parse repophlan demo #1

genomesubsampler/parseRepophlan.py

@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+
+# ----------------------------------------------------------------------------
+# Copyright (c) 2017--, genome-subsampler development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file COPYING.txt, distributed with this software.
+# ----------------------------------------------------------------------------
+
+#
+# parser for RepoPhlAn-downloaded genomes
+#
+
+import click
+import pandas as pd
+
+
+def parse_repophlan(repophlan_wscores_fp):
+    """ Extract number of HGTs found.
+
+    Parameters
+    ----------
+    repophlan_wscores_fp: string
+        file path to RepoPhlAn summary table with scores
+
+    Returns
+    -------
+    list of string
+        Human-readable report of basic statistics of genomes
+    """
+    df = pd.read_table(repophlan_wscores_fp, index_col=0, header=0)
+    out = []
+    out.append('Total number of genomes: %s.' % df.shape[0])
+    out.append('Number of RefSeq genomes: %s.'
+               % df['assembly_accession'].str.contains('GCF_').sum())
+    out.append('With genome sequences (fna): %s.' % df['fna_lname'].count())
+    out.append('With protein sequences (faa): %s.' % df['faa_lname'].count())
+    out.append('With protein-coding DNA sequences (ffn): %s.'
+               % df['ffn_lname'].count())
+    out.append('With RNA-coding DNA sequences (frn): %s.'
+               % df['frn_lname'].count())
+    return out
+
+
+@click.command()
+@click.option('--repophlan-wscores-fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=True,
+                              file_okay=True),
+              help='RepoPhlAn summary table with scores')
+def _main(repophlan_wscores_fp):
+    """ Parser for RepoPhlAn-downloaded genomes
+    """
+    out = parse_repophlan(repophlan_wscores_fp)
+    click.echo('\n'.join(out))
+    click.echo('Task completed.')
+
+
+if __name__ == "__main__":
+    _main()