Python SnakeModule Exemples

Exemple #1

import os
import assnake

snake_module = assnake.SnakeModule(name='assnake-core-mapping',
                                   install_dir=os.path.dirname(
                                       os.path.abspath(__file__)))

Exemple #2

import os, assnake

import assnake_anvio.result
from assnake.utils import read_yaml

this_dir = os.path.dirname(os.path.abspath(__file__))

snake_module = assnake.SnakeModule(name='assnake-anvio',
                                   install_dir=this_dir,
                                   results=[assnake_anvio.result],
                                   snakefiles=[],
                                   invocation_commands=[])

Exemple #3

Fichier : snake_module_setup.py Projet : ASSNAKE/assnake-core-binning

import os
import assnake
# from assnake_core_assembly.megahit.cmd_megahit import megahit_invocation
from assnake.utils.general import read_yaml
from assnake_core_binning.checkm.invocation_commands import chekcm_invocation
from assnake_core_binning.metabat2.invocation_commands import metabat2_invocation

this_dir = os.path.dirname(os.path.abspath(__file__))
snake_module = assnake.SnakeModule(
    name='assnake-core-binning',
    install_dir=this_dir,
    snakefiles=['./metabat2/metabat2.smk', './checkm/checkm.smk'],
    invocation_commands=[chekcm_invocation, metabat2_invocation],
    wc_configs=[])

Exemple #4

Fichier : snake_module_setup.py Projet : PollyTikhonova/assnake-core-preprocessing

import os, assnake

snake_module = assnake.SnakeModule(
    name='assnake-core-preprocessing',
    install_dir=os.path.dirname(os.path.abspath(__file__)),
)

Exemple #5

Fichier : __init__.py Projet : ASSNAKE/assnake-core-taxonomy

import os
import assnake

from assnake_core_taxonomy.metaphlan2.init_metaphlan2 import mp2_init
from assnake_core_taxonomy.metaphlan2.loaders import load_metaphlan2

snake_module = assnake.SnakeModule(
    name='assnake-core-taxonomy',
    install_dir=os.path.dirname(os.path.abspath(__file__)),
    initialization_commands=[mp2_init],
    dataset_methods={'load_metaphlan2': load_metaphlan2})

Exemple #6

Fichier : snake_module_setup.py Projet : ASSNAKE/assnake-dada2

import os
import assnake

from assnake_dada2.invocation_commands import dada2_full
from assnake_dada2.init_dada2 import dada2_init

snake_module = assnake.SnakeModule(
    name='assnake-dada2',
    install_dir=os.path.dirname(os.path.abspath(__file__)),
    snakefiles=[
        './assign_taxa/workflow.smk',
        './remove_chimeras/workflow.smk',
        './make_seqtab/workflow.smk',
        './derep_infer_merge/workflow.smk',
        './idtaxa/workflow.smk',
        #    './derep_infer_pooled/workflow.smk',
        './track_reads/workflow.smk',
    ],
    invocation_commands=[dada2_full],
    initialization_commands=[dada2_init])

Exemple #7

Fichier : snake_module_setup.py Projet : ASSNAKE/assnake-transcriptome

import os
import assnake

snake_module = assnake.SnakeModule(
    name='assnake-transcriptome',
    install_dir=os.path.dirname(os.path.abspath(__file__)),
)

Exemple #8

import os, assnake

import assnake_core_assembly.megahit.result as megahit


snake_module = assnake.SnakeModule(name='assnake-core-assembly',
                                   install_dir=os.path.dirname(os.path.abspath(__file__)),
                                #    results = [megahit]
                                   )