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Commit dbe6a5d7 authored by Lannoy, Carlos de's avatar Lannoy, Carlos de
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small fixes, update env

parent 68456266
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......@@ -14,4 +14,6 @@ dependencies:
- hyperopt=0.2.5
- seaborn=0.11.1
- numpy=1.19.5
- pytables=3.6.1
\ No newline at end of file
- pytables=3.6.1
- kmer-jellyfish=2.3.0
- scikit-learn=0.24.2
import os
import os, sys
import pandas as pd
from os.path import basename
from shutil import copy
......@@ -6,6 +6,11 @@ from pathlib import Path
from distutils.dir_util import copy_tree
from sklearn.model_selection import StratifiedKFold
from jinja2 import Template
__location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
baseless_location = os.path.realpath(f'{__location__}/..')
sys.path.append(baseless_location)
from argparse_dicts import get_validate_parser
from helper_functions import parse_input_path, parse_output_path
from snakemake import snakemake
......@@ -17,8 +22,7 @@ args = parser.parse_args()
nn_target_list = [pth.name for pth in Path(args.primed_nn_dir).iterdir() if pth.is_dir()]
__location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
baseless_location = os.path.realpath(f'{__location__}/..')
with open(args.parameter_file, 'r') as pf: params = yaml.load(pf, Loader=yaml.FullLoader)
primed_nn_dir = args.primed_nn_dir
if primed_nn_dir[-1] != '/': primed_nn_dir += '/'
......@@ -44,7 +48,7 @@ fast5_basename_list = [basename(f) for f in fast5_list]
fast5_df = pd.DataFrame({'read_id': fast5_basename_list,
'fn': fast5_list,
'species': [gt_df.species_short.get(ff) for ff in fast5_basename_list]}
'species': [gt_df.species_short.get(ff, 'unknown') for ff in fast5_basename_list]}
).set_index('read_id')
fast5_df.drop(fast5_df.query('species == "unknown"').index, axis=0, inplace=True)
......
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