class StreamIEO(object):
def __init__(self, logname):
"""
A class that individually threads the capture of the stdout stream and the stderr stream of a system command.
The stdout/stderr are queued in the order they occur. As the que populates another thread, parse the que and
prints to the screen using the LogIT class.
"""
self.io_q = Queue()
self.process = None
self.streamieolog = LogIt().default(logname="%s - streamieo" % logname,
logfile=None)
def streamer(self, cmd):
self.process = Popen(cmd,
stdout=PIPE,
stderr=PIPE,
shell=True,
encoding='utf-8')
# Add the command line to the que
self.io_q.put(("STDIN", cmd))
# Watch the standard output and add it to the que
Thread(target=self._stream_watcher,
name='stdout-watcher',
args=('STDOUT', self.process.stdout)).start()
# Watch the standard error and add it to the que
Thread(target=self._stream_watcher,
name='stderr-watcher',
args=('STDERR', self.process.stderr)).start()
# As items are added, print the stream.
Thread(target=self._printer, name='_printer').start()
def _stream_watcher(self, identifier, stream):
# Watch the stream and add to the que dynamically
# This runs in tandem with the printer. So as the stdout/stderr streams are queued here,
# the que is parsed and printed in the printer function.
for line in stream:
self.io_q.put((identifier, line))
if not stream.closed:
stream.close()
def _printer(self):
# Prints the que as it is populated with stdout/stderr dynamically.
while True:
try:
# Block for 1 second.
item = self.io_q.get(True, 1)
except Empty:
# No output in either streams for a second. Are we done?
if self.process.poll() is not None:
break
else:
identifier, line = item
if identifier == "STDIN":
self.streamieolog.warn("Command: " + line.strip())
elif identifier == "STDERR":
self.streamieolog.error(line.strip())
elif identifier == "STDOUT":
self.streamieolog.info(line.strip())
else:
self.streamieolog.critical(identifier + ':' + line.strip())
def archive(database_path, archive_path, option, delete_flag=False):
"""Archive a database directory from a Cookie templated directory structure.
This utility creates a YAML config dictionary that contains path-like
objects for archiving. The original data
can be moved to the archive path or deleted all together.
:param database_path: A path to a folder that consists of the desired data.
:param archive_path: A path to an output folder for archived data.
:param option: An option for the archiving strategy. Will be one of the
keys in the archive_options.
:param delete_flag: A flag for deleting the original data. USE WITH CAUTION.
:return: Returns a list of paths to the *.tar.xz archive of the data
and/or a path to the original data.
"""
archive_dict = {}
archive_list = []
archive_log = LogIt().default(logname="Archive", logfile=None)
if option == "Full":
full_path = Path(database_path) / archive_options["Full"]
for folder in os.listdir(str(full_path)):
if os.path.isdir(folder):
archive_dict[folder] = database_path / Path(folder)
elif isinstance(option, list):
for opt in option:
other_path = Path(database_path) / archive_options[opt]
archive_dict[opt] = other_path
else:
other_path = Path(database_path) / archive_options[option]
archive_dict[option] = other_path
for arch_name, data_path in archive_dict.items():
root_dir = str(data_path.parent)
base_dir = str(data_path.stem)
d = datetime.datetime.now().strftime(fmt="%Y-%m-%d_%H%M")
output_pathname = archive_path / Path(arch_name + "." + d)
# Archive the desired data.
data_size = get_size(start_path=str(data_path))
archive_log.info("Archiving %s of data." % data_size)
archive_filename = shutil.make_archive(base_name=str(output_pathname),
format="xztar",
root_dir=root_dir,
base_dir=base_dir)
archive_size = get_size(archive_filename)
archive_log.warning("A %s archive file was created at %s." %
(archive_filename, archive_size))
# TODO-ROB: Logging. And log to a README.md file.
# Delete the files if desired.
if delete_flag:
archive_log.critical(
"The original data will be deleted recursively at %s." %
data_path)
from OrthoEvol import OrthoEvolWarning
OrthoEvolWarning(
"You're about to delete your database (%s). Are you sure??" %
data_path)
shutil.rmtree(path=data_path)
archive_list.append(str(archive_filename))
else:
archive_log.critical(
"The original data will be moved recursively from %s to %s." %
(data_path, output_pathname))
output_pathname.mkdir()
shutil.move(src=str(data_path), dst=str(output_pathname))
shutil.move(src=str(archive_filename), dst=str(output_pathname))
archive_list.append(str(output_pathname))
Path(data_path).mkdir(parents=True, exist_ok=True)
return archive_list
class GenBank(object):
"""This class will handle GenBank files in various ways."""
def __init__(self,
project,
project_path=None,
solo=False,
multi=True,
archive=False,
min_fasta=True,
blast=OrthoBlastN,
**kwargs):
"""Handle GenBank files in various ways.
