dgenies.config_reader module

dgenies.database module

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

Bases: peewee.Model

DoesNotExist

alias of dgenies.database.BaseModelDoesNotExist

classmethod connect()

id = <AutoField: BaseModel.id>

class dgenies.database.Database

Bases: object

nb_open = 0

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

Bases: dgenies.database.BaseModel

DoesNotExist

alias of dgenies.database.GalleryDoesNotExist

id = <AutoField: Gallery.id>

job = <ForeignKeyField: Gallery.job>

job_id = <ForeignKeyField: Gallery.job>

name = <CharField: Gallery.name>

picture = <CharField: Gallery.picture>

query = <CharField: Gallery.query>

target = <CharField: Gallery.target>

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

Bases: dgenies.database.BaseModel

DoesNotExist

alias of dgenies.database.JobDoesNotExist

batch_type = <CharField: Job.batch_type>

date_created = <DateTimeField: Job.date_created>

email = <CharField: Job.email>

error = <CharField: Job.error>

gallery_set

id = <AutoField: Job.id>

id_job = <CharField: Job.id_job>

id_process = <IntegerField: Job.id_process>

mem_peak = <IntegerField: Job.mem_peak>

options = <CharField: Job.options>

status = <CharField: Job.status>

time_elapsed = <IntegerField: Job.time_elapsed>

tool = <CharField: Job.tool>

class dgenies.database.MyRetryDB(database, thread_safe=True, autorollback=False, field_types=None, operations=None, autocommit=None, autoconnect=True, **kwargs)

Bases: dgenies.database.RetryOperationalError, peewee.MySQLDatabase

class dgenies.database.RetryOperationalError

Bases: object

execute_sql(sql, params=None, commit=True)

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

Bases: dgenies.database.BaseModel

DoesNotExist

alias of dgenies.database.SessionDoesNotExist

ask_for_upload(change_status=False)

date_created = <DateTimeField: Session.date_created>

id = <AutoField: Session.id>

keep_active = <BooleanField: Session.keep_active>

last_ping = <DateTimeField: Session.last_ping>

classmethod new(keep_active=False)

ping()

s_id = <CharField: Session.s_id>

status = <CharField: Session.status>

upload_folder = <CharField: Session.upload_folder>

dgenies.tools module

class dgenies.tools.Tool(name, exec, command_line, all_vs_all, max_memory, label=None, threads=1, exec_cluster=None, threads_cluster=None, parser=None, split_before=False, help=None, order=None, options=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

• label – Name to display for user

• 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

• options – list of options for the tool

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_tools_options(tool_name, chosen_options)

Transform options chosen in javascript into parameters

Returns

True is chosen options are valid + a string containing optional parameters to use with tool

Return type

boolean, str

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.legal(page)

Display legal things

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 reference

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