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Refactoring/build #16

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merged 4 commits into from
May 10, 2024
Merged

Refactoring/build #16

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c5f4732
updated blast build class
mattheww95 May 10, 2024
a6b7b3c
Created metadata info class
mattheww95 May 10, 2024
79fc152
updated extract messages
mattheww95 May 10, 2024
99d16f2
Updated string constants
mattheww95 May 10, 2024
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137 changes: 61 additions & 76 deletions locidex/build.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,79 +2,78 @@
from datetime import datetime
import pandas as pd
import os, sys
from pathlib import Path
from argparse import (ArgumentParser, ArgumentDefaultsHelpFormatter, RawDescriptionHelpFormatter)
from locidex.version import __version__
from locidex.constants import DBFiles
from locidex.classes import run_command
from locidex.constants import DBConfig
from locidex.constants import DBConfig, MetadataFields
from locidex.classes.blast import BlastMakeDB
from locidex.manifest import DBData
import getpass

import logging
import sys

logger = logging.getLogger(__name__)
logging.basicConfig(filemode=sys.stderr, level=logging.INFO)

class locidex_build:
input_file = None
outdir = None
blast_dir = None
is_dna = False
is_protein = False
df = None
config = {}
meta = {}
num_seqs = 0
status = True
messages = []


def __init__(self, input_file: os.PathLike, outdir: os.PathLike, config: DBConfig, seq_columns={'nucleotide':'dna_seq','protein':'aa_seq'},force=False,parse_seqids=False):


def __init__(self, input_file: os.PathLike, outdir: os.PathLike, config: DBConfig,
seq_columns={DBData.nucleotide_name():'dna_seq',DBData.protein_name():'aa_seq'},force=False,parse_seqids=False,translation_table: int = 11):
self.input_file = input_file
self.translation_table = translation_table
self.outdir = outdir
self.force = force
self.status = self.init_dir(self.outdir)
self.parse_seqids = parse_seqids
if not self.status:
return

self.status = self.blast_dir = os.path.join(outdir,'blast')
self.is_dna = False
self.is_protein = False
self.blast_dir = outdir.joinpath("blast")

self.init_dir(self.blast_dir)
if not self.status:
return

self.df = self.read_data( self.input_file)
self.df = self.read_data(self.input_file)
self.config = config
self.config.db_num_seqs = len(self.df)

for t in seq_columns:
col_name = seq_columns[t]
s = self.is_seqtype_present(col_name)
if s:
outfile = os.path.join(self.blast_dir, t)
if t == 'nucleotide':
outfile = self.blast_dir.joinpath(t)
if t == DBData.nucleotide_name():
self.is_dna = True
self.config.nucleotide_db_name = t
blast_method = 'nucl'
elif t == 'protein':

blast_method = DBData.nucleotide_db_type()
elif t == DBData.protein_name():
self.is_protein = True
self.config.protein_db_name = t
blast_method = 'prot'
self.create_seq_db(t, col_name, outfile, blast_method)
blast_method = DBData.protein_db_type()
self.init_dir(outfile)
out_fasta = outfile.joinpath("{}.fasta".format(t))
self.write_seq_file(out_fasta, col_name)
creating_db = BlastMakeDB(input_file=out_fasta,
db_type=blast_method,
parse_seqids=self.parse_seqids,
output_db_path=out_fasta)
creating_db.makeblastdb()
self.config.is_nucl = self.is_dna
self.config.is_prot = self.is_protein
self.get_metadata(self.df,columns_to_exclude=list(seq_columns.values()))

def create_seq_db(self,stype,col_name,outfile,blast_method='nucl'):
self.init_dir(outfile)
f = os.path.join(outfile,"{}.fasta".format(stype))
self.write_seq_file(f,col_name)
(stdout,stderr) = self.makeblastdb(fasta_file=f,outfile=os.path.join(outfile,stype),blast_method=blast_method)
self.messages.append(stderr)

def init_dir(self,d):
if os.path.isdir(d) and not self.force:
self.messages.append(f'Error {d} exists, if you would like to overwrite, then specify --force')
return False

if not os.path.isdir(d):
os.makedirs(d, 0o755)

def init_dir(self, d: Path):
logger.info("Checking if directory {} exists.".format(d))
try:
d.mkdir(parents=True, exist_ok=self.force, mode=0o755)
except FileExistsError:
logger.critical("Database file {} already exists. To overwrite please run with --force".format(d))
sys.exit(17)
return True


