import logging
import math
from subprocess import PIPE
from pynpact.steps import extract, nprofile, acgt_gamma
from pynpact import binfile
from pynpact import capproc, parsing
from pynpact.util import Hasher, reducedict, which, replace_ext
from pynpact.steps import producer, enqueue
log = logging.getLogger('pynpact.steps.allplots')
statuslog = logging.getLogger('pynpact.statuslog')
BIN = binfile('Allplots')
KEYS = ['first_page_title', 'following_page_title',
'length', 'startBase', 'endBase', 'period',
'basesPerGraph', 'graphsPerPage', 'x-tics',
'nucleotides', 'alternate_colors', 'basename']
FILE_KEYS = ['File_of_unbiased_CDSs',
'File_of_conserved_CDSs',
'File_of_new_CDSs',
'File_of_published_rejected_CDSs',
'File_of_stretches_where_CG_is_asymmetric',
'File_of_published_accepted_CDSs',
'File_of_potential_new_CDSs',
'File_of_blocks_from_new_ORFs_as_cds',
'File_of_blocks_from_annotated_genes_as_cds',
'File_of_GeneMark_regions',
import logging
import sys
import json
from path import Path
from pynpact import binfile
from pynpact import capproc, parsing
from pynpact.util import Hasher, reducedict
from pynpact.steps import producer, enqueue
logger = logging.getLogger('pynpact.steps.nprofile')
statuslog = logging.getLogger('pynpact.statuslog')
BIN = binfile('nprofile')
KEYS = ['nucleotides', 'length', 'window_size', 'step', 'period', 'ddna', 'stderr']
OUTPUTKEY = 'File_list_of_nucleotides_in_200bp windows'
JSONOUTPUTKEY = 'nprofileData'
def plan(config, executor):
if 'nprofile' in config:
return
config['nprofile'] = True
parsing.length(config)
rconfig = reducedict(config, KEYS)
h = Hasher()
h.hashdict(rconfig)
import os.path
import sys
import logging
from pynpact import capproc, parsing
from pynpact import binfile, DATAPATH
from pynpact.util import Hasher, reducedict, mkdtemp_rename
from pynpact.steps import producer, enqueue
log = logging.getLogger("pynpact.steps.acgt_gamma")
statuslog = logging.getLogger("pynpact.statuslog")
BIN = binfile("acgt_gamma")
OUTPUTKEY = "acgt_gamma_output"
def plan(config, executor):
"Identifying ORFs with significant 3-base periodicities."
if config.get("skip_prediction", False):
return
assert os.path.exists(DATAPATH), "Missing pynpact/data for acgt_gamma prediction. " "Expected at " + DATAPATH
rconfig = reducedict(config, ["filename", "significance", "GeneDescriptorSkip1"])
h = Hasher().hashdict(rconfig)
h.hashfiletime(config["filename"])
h.hashfiletime(BIN)
outdir = parsing.derive_filename(config, h.hexdigest(), ".predict")
log.debug("Adding prediction filenames to config dict.")
# strip 4 characters off here b/c that's how acgt_gamma does
"""
from __future__ import absolute_import
import logging
import os.path
import sys
from pynpact import binfile, InvalidGBKException
from pynpact import capproc, parsing
from pynpact.util import Hasher, reducedict
from pynpact.steps import producer, enqueue
logger = logging.getLogger('pynpact.steps.extract')
statuslog = logging.getLogger('pynpact.statuslog')
BIN = binfile("extract")
KEYS = ['GeneDescriptorKey1', 'GeneDescriptorKey2',
'GeneDescriptorSkip1', 'GeneDescriptorSkip2',
'filename']
OUTPUTKEY = 'File_of_published_accepted_CDSs'
def plan(config, executor):
if parsing.isgbk(config):
logger.debug(
"GBK file, extracting known gene names %s", config['filename'])
rconfig, hash = get_hash(config)
target_file = parsing.derive_filename(config, hash, 'genes')
config[OUTPUTKEY] = target_file