dgenies.config_reader module

dgenies.database module

class dgenies.database.BaseModel(*args, **kwargs)

Bases: peewee.Model

DoesNotExist

alias of BaseModelDoesNotExist

_data = None

_meta = <ModelOptions: basemodel>

classmethod connect()

id = <peewee.PrimaryKeyField object>

class dgenies.database.Database

Bases: object

nb_open = 0

class dgenies.database.Gallery(*args, **kwargs)

Bases: dgenies.database.BaseModel

DoesNotExist

alias of GalleryDoesNotExist

_data = None

_meta = <ModelOptions: gallery>

id = <peewee.PrimaryKeyField object>

job = <peewee.ForeignKeyField object>

job_id = <peewee.ForeignKeyField object>

name = <peewee.CharField object>

picture = <peewee.CharField object>

query = <peewee.CharField object>

target = <peewee.CharField object>

class dgenies.database.Job(*args, **kwargs)

Bases: dgenies.database.BaseModel

DoesNotExist

alias of JobDoesNotExist

_data = None

_meta = <ModelOptions: job>

batch_type = <peewee.CharField object>

date_created = <peewee.DateTimeField object>

email = <peewee.CharField object>

error = <peewee.CharField object>

gallery_set

Back-reference to expose related objects as a SelectQuery.

id = <peewee.PrimaryKeyField object>

id_job = <peewee.CharField object>

id_process = <peewee.IntegerField object>

mem_peak = <peewee.IntegerField object>

status = <peewee.CharField object>

time_elapsed = <peewee.IntegerField object>

tool = <peewee.CharField object>

class dgenies.database.MyRetryDB(database, threadlocals=True, autocommit=True, fields=None, ops=None, autorollback=False, use_speedups=True, **connect_kwargs)

Bases: playhouse.shortcuts.RetryOperationalError, peewee.MySQLDatabase

class dgenies.database.Session(*args, **kwargs)

Bases: dgenies.database.BaseModel

DoesNotExist

alias of SessionDoesNotExist

_data = None

_meta = <ModelOptions: session>

ask_for_upload(change_status=False)

date_created = <peewee.DateTimeField object>

id = <peewee.PrimaryKeyField object>

keep_active = <peewee.BooleanField object>

last_ping = <peewee.DateTimeField object>

classmethod new(keep_active=False)

ping()

s_id = <peewee.CharField object>

status = <peewee.CharField object>

upload_folder = <peewee.CharField object>

dgenies.tools module

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)

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

dgenies.views.ask_upload()

Ask for upload: to keep a max number of concurrent uploads

dgenies.views.build_fasta(id_res)

Generate the fasta file of query

Parameters:id_res (str) – job id

dgenies.views.build_query_as_reference(id_res)

Build fasta of query with contigs order like reference

Parameters:id_res (str) – job id

dgenies.views.contact()

Contact page

dgenies.views.delete_job(id_res)

Delete a job

Parameters:id_res (str) – job id

dgenies.views.dl_fasta(id_res, filename)

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)

dgenies.views.documentation_dotplot()

Documentation dotplot page

dgenies.views.documentation_formats()

Documentation formats page

dgenies.views.documentation_result()

Documentation result page

dgenies.views.documentation_run()

Documentation run page

dgenies.views.download_file(id_res, filename)

Download a file from a job

Parameters:

• id_res (str) – job id
• filename (str) – file name

dgenies.views.download_paf(id_res)

Download PAF file of a job

Parameters:id_res (str) – job id

dgenies.views.free_noise(id_res)

Remove noise from the dot plot

Parameters:id_res (str) – job id

dgenies.views.gallery()

Gallery page

dgenies.views.gallery_file(filename)

Getting gallery illustration

Parameters:filename – filename of the PNG file

dgenies.views.get_backup_file(id_res)

Download archive backup file of a job

Parameters:id_res (str) – job id

dgenies.views.get_file(file, gzip=False)

Download a file

Parameters:

• file (str) – filename
• gzip (bool) – is file gzipped?

dgenies.views.get_filter_out(id_res, type_f)

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)

dgenies.views.get_filter_out_query(id_res)

Download query filtered fasta, when it has been filtered before job run

Parameters:id_res (str) – job id

dgenies.views.get_filter_out_target(id_res)

Download target filtered fasta, when it has been filtered before job run

Parameters:id_res (str) – job id

dgenies.views.get_graph()

Get dot plot data for a job

dgenies.views.get_query_as_reference(id_res)

Get fasta of query with contigs order like reference

Parameters:id_res (str) – job id

dgenies.views.get_viewer_html(id_res)

Get HTML file with offline interactive viewer inside

Parameters:id_res (str) – job id

dgenies.views.global_templates_variables()

Global variables used for any view

dgenies.views.install()

Documentation: how to install? page

dgenies.views.launch_analysis()

Launch the job

dgenies.views.main()

Index page

dgenies.views.no_assoc(id_res)

Get contigs that match with None target

Parameters:id_res (str) – job id

dgenies.views.ping_upload()

When upload waiting, ping to be kept in the waiting line

dgenies.views.post_query_as_reference(id_res)

Launch build fasta of query with contigs order like reference

Parameters:id_res (str) – job id

dgenies.views.qt_assoc(id_res)

Query - Target association TSV file

Parameters:id_res – Returns:

dgenies.views.result(id_res)

Result page

Parameters:id_res (str) – job id

dgenies.views.reverse_contig(id_res)

Reverse contig order

Parameters:id_res (str) – job id

dgenies.views.run()

Run page

dgenies.views.run_test()

Run test page (used to simulate a real client run)

dgenies.views.send_mail(id_res)

Send mail

Parameters:id_res (str) – job id

dgenies.views.sort_graph(id_res)

Sort dot plot to referene

Parameters:id_res (str) – job id

dgenies.views.status(id_job)

Status page

Parameters:id_job (str) – job id

dgenies.views.summary(id_res)

Get Dot plot summary data

Parameters:id_res (str) – job id

dgenies.views.upload()

Do upload of a file