def read_data(self,f):
if os.path.isfile(f) and os.path.getsize(f) > 0:
Expand All @@ -99,21 +98,6 @@ def write_seq_file(self,f,col_name):
oh.write(f">{id}\n{data[id]}\n")
oh.close()

def makeblastdb(self,fasta_file,outfile,blast_method):
dbtype = 'nucl'
if blast_method == 'prot':
dbtype = 'prot'
command = ['makeblastdb',
'-in', fasta_file,
'-dbtype', dbtype]
if self.parse_seqids:
command.append('-parse_seqids')
if outfile != None:
command+= ['-out',outfile]
command = " ".join([str(x) for x in command])

return run_command(command)

def get_metadata(self,df,columns_to_exclude=['dna_seq','aa_seq']):
columns_to_exclude = set(columns_to_exclude)
columns_to_include = []
Expand All @@ -122,33 +106,34 @@ def get_metadata(self,df,columns_to_exclude=['dna_seq','aa_seq']):
columns_to_include.append(col)
subset = df[columns_to_include]
self.meta = {
"info": {
"num_seqs": len(df),
"is_cds": "True",
"trans_table": 11,
"dna_min_len": min(df['dna_min_len'].tolist()),
"dna_max_len": max(df['dna_min_len'].tolist()),
"dna_min_ident": min(df['dna_min_ident'].tolist()),
"aa_min_len": min(df['aa_min_len'].tolist()),
"aa_max_len": max(df['aa_min_len'].tolist()),
"aa_min_ident": min(df['aa_min_ident'].tolist()),
},
"info": MetadataFields(
num_seqs=len(df),
is_cds=True,
trans_table=self.translation_table,
dna_min_len=min(df['dna_min_len'].tolist()),
dna_max_len=max(df['dna_min_len'].tolist()),
dna_min_ident=min(df['dna_min_ident'].tolist()),
aa_min_len=min(df['aa_min_len'].tolist()),
aa_max_len= max(df['aa_min_len'].tolist()),
aa_min_ident= min(df['aa_min_ident'].tolist())).to_dict(),
"meta": subset.to_dict(orient='index')
}

def add_args(parser=None):

translation_table_def = 11
default_version = "1.0.0"
if parser is None:
parser = ArgumentParser(
description="Locidex: Build a locidex database",)
parser.add_argument('-i','--input_file', type=str, required=True,help='Input tsv formated for locidex')
parser.add_argument('-o', '--outdir', type=str, required=True, help='Output directory to put results')
parser.add_argument('-n', '--name', type=str, required=False, help='DB name',default='Locidex Database')
parser.add_argument('-a', '--author', type=str, required=False, help='Author Name for Locidex Database',default='')
parser.add_argument('-c', '--db_ver', type=str, required=False, help='Version code for locidex db',
default='1.0.0')
parser.add_argument('-n', '--name', type=str, required=True, help='Database name',default='Locidex Database')
parser.add_argument('-a', '--author', type=str, required=False, help='Author Name for Locidex Database. Default: {}'.format(getpass.getuser()),default=getpass.getuser())
parser.add_argument('-c', '--db_ver', type=str, required=False, help='Version code for locidex db: {}'.format(default_version),
default=default_version)
parser.add_argument('-e', '--db_desc',type=str, required=False, help='Version code for locidex db',
default='')
parser.add_argument("-t", "--translation_table", type=int, required=False, help="Translation table to use: {}".format(translation_table_def), default=translation_table_def)
parser.add_argument('-V', '--version', action='version', version="%(prog)s " + __version__)
parser.add_argument('-f', '--force', required=False, help='Overwrite existing directory',
action='store_true')
Expand All @@ -161,7 +146,7 @@ def run(cmd_args=None):
if cmd_args is None:
parser = add_args()
cmd_args = parser.parse_args()
#cmd_args = parse_args()

input_file = cmd_args.input_file
outdir = cmd_args.outdir
force = cmd_args.force
Expand All @@ -181,7 +166,7 @@ def run(cmd_args=None):
print(f'Error {input_file} does not exist, please check path and try again')
sys.exit()

obj = locidex_build(input_file, outdir,config=config,seq_columns={'nucleotide':'dna_seq','protein':'aa_seq'},force=force)
obj = locidex_build(Path(input_file), Path(outdir),config=config,seq_columns={'nucleotide':'dna_seq','protein':'aa_seq'},force=force)

if obj.status == False:
print(f'Error something went wrong building the db, check error messages {obj.messages}')
Expand Down
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