move low quality genomes from input directory to output directory (fo…

python_scripts/filter_genomes.py

@@ -0,0 +1,110 @@
+#!/bin/python
+
+# ----------------------------------------------------------------------------
+# Copyright (c) 2016--, Evguenia Kopylova.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+# ----------------------------------------------------------------------------
+
+# Move low quality genomes from input folder to output folder.
+
+import click
+from os.path import join, basename, exists
+from os import listdir, makedirs
+import shutil
+import logging
+
+
+def get_logger(log_fp):
+    """ Get logging instance.
+    """
+    logger = logging.getLogger('log')
+    log_handler = logging.FileHandler(log_fp)
+    formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s')
+    log_handler.setFormatter(formatter)
+    logger.addHandler(log_handler)
+    logger.setLevel(logging.DEBUG)
+
+    return logger
+
+
+def get_genomes_ids(repophlan_scores_fp):
+    """Return genome IDs to keep.
+    """
+    genomes = set()
+    # Get quality filtered genome ID and filepath to .fna.bz2
+    with open(repophlan_scores_fp) as repophlan_scores_f:
+        # header
+        line = repophlan_scores_f.readline()
+        line = line.strip().split('\t')
+        fna_idx = line.index('faa_lname')
+        for line in repophlan_scores_f:
+            line = line.strip().split('\t')
+            filename = basename(line[fna_idx])
+            if filename not in genomes:
+                genomes.add(filename)
+            else:
+                raise ValueError('Duplicate file name: %s' % filename)
+    return genomes
+
+
+def filter_genomes(all_genomes_bz2_dp,
+                   genomes,
+                   low_quality_genomes_dp,
+                   logger):
+    """Move low quality genomes into another directory.
+    """
+    files_moved = 0
+    files_kept = 0
+    for filename in listdir(all_genomes_bz2_dp):
+        if filename.endswith('.faa.bz2'):
+            if filename not in genomes:
+                src = join(all_genomes_bz2_dp, filename)
+                dst = join(low_quality_genomes_dp, filename)
+                logger.info('Moving %s' % filename)
+                shutil.move(src, dst)
+                files_moved += 1
+            else:
+                files_kept += 1
+        else:
+            continue
+    logger.info('Total files moved to %s: %s' % (
+        low_quality_genomes_dp, files_moved))
+    logger.info('Total files kept in %s: %s' % (
+        all_genomes_bz2_dp, files_kept))
+
+
+@click.command()
+@click.option('--all-genomes-bz2-dp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=True,
+                              file_okay=True),
+              help='Directory path to all 54K genomes (.faa)')
+@click.option('--repophlan-scores-fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=False,
+                              file_okay=True),
+              help='Filepath to RepoPhlAn screened results')
+@click.option('--low-quality-genomes-dp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=False,
+                              file_okay=True),
+              help='Output directory path to low quality genomes')
+@click.option('--log-fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=False,
+                              file_okay=True),
+              help='Filepath to log file')
+def main(all_genomes_bz2_dp,
+         repophlan_scores_fp,
+         low_quality_genomes_dp,
+         log_fp):
+    logger = get_logger(log_fp)
+    genomes = get_genomes_ids(repophlan_scores_fp)
+    if not exists(low_quality_genomes_dp):
+        makedirs(low_quality_genomes_dp)
+    filter_genomes(all_genomes_bz2_dp,
+                   genomes,
+                   low_quality_genomes_dp,
+                   logger)
+
+if __name__ == '__main__':
+    main()