rename sample ids

python_scripts/add_metadata_columns.py

@@ -0,0 +1,119 @@
+#!/usr/bin/env 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.
+#-----------------------------------------------------------------------------
+
+"""
+Add metadata columns from super metadata file to reduced metadata file.
+"""
+
+import click
+from collections import OrderedDict
+
+
+def add_columns(qiime_mapping_file_fp,
+                cgc_mapping_file_fp,
+                metadata_column,
+                output_fp):
+    """Copy metadata columns from CGC metadata file to QIIME metadata file.
+
+    Parameters
+    ----------
+    qiime_mapping_file_fp: str
+        Filepath to QIIME mapping file
+    cgc_mapping_file_fp: str
+        Filepath to CGC mapping file
+    metadata_column: tuple
+        Metadata columns to copy from CGC to QIIME mapping file
+    output_fp: str
+        Filepath to updated QIIME mapping file
+    """
+    qiime_mapping_file = {}
+    qiime_mapping_header = ""
+    with open(qiime_mapping_file_fp) as qiime_f:
+        for line in qiime_f:
+            line = line.strip().split('\t')
+            if line[0] == '#SampleID':
+                qiime_mapping_header = line
+                continue
+            # use filename as key
+            key = line[3]
+            qiime_mapping_file[key] = line
+
+    cgc_mapping_header = []
+    cgc_metadata_columns = OrderedDict()
+    # initialize list indexes to 0
+    for name in metadata_column:
+        cgc_metadata_columns[str(name)] = 0
+    files_searched = set()
+    with open(cgc_mapping_file_fp) as cgc_f:
+        for line in cgc_f:
+            line = line.strip().split('\t')
+            if line[0] == "case_name":
+                cgc_mapping_header = line
+                # set correct index values for metadata columns in CGC header
+                for key in cgc_metadata_columns:
+                    cgc_metadata_columns[key] = cgc_mapping_header.index(key)+1
+                continue
+            # use filename as key
+            key_file = line[22]
+            if key_file in files_searched:
+                continue
+            if key_file in qiime_mapping_file:
+                for key_column, value in cgc_metadata_columns.iteritems():
+                    qiime_mapping_file[key_file].append(line[value])
+                files_searched.add(key_file)
+
+    # output updated QIIME mapping file
+    num_columns_qiime = len(qiime_mapping_header)
+    num_columns_cgc = len(cgc_metadata_columns)
+    with open(output_fp, 'w') as output_f:
+        output_f.write('\t'.join(map(str,qiime_mapping_header[:-1])))
+        for key in cgc_metadata_columns:
+            output_f.write('\t%s' % key)
+        output_f.write('\t%s' % qiime_mapping_header[-1])
+        output_f.write('\n')
+        for key in qiime_mapping_file:
+            # Output QIIME mapping file up to Description column
+            output_f.write('\t'.join(map(str,qiime_mapping_file[key][:num_columns_qiime-1])))
+            output_f.write('\t')
+            # Output added keys from CGC mapping file
+            output_f.write('\t'.join(map(str,qiime_mapping_file[key][num_columns_qiime:])))
+            # Output Description column
+            output_f.write('\t%s' % qiime_mapping_file[key][num_columns_qiime-1])
+            output_f.write('\n')
+
+
+@click.command()
+@click.option('--qiime-mapping-file-fp', required=False,
+              type=click.Path(resolve_path=True, readable=True, exists=True,
+                              file_okay=True),
+              help='Filepath to QIIME metadata file')
+@click.option('--cgc-mapping-file-fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=True,
+                              file_okay=True),
+              help='Filepath to CGC metadata file')
+@click.option('--metadata-column', type=str, required=True, multiple=True,
+              help="Metadata column to add from CGC to QIIME mapping file")
+@click.option('--output-fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=False,
+                              file_okay=True),
+              help='Filepath to updated QIIME mapping file')
+def main(qiime_mapping_file_fp,
+         cgc_mapping_file_fp,
+         metadata_column,
+         output_fp):
+    # rename sample ids in mapping file
+    add_columns(qiime_mapping_file_fp,
+                cgc_mapping_file_fp,
+                metadata_column,
+                output_fp)
+
+
+if __name__ == "__main__":
+    main()

python_scripts/rename_sample_ids.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env 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.
+#-----------------------------------------------------------------------------
+
+"""
+Rename sample IDs in mapping file and BIOM table for combined analysis of
+multiple disease types in CGC TCGA analysis.
+"""
+
+import click
+from os.path import splitext, join
+from biom.table import Table
+from biom.util import biom_open
+from biom import load_table
+
+
+def rename_sample_ids(mapping_file_fp,
+                      biom_fp,
+                      count_start):
+    """Rename sample IDs to join mapping files
+
+    Parameters
+    ----------
+    mapping_file_fp: tuple
+        Filepath to mapping file
+    biom_fp: str
+        Filepath to BIOM table
+    count_start: int
+        First new sample ID name (ascending in order)
+    """
+    output_mapping_file_fp = "%s_modified.txt" % splitext(mapping_file_fp)[0]
+    id_map = {}
+    modified_id = count_start
+    with open(output_mapping_file_fp, 'w') as output_f:
+        with open(mapping_file_fp, 'r') as mapping_f:
+            for line in mapping_f:
+                if line.startswith('#SampleID'):
+                    output_f.write(line)
+                    continue
+                line = line.strip().split('\t')
+                curr_sample_id = line[0]
+                new_sample_id = "s%s" % modified_id
+                id_map[curr_sample_id] = new_sample_id
+                line[0] = new_sample_id
+                output_f.write('\t'.join(map(str,line)))
+                output_f.write('\n')
+                modified_id += 1
+
+    # update IDs in BIOM table to match modified mapping file
+    output_biom_fp = "%s_modified.biom" % splitext(biom_fp)[0]
+    table = load_table(biom_fp)
+    table.update_ids(id_map, axis='sample')
+    with biom_open(output_biom_fp, 'w') as f:
+            table.to_hdf5(h5grp=f, generated_by="tcga-rename-sample-ids")
+
+
+@click.command()
+@click.option('--mapping-file-fp', required=False,
+              type=click.Path(resolve_path=True, readable=True, exists=True,
+                              file_okay=True),
+              help='Filepath to mapping file')
+@click.option('--biom-fp', required=True,
+              type=click.Path(resolve_path=True, readable=True, exists=True,
+                              file_okay=True),
+              help='Filepath to BIOM table')
+@click.option('--count-start', required=True, type=int,
+              help='First new sample ID name (ascending in order)')
+def main(mapping_file_fp,
+         biom_fp,
+         count_start):
+    # rename sample ids in mapping file
+    rename_sample_ids(mapping_file_fp,
+                      biom_fp,
+                      count_start)
+
+
+if __name__ == "__main__":
+    main()