoesNotExist
¶ alias of
SessionDoesNotExist
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_data
= None¶
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_meta
= <ModelOptions: session>¶
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date_created
= <peewee.DateTimeField object>¶
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id
= <peewee.PrimaryKeyField object>¶
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keep_active
= <peewee.BooleanField object>¶
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last_ping
= <peewee.DateTimeField object>¶
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s_id
= <peewee.CharField object>¶
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status
= <peewee.CharField object>¶
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upload_folder
= <peewee.CharField object>¶
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dgenies.tools module¶
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class
dgenies.tools.
Tool
(name, exec, command_line, all_vs_all, max_memory, threads=1, exec_cluster=None, threads_cluster=None, parser=None, split_before=False, help=None, order=None)[source]¶ Bases:
object
Create a new tool
Parameters: - command_line – command line to launch the tool
- all_vs_all – command line in all_vs_all mode (None if not available for the tool)
- max_memory – max memory the tool is supposed to use (ex: 40G) - for cluster submissions
- parser – name of the function in dgenies.lib.functions to launch after mapping to have a correct PAF out file
- split_before (bool) – True to split contigs before mapping
- help – help message to show in run form
- order – order to show in run mode
dgenies.views module¶
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dgenies.views.
build_fasta
(id_res)[source]¶ Generate the fasta file of query
Parameters: id_res (str) – job id
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dgenies.views.
build_query_as_reference
(id_res)[source]¶ Build fasta of query with contigs order like reference
Parameters: id_res (str) – job id
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dgenies.views.
dl_fasta
(id_res, filename)[source]¶ Download fasta file
Parameters: - id_res (str) – job id
- filename (str) – file name (not used, but can be in the URL to define download filename to the browser)
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dgenies.views.
download_file
(id_res, filename)[source]¶ Download a file from a job
Parameters: - id_res (str) – job id
- filename (str) – file name
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dgenies.views.
download_paf
(id_res)[source]¶ Download PAF file of a job
Parameters: id_res (str) – job id
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dgenies.views.
free_noise
(id_res)[source]¶ Remove noise from the dot plot
Parameters: id_res (str) – job id
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dgenies.views.
gallery_file
(filename)[source]¶ Getting gallery illustration
Parameters: filename – filename of the PNG file
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dgenies.views.
get_backup_file
(id_res)[source]¶ Download archive backup file of a job
Parameters: id_res (str) – job id
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dgenies.views.
get_file
(file, gzip=False)[source]¶ Download a file
Parameters: - file (str) – filename
- gzip (bool) – is file gzipped?
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dgenies.views.
get_filter_out
(id_res, type_f)[source]¶ Download filter fasta, when it has been filtered before job run
Parameters: - id_res (str) – job id
- type_f (str) – type of fasta (query or target)
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dgenies.views.
get_filter_out_query
(id_res)[source]¶ Download query filtered fasta, when it has been filtered before job run
Parameters: id_res (str) – job id
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dgenies.views.
get_filter_out_target
(id_res)[source]¶ Download target filtered fasta, when it has been filtered before job run
Parameters: id_res (str) – job id
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dgenies.views.
get_query_as_reference
(id_res)[source]¶ Get fasta of query with contigs order like reference
Parameters: id_res (str) – job id
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dgenies.views.
get_viewer_html
(id_res)[source]¶ Get HTML file with offline interactive viewer inside
Parameters: id_res (str) – job id
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dgenies.views.
no_assoc
(id_res)[source]¶ Get contigs that match with None target
Parameters: id_res (str) – job id
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dgenies.views.
post_query_as_reference
(id_res)[source]¶ Launch build fasta of query with contigs order like reference
Parameters: id_res (str) – job id
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dgenies.views.
qt_assoc
(id_res)[source]¶ Query - Target association TSV file
Parameters: id_res – Returns: