<commit_before># -*- coding: utf-8 -*-
import os.path
import logging

import click
from sqlalchemy.exc import IntegrityError

from chanjo.store.api import ChanjoDB
from .utils import validate_stdin
from .link import link_elements
from .sambamba import load_transcripts

log = logging.getLogger(__name__)


@click.command()
@click.option('-s', '--sample', help='override sample id from file')
@click.option('-g', '--group', help='id to group related samples')
@click.option('-n', '--name', help='display name for sample')
@click.option('-gn', '--group-name', help='display name for sample group')
@click.option('-r', '--threshold', type=int,
              help='completeness level to disqualify exons')
@click.argument('bed_stream', callback=validate_stdin,
                type=click.File(encoding='utf-8'), default='-', required=False)<commit_msg>set threshold default for loading transcripts<commit_after># -*- coding: utf-8 -*-
import os.path
import logging

import click
from sqlalchemy.exc import IntegrityError

from chanjo.store.api import ChanjoDB
from .utils import validate_stdin
from .link import link_elements
from .sambamba import load_transcripts

log = logging.getLogger(__name__)


@click.command()
@click.option('-s', '--sample', help='override sample id from file')
@click.option('-g', '--group', help='id to group related samples')
@click.option('-n', '--name', help='display name for sample')
@click.option('-gn', '--group-name', help='display name for sample group')
@click.option('-r', '--threshold', default=10,
              help='completeness level to disqualify exons')
@click.argument('bed_stream', callback=validate_stdin,
                type=click.File(encoding='utf-8'), default='-', required=False)
{'fraction_non_alphanumeric': 0.15491329479768787, 'fraction_numerical': 0.003468208092485549, 'mean_word_length': 4.731788079470198, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7203873', 'n_tokens_mistral': 531, 'n_tokens_neox': 508, 'n_words': 148}