<commit_before>"""
count number of reads mapping to features of transcripts

"""
import os
import sys
import itertools

# soft imports
try:
    import pandas as pd
    import gffutils
except ImportError:
    pd, gffutils = None, None, None

from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction
from bcbio.log import logger
from bcbio import bam
import bcbio.pipeline.datadict as dd

def combine_count_files(files, out_file=None, ext=".fpkm"):
    """
    combine a set of count files into a single combined file
    """
    assert all([file_exists(x) for x in files]), \<commit_msg>Remove soft imports of pandas and gffutils.<commit_after>"""
count number of reads mapping to features of transcripts

"""
import os
import sys
import itertools
import pandas as pd
import gffutils

from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction
from bcbio.log import logger
from bcbio import bam
import bcbio.pipeline.datadict as dd

def combine_count_files(files, out_file=None, ext=".fpkm"):
    """
    combine a set of count files into a single combined file
    """
    assert all([file_exists(x) for x in files]), \
{'fraction_non_alphanumeric': 0.07208717518860017, 'fraction_numerical': 0.0, 'mean_word_length': 4.4520547945205475, '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': '472724', 'n_tokens_mistral': 360, 'n_tokens_neox': 353, 'n_words': 142}