It allows for refseq-release .gbff files to be downloaded from NCBI
and uploaded to a BioSQL database (biopython). Single .gbk files can be
downloaded from the .gbff, and uploaded to a custom BopSQL database for
faster acquisition of GenBank data.
:param project: The name of the project.
:param project_path: The relative path to the project.
:param solo: A flag for adding single fasta files.
:param multi: A flag for adding multi-fasta files.
:param archive: A flag for archiving current GenBank Data. # TODO
:param min_fasta: A flag for minimizing FASTA file headers.
:param blast: The blast parameter is used for composing various
Orthologs.Blast classes. Can be a class, a dict,
or none.
:returns: .gbff files/databases, .gbk files/databases, & FASTA files.
"""
# TODO-ROB: Change the way the file systems work.
self.project = project
self.project_path = project_path
self.solo = solo
self.multi = multi
self.min_fasta = min_fasta
self.genbanklog = LogIt().default(logname="GenBank", logfile=None)
# Configuration of class attributes
add_self = attribute_config(self,
composer=blast,
checker=OrthoBlastN,
checker2=BaseComparativeGenetics,
project=project,
project_path=project_path)
for var, attr in add_self.__dict__.items():
setattr(self, var, attr)
# Configuration
# FIXME AttributeError: 'GenBank' object has no attribute 'user_db'
self.target_gbk_db_path = self.user_db / Path(self.project)
Path.mkdir(self.target_gbk_db_path, parents=True, exist_ok=True)
# Make a list of BioSQL database(.db) files that contain GenBank info
self.db_files_list = []
for FILE in os.listdir(str(self.ncbi_db_repo)):
if FILE.endswith('.db'):
self.db_files_list.append(str(FILE))
@staticmethod
def name_fasta_file(path, gene, org, feat_type, feat_type_rank, extension,
mode):
"""Name a fasta file.
Provide a uniquely named FASTA file:
* Coding sequence:
* Single - "<path>/<gene>_<organism><feat_type_rank>.<extension>"
* Multi - "<path>/<gene><feat_type_rank>.<extension>"
* Other:
* Single - "<path>/<gene>_<organism>_<feat_type_rank>.<extension>"
* Multi - "<path>/<gene>_<feat_type_rank>.<extension>"
:param path: The path where the file will be made.
:param gene: The gene name.
:param org: The organism name.
:param feat_type: The type of feature from the GenBank record.
(CDS, UTR, misc_feature, variation, etc.)
:param feat_type_rank: The feature type + the rank.
(There can be multiple misc_features and
variations)
:param extension: The file extension.
(".ffn", ".faa", ".fna", ".fasta")
:param mode: The mode ("w" or "a") for writing the file. Write to a
solo-FASTA file. Append a multi-FASTA file.
:return: The uniquely named FASTA file.
"""
# Create path variables. (typically raw_data/<gene>/GENBANK
feat_path = path
# Create a format-able string for file names
if feat_type_rank is "CDS":
single = '%s_%s%s%s'
multi = '%s%s%s'
else:
single = '%s_%s_%s%s'
multi = '%s_%s%s'
# Create different names based on fasta file type
if mode == 'w':
file_path = feat_path / Path(
single % (gene, org, feat_type_rank, extension))
elif mode == 'a':
file_path = feat_path / Path(multi %
(gene, feat_type_rank, extension))
# Make the base directory and return an open file.
makedirectory(feat_path)
file = open(file_path, mode)
return file
@staticmethod
def protein_gi_fetch(feature):
"""Retrieve the protein gi number.
:param feature: Search the protein feature for the GI number.
:return: The protein GI number as a string.
"""
# Find the protein gi number under the features qualifiers.
for x in feature.qualifiers:
if 'GI' in x:
_, _, p_gi = x.partition(':')
return p_gi
def create_post_blast_gbk_records(self, org_list, gene_dict):
"""Create a single GenBank file for each ortholog.
After a blast has completed and the accession numbers have been compiled
into an accession file, this class searches a local NCBI refseq release
database composed of GenBank records. This method will create a single
GenBank file (.gbk) for each ortholog with an accession number.
The create_post_blast_gbk_records is only callable if the
the instance is composed by one of the Blast classes. This method also
requires an NCBI refseq release database to be set up with the proper
GenBank Flat Files (.gbff) files.
:param org_list: List of organisms
:param gene_dict: A nested dictionary for accessing accession numbers.
(e.g. gene_dict[GENE][ORGANISM} yields an accession
number)
:return: Does not return an object, but creates genbank files.
"""
# Parse the tier_frame_dict to get the tier
for G_KEY, _ in self.tier_frame_dict.items():
tier = G_KEY
# Parse the tier based transformed dataframe to get the gene
for GENE in self.tier_frame_dict[tier].T:
# Parse the organism list to get the desired accession number
for ORGANISM in org_list:
accession = str(gene_dict[GENE][ORGANISM])
accession, _, version = accession.partition('.')
# When parsing a GenBank database, the version needs to be removed.
accession = accession.upper()
server_flag = False
# Search the databases and create a GenBank file.
self.get_gbk_file(accession,
GENE,
ORGANISM,
server_flag=server_flag)
def get_gbk_file(self, accession, gene, organism, server_flag=None):
"""Search a GenBank database for a target accession number.
This function searches through the given NCBI databases (created by
uploading NCBI refseq .gbff files to a BioPython BioSQL database) and
creates single GenBank files. This function can be used after a
blast or on its own. If used on it's own then the NCBI .db files must
be manually moved to the proper directories.
:param accession: Accession number of interest without the version.
:param gene: Target gene of the accession number parameter.
:param organism: Target organism of the accession number parameter.
:param server_flag: (Default value = None)
:return:
"""
gene_path = self.raw_data / Path(gene) / Path('GENBANK')
Path.mkdir(gene_path, parents=True, exist_ok=True)
# Parse each database to find the proper GenBank record
for FILE in self.db_files_list:
db_file_path = self.ncbi_db_repo / Path(FILE)
# Stop searching if the GenBank record has been created.
if server_flag is True:
break
server = BioSeqDatabase.open_database(driver='sqlite3',
db=str(db_file_path))
# Parse the sub-databases
for SUB_DB_NAME in server.keys():
db = server[SUB_DB_NAME]
try:
record = db.lookup(accession=accession)
gbk_file = '%s_%s.gbk' % (gene, organism)
gbk_file_path = gene_path / Path(gbk_file)
with open(gbk_file_path, 'w') as GB_file:
GB_file.write(record.format('genbank'))
self.genbanklog.info(GB_file.name, 'created')
# Make sure we have the correct GenBank file.
self.gbk_quality_control(gbk_file_path, gene, organism)
# Stop searching if the GenBank record has been created.
server_flag = True
break
except IndexError:
self.genbanklog.critical(
'Index Error in %s. Moving to the next database...' %
SUB_DB_NAME)
continue
# If the file has not been created after searching, then raise an error
if server_flag is not True:
self.genbanklog.critical(
"The GenBank file was not created for %s (%s, %s)." %
(accession, gene, organism))
raise FileNotFoundError
def gbk_quality_control(self, gbk_file, gene, organism):
"""Ensures the quality or validity of the retrieved genbank record.
It takes the GenBank record and check to make sure the Gene and Organism
from the GenBank record match the Gene and Organism from the accession
file. If not, then the Blast has returned the wrong accession number.
:param gbk_file: The path to a GenBank file.
:param gene: A gene name from the Accession file.
:param organism: A gene name from the Accession file.
:return:
"""
# TODO-ROB: Check the bad data here against the misssing/duplicate files
record = SeqIO.read(gbk_file, 'genbank')
gene_flag = False
organism_flag = False
accession = record.id
self.gbk_gene_synonym = {}
self.duplicated_dict["validated"] = {}
# Get the organism name from the GenBank file
gbk_organism = record.features[0].qualifiers[
"organism"] # A list with one entry
if len(gbk_organism) == 1:
gbk_organism = gbk_organism[0]
gbk_organism = gbk_organism.replace(" ", "_")
else:
self.genbanklog.critical(
"Two organisms exist in the GenBank file. Is this normal?")
raise BrokenPipeError
# Check to make sure the organism in the GenBank file matches the
# organism from the accession file
if gbk_organism == organism:
self.genbanklog.info(
"The GenBank organism, %s, has been verified for %s." %
(organism, gene))
else:
organism_flag = True
# Get the gene from the GenBank files
gbk_genes = record.features[1].qualifiers["gene"]
# Get the synonyms from the GenBank file if they exist and add them to
# the list.
if "gene_synonym" in str(record.features[1].qualifiers.keys()):
base_gene_name = gbk_genes
gbk_genes.extend(record.features[1].qualifiers["gene_synonym"])
# Create a dictionary from the synonyms
self.gbk_gene_synonym[base_gene_name] = []
self.gbk_gene_synonym[base_gene_name].extend(gbk_genes)
# Check to make sure the gene in the GenBank file matches the gene from
# the accession file
for gbk_gene in gbk_genes:
if gbk_gene == gene:
gene_flag = False
self.genbanklog.info(
"The GenBank gene, %s, has been verified for %s." %
(gene, organism))
break
else:
gene_flag = True
# TODO-ROB: Add a verified key to the duplicates dictionary.
# Raise errors.
if organism_flag is True and gene_flag is True:
self.genbanklog.critical(
"The organisms don't match.\n\tGenBank: %s \n\tAccession File: %s"
% (gbk_organism, organism))
self.genbanklog.critical(
"The genes don't match. \n\tGenBank: %s \n\tAccession File: %s"
% (gbk_genes, gene))
raise BrokenPipeError
elif organism_flag is True:
self.genbanklog.critical(
"The organisms don't match.\n\tGenBank: %s \n\tAccession File: %s"
% (gbk_organism, organism))
raise BrokenPipeError
elif gene_flag is True:
self.genbanklog.critical(
"The genes don't match. \n\tGenBank: %s \n\tAccession File: %s"
% (gbk_genes, gene))
raise BrokenPipeError
self.duplicated_dict["validated"][accession] = [gene, organism]
def gbk_upload(self):
"""Upload a BioSQL database with target GenBank data (.gbk files).
This method is only usable after creating GenBank records with this
class. It uploads a BioSQL databases with target GenBank data (.gbk
files). This creates a compact set of data for each project.
:return: Does not return an object.
"""
t_count = 0
# Parse the tier dictionary
for TIER in self.tier_frame_dict.keys():
db_name = str(TIER) + '.db'
db_file_path = self.target_gbk_db_path / Path(db_name)
# Create the db file if it exists
if os.path.isfile(str(db_file_path)) is False:
self.genbanklog.warn(
'Copying Template BioSQL Database... This may take a few minutes...'
)
shutil.copy2('Template_BioSQL_DB.db', str(db_file_path))
# If it already exists then the database is bad, or needs to be update. Delete it.
else:
# TODO-ROB: This part is broken until the template db creation and management is added
os.remove(str(db_file_path))
self.genbanklog.warn(
'Copying Template BioSQL Database... This may take a few minutes...'
)
shutil.copy2('Template_BioSQL_DB.db', str(db_file_path))
server = BioSeqDatabase.open_database(driver='sqlite3',
db=str(db_file_path))
gene_path = self.raw_data
# Parse the raw_data folder to get the name of each gene.
for GENE in os.listdir(str(gene_path)):
sub_db_name = GENE
genbank_path = gene_path / Path(GENE) / Path('GENBANK')
# Parse the GenBank file names for each gene in order to upload them to a custom BioSQL database
for FILE in os.listdir(str(genbank_path)):
# Try to load the database.
try:
if sub_db_name not in server.keys():
server.new_database(sub_db_name)
db = server[sub_db_name]
count = db.load(SeqIO.parse(FILE, 'genbank'))
server.commit()
self.genbanklog.info('Server Commited %s' %
sub_db_name)
self.genbanklog.info('%s database loaded with %s.' %
(db.dbid, FILE))
self.genbanklog.info(
"That file contains %s genbank records." %
str(count))
t_count = t_count + count
self.genbanklog.info(
'The total number of files loaded so far is %i.' %
t_count)
# If the database cannot be loaded then rollback the server and raise an error.
except BaseException:
server.rollback()
# Try to delete the sub database and commit
try:
del server[sub_db_name]
server.commit()
# If it cannot be deleted then raise an error.
except BaseException:
raise
raise
def get_fasta_files(self, acc_dict, db=True):
"""Create FASTA files for each GenBank record in the accession dictionary.
It can search through a BioSQL database or it can crawl a directory
for .gbk files.
:param acc_dict: An accession dictionary like the one created by
CompGenObjects.
:param db: A flag that determines whether or not to use the custom
BioSQL database or to use .gbk files.
(Default value = True)
:return: Returns FASTA files for each GenBank record.
"""
# Get FASTA files from the BioSQL GenBank databases.
if db is True:
# Parse the directory that contains the databases for the project of interest.
for database in os.listdir(str(self.target_gbk_db_path)):
server = BioSeqDatabase.open_database(driver="sqlite3",
db=database)
try:
for db_name in server.keys():
db = server[db_name]
# For each GenBank record in the database write a set of FASTA files.
for item in db.keys():
record = db.lookup(item)
self.write_fasta_files(record, acc_dict)
self.genbanklog.info(
"FASTA files for %s created from BioSQL database."
% item)
except:
raise ()
# Get FASTA files from the GenBank files.
# TODO-ROB change this. Broken by new directory structure
# TODO-ROB directory looks like /raw_data/Gene_1/GENBANK/*.gbk
elif db is False:
# Parse the directory that contain the GenBank records for the project of interest.
for _, _, gbk_files in os.walk(str(self.target_gbk_files_path)):
# For each genbank record write a set of FASTA files.
for gbk_file in gbk_files:
if Path(gbk_file).suffix is '.gbk':
record = SeqIO.read(gbk_file, 'genbank')
self.write_fasta_files(record, acc_dict)
self.genbanklog.info("FASTA files for %s created." %
gbk_file)
def write_fasta_files(self, record, acc_dict):
"""Create a dictionary for formatting the FASTA header & sequence.
:param record: A GenBank record created by BioPython.
:param acc_dict: Accession dictionary from the CompGenObjects class.
:return:
"""
feat_type_list = []
for feature in record.features:
# XXX Set up variables to use for dictionary values !!!
# Basic variables.
accession = record.id
gene = acc_dict[accession][0]
organism = acc_dict[accession][1]
# Variable for minimalistic FASTA files.
genus, sep, species = organism.partition('_')
min_org = str(''.join([genus[0], sep, species[0:28]]))
# Keep a list of feature types to identify duplicates (for naming the FASTA files).
# The first iteration of the feature type contains no number.
# The following iterations are concatenated with a number.
feat_type = str(feature.type)
feat_type_list.append(feat_type)
duplicate_num = feat_type_list.count(feat_type)
if duplicate_num == 1:
feat_type_rank = feat_type
else:
feat_type_rank = feat_type + str(duplicate_num)
# XXX END !!!
# TODO-ROB: Remove the GI number stuff here or at least prepare for
# file with no GI.
# Create a dictionary and format FASTA file entries.
fmt = {
'na_gi': str(record.annotations['gi']),
'aa_gi': str(self.protein_gi_fetch(feature)),
'na_acc_n': str(accession),
'aa_acc_n': str(feature.qualifiers['protein_id'][0]),
'na_description': str(record.description),
'aa_description': str(feature.qualifiers['product'][0]),
'na_seq': str(feature.extract(record.seq)),
'aa_seq': str(feature.qualifiers['translation'][0]),
'na_misc_feat': str(feature.qualifiers['note'][0]),
'org': str(organism),
'gene': str(gene),
'min_org': str(min_org),
'feat_type': str(feat_type),
'feat_type_rank': str(feat_type_rank),
'path': str(self.raw_data / Path(gene) / Path('GENBANK'))
