<commit_before>#!/usr/bin/env python
"""
align FASTQ, SAM, or BAM file (gzip and bzip2 supported)
with bowtie2, produces BAM files (sorted and indexed)
output will be in ./align2
In align2, there will be a folder for each reference genome
    e.g. align2/ref1 , align2/ref2, align2/ref1, align2/ref2
In reference folder, there will be a folder for uniquely mapped alignments
     and alignments including random sampling where necessary
    (folder names are unique, random, respectively)
    e.g. align2/ref1/random, align2/ref1/unique, etc.
"""
import pysam
import logging
import os
from os import getcwd, environ, curdir, makedirs, devnull
from os.path import join, exists, splitext
from textwrap import dedent
import sys
from tempfile import mkdtemp
from subprocess import Popen, PIPE, STDOUT
import scripter
from scripter import assert_path, path_to_executable, Usage, \
                     exit_on_Usage, InvalidFileException, get_logger, \
                     Environment, critical, debug
from seriesoftubes.tubes.polledpipe import PolledPipe
from seriesoftubes.tubes import wait_for_job
from seriesoftubes.fnparsers import BowtieFilenameParser
from seriesoftubes.converters.bamtofastq import UnpairedBAMToFastqConverter
from seriesoftubes.converters.bamtofastqpair import PairedBAMToFastqConverter
    
from pkg_resources import get_distribution
__version__ = get_distribution('seriesoftubes').version
VERSION = __version__

def main():
    e = Environment(version=VERSION, doc=__doc__)
    e.set_filename_parser(BowtieFilenameParser)
    # let bowtie2 do the multiprocessing
    e.override_num_cpus(1)<commit_msg>removed bad imports<commit_after>#!/usr/bin/env python
"""
align FASTQ, SAM, or BAM file (gzip and bzip2 supported)
with bowtie2, produces BAM files (sorted and indexed)
output will be in ./align2
In align2, there will be a folder for each reference genome
    e.g. align2/ref1 , align2/ref2, align2/ref1, align2/ref2
In reference folder, there will be a folder for uniquely mapped alignments
     and alignments including random sampling where necessary
    (folder names are unique, random, respectively)
    e.g. align2/ref1/random, align2/ref1/unique, etc.
"""
import pysam
import logging
import os
from os import getcwd, environ, curdir, makedirs, devnull
from os.path import join, exists, splitext
from textwrap import dedent
import sys
from tempfile import mkdtemp
from subprocess import Popen, PIPE, STDOUT
import scripter
from scripter import assert_path, path_to_executable, Usage, \
                     exit_on_Usage, InvalidFileException, get_logger, \
                     Environment, critical, debug
from seriesoftubes.tubes.polledpipe import PolledPipe
from seriesoftubes.tubes import wait_for_job
from seriesoftubes.fnparsers import BowtieFilenameParser
    
from pkg_resources import get_distribution
__version__ = get_distribution('seriesoftubes').version
VERSION = __version__

def main():
    e = Environment(version=VERSION, doc=__doc__)
    e.set_filename_parser(BowtieFilenameParser)
    # let bowtie2 do the multiprocessing
    e.override_num_cpus(1)
{'fraction_non_alphanumeric': 0.06129032258064516, 'fraction_numerical': 0.011612903225806452, 'mean_word_length': 4.6075949367088604, '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': '3901839', 'n_tokens_mistral': 959, 'n_tokens_neox': 909, 'n_words': 313}