<commit_before># cython: profile=True
#cimport csamtools
from pysam.csamtools cimport *

import collections, array, struct
import CGAT.Experiment as E

import os
import sys
import string
import re
import optparse
import math
import time
import tempfile
import subprocess
import types
import bisect
import array
import collections
import itertools
import CGAT.GTF as GTF
import CGAT.Bed as Bed
import CGAT.IOTools as IOTools
import CGAT.Experiment as E
import CGAT.IndexedFasta as IndexedFasta
import CGAT.Stats as Stats
import CGAT.SequenceProperties as SequenceProperties
import CGAT.Genomics as Genomics
import CGAT.Intervals as Intervals

import bx
import bx.bbi.bigwig_file
import bx.intervals.io
import bx.intervals.intersection
import alignlib
import numpy
import CGAT.IndexedGenome as IndexedGenome
import pysam


class Counter:
    """
    This class does not remove small exons/introns,
    so beware ENSEMBL that stores frameshifts as mini-exons.
    """

    header = [ "contig", "strand" ]

    mMinIntronSize = 10

    def __init__(self, fasta = None, section = None, 
                 options = None, prefix = None):

        self.fasta = fasta
        self.section = section
        self.options = options
        <commit_msg>gtf2table.py - changed alignlib to alignlib-lite<commit_after># cython: profile=True
#cimport csamtools
from pysam.csamtools cimport *

import collections, array, struct
import CGAT.Experiment as E

import os
import sys
import string
import re
import optparse
import math
import time
import tempfile
import subprocess
import types
import bisect
import array
import collections
import itertools
import CGAT.GTF as GTF
import CGAT.Bed as Bed
import CGAT.IOTools as IOTools
import CGAT.Experiment as E
import CGAT.IndexedFasta as IndexedFasta
import CGAT.Stats as Stats
import CGAT.SequenceProperties as SequenceProperties
import CGAT.Genomics as Genomics
import CGAT.Intervals as Intervals
import CGAT.IndexedGenome as IndexedGenome

import numpy
import pysam

class Counter:
    """
    This class does not remove small exons/introns,
    so beware ENSEMBL that stores frameshifts as mini-exons.
    """

    header = [ "contig", "strand" ]

    mMinIntronSize = 10

    def __init__(self, fasta = None, section = None, 
                 options = None, prefix = None):

        self.fasta = fasta
        self.section = section
        self.options = options
        
{'fraction_non_alphanumeric': 0.052740863787375414, 'fraction_numerical': 0.0020764119601328905, 'mean_word_length': 3.686770428015564, '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': '1840370', 'n_tokens_mistral': 772, 'n_tokens_neox': 715, 'n_words': 266}