Remove xcor file.

cross_correlation/xcor.py

-#!/usr/bin/env python3
-
-'''Compute cross-correlation analysis.'''
-
-import os
-import argparse
-import shutil
-import logging
-from multiprocessing import cpu_count
-import sys
-sys.path.append(os.path.abspath('../python_utils'))
-import utils
-
-EPILOG = '''
-For more details:
-        %(prog)s --help
-'''
-
-# SETTINGS
-
-logger = logging.getLogger(__name__)
-logger.addHandler(logging.NullHandler())
-logger.propagate = False
-logger.setLevel(logging.INFO)
-
-
-def get_args():
-    '''Define arguments.'''
-
-    parser = argparse.ArgumentParser(
-        description=__doc__, epilog=EPILOG,
-        formatter_class=argparse.RawDescriptionHelpFormatter)
-
-    parser.add_argument('-t', '--tag',
-                        help="The tagAlign file to qc on.",
-                        required=True)
-
-    parser.add_argument('-p', '--paired',
-                        help="True/False if paired-end or single end.",
-                        default=False,
-                        action='store_true')
-
-    args = parser.parse_args()
-    return args
-
-# Functions
-
-
-def check_tools():
-    '''Checks for required componenets on user system'''
-
-    logger.info('Checking for required libraries and components on this system')
-
-    r_path = shutil.which("R")
-    if r_path:
-        logger.info('Found R: %s', r_path)
-    else:
-        logger.error('Missing R')
-        raise Exception('Missing R')
-
-
-def xcor(tag, paired):
-    '''Use spp to calculate cross-correlation stats.'''
-
-    tag_basename = os.path.basename(utils.strip_extensions(tag, ['.gz']))
-
-    uncompressed_tag_filename = tag_basename
-    out, err = utils.run_pipe([
-        'gzip -dc %s > ' % (tag)], outfile=uncompressed_tag_filename)
-
-    # Subsample tagAlign file
-    numReads = 15000000
-
-    subsampled_tag_filename = \
-        tag_basename + ".%d.tagAlign.gz" % (numReads/1000000)
-    steps = [
-        'grep -v "chrM" %s' % (uncompressed_tag_filename),
-        'shuf -n %d --random-source=%s' % (numReads, uncompressed_tag_filename)
-    ]
-    if paired:
-        steps.extend([r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'"""])
-
-    steps.extend(['gzip -nc'])
-
-    out, err = utils.run_pipe(steps, outfile=subsampled_tag_filename)
-
-    # Calculate Cross-correlation QC scores
-    cc_scores_filename = subsampled_tag_filename + ".cc.qc"
-    cc_plot_filename = subsampled_tag_filename + ".cc.plot.pdf"
-
-    # CC_SCORE FILE format
-    # Filename <tab>
-    # numReads <tab>
-    # estFragLen <tab>
-    # corr_estFragLen <tab>
-    # PhantomPeak <tab>
-    # corr_phantomPeak <tab>
-    # argmin_corr <tab>
-    # min_corr <tab>
-    # phantomPeakCoef <tab>
-    # relPhantomPeakCoef <tab>
-    # QualityTag
-
-    run_spp_command = shutil.which("run_spp.R")
-    out, err = utils.run_pipe([
-        "Rscript %s -c=%s -p=%d -filtchr=chrM -savp=%s -out=%s" %
-        (run_spp_command, subsampled_tag_filename, cpu_count(),
-         cc_plot_filename, cc_scores_filename)
-    ])
-
-    return cc_scores_filename
-
-
-def main():
-    args = get_args()
-    paired = args.paired
-    tag = args.tag
-
-    # Create a file handler
-    handler = logging.FileHandler('xcor.log')
-    logger.addHandler(handler)
-
-    # Check if tools are present
-    check_tools()
-
-    # Calculate Cross-correlation
-    xcor_filename = xcor(tag, paired)
-
-
-if __name__ == '__main__':
-    main()