}
# Set up minimalistic FASTA headers and sequence entries for Nucleic Acid and Amino Acid sequences.
na_entry = ">{min_org}\n{na_seq}\n".format(**fmt)
aa_entry = ">{min_org}\n{aa_seq}\n".format(**fmt)
# For full FASTA headers/sequences set min_fasta to False
if self.min_fasta is False:
na_entry = ">gi|{na_gi}|ref|{na_acc_n}| {na_description}\n{na_seq}\n".format(
**fmt)
aa_entry = ">gi|{aa_gi}|reg|{aa_acc_n}| {aa_description} {org}\n{aa_seq}\n".format(
**fmt)
# ######### End ######### #
# ############ Write desired FASTA files ############ #
if self.solo is True:
self.solo_fasta(na_entry, aa_entry, fmt)
if self.multi is True:
self.multi_fasta(na_entry, aa_entry, fmt)
def solo_fasta(self, na_entry, aa_entry, fmt):
"""This method writes a sequence of a feature to a uniquely named file using a dictionary for formatting.
:param na_entry: A string representing the Nucleic Acid sequence data in FASTA format.
:param aa_entry: A string representing the Amino Acid sequence data in FASTA format.
:param fmt: A dictionary for formatting the FASTA entries and the file names.
:return: Does not return an object, but creates single entry FASTA files.
"""
mode = 'w'
# Create the desired variables from the formatter dictionary.
feat_type = fmt['feat_type']
feat_type_rank = fmt['feat_type_rank']
path = fmt['path']
gene = fmt['gene']
org = fmt['org']
if feat_type == "CDS":
# Create a .ffn file (FASTA for Coding Nucleic Acids)
extension = '.ffn'
file = self.name_fasta_file(path, gene, org, feat_type,
feat_type_rank, extension, mode)
file.write(na_entry)
file.close()
# Create a .faa file (FASTA for Amino Acids)
extension = '.faa'
file = self.name_fasta_file(path, gene, org, 'Protein',
feat_type_rank, extension, mode)
file.write(aa_entry)
file.close()
elif feat_type == "misc_feature":
# Create a custom entry for miscellaneous features.
na_entry = ">gi|{na_gi}|ref|{na_acc_n}| {na_description} Feature: {na_misc_feat}\n{na_seq}\n".format(
**fmt)
# Creates .fna files (generic FASTA file for Nucleic Acids)
extension = '.fna'
file = self.name_fasta_file(path, gene, org, feat_type,
feat_type_rank, extension, mode)
file.write(na_entry)
file.close()
elif feat_type != "variation":
# Creates .fasta files (generic FASTA file)
extension = '.fasta'
file = self.name_fasta_file(path, gene, org, 'Other',
feat_type_rank, extension, mode)
file.write(na_entry)
file.close()
def multi_fasta(self, na_entry, aa_entry, fmt):
"""Append an othologous sequence of a feature to a uniquely named file.
Usese a dictionary for formatting.
:param na_entry: A string representing the Nucleic Acid sequence data in FASTA format.
:param aa_entry: A string representing the Amino Acid sequence data in FASTA format.
:param fmt: A dictionary for formatting the FASTA entries and the file names.
:return: Does not return an object, but creates or appends to a multi entry FASTA file.
"""
mode = 'a'
# Create the desired variables from the formatter dictionary.
feat_type = fmt['feat_type']
feat_type_rank = fmt['feat_type_rank']
path = fmt['path']
gene = fmt['gene']
org = fmt['org']
if feat_type == "CDS":
# Create a MASTER .ffn file (multi-FASTA file for Coding Nucleic Acids)
extension = '.ffn'
file = self.name_fasta_file(path, gene, org, feat_type,
feat_type_rank, extension, mode)
file.write(na_entry)
file.close()
# Create a MASTER .faa file (multi-FASTA file for Amino Acids)
extension = '.faa'
file = self.name_fasta_file(path, gene, org, feat_type,
feat_type_rank, extension, mode)
file.write(aa_entry)
file.close()
elif feat_type == "misc_feature":
na_entry = ">gi|{na_gi}|ref|{na_acc_n}| {na_description} Feature: {na_misc_feat}\n{na_seq}\n".format(
**fmt)
# Creates .fna files (generic FASTA file for Nucleic Acids)
extension = '.fna'
file = self.name_fasta_file(path, gene, org, feat_type,
feat_type_rank, extension, mode)
file.write(na_entry)
file.close()