Mercurial > repos > jpayne > table_ops
view table-union.py @ 6:6ffd502b3cf1
planemo upload
author | jpayne |
---|---|
date | Tue, 30 Jan 2018 12:40:45 -0500 |
parents | 8c5fb0c5e560 |
children | 4eaafbdfb8bf |
line wrap: on
line source
#!/usr/bin/env python3 import csv import sys def main(files): header = [] items = [] possible_identity_headers = None for fi in files: with open(fi, 'rU') as table: reader = csv.DictReader(table, delimiter='\t', dialect='excel-tab') rows = list(reader) for field in reader.fieldnames: if field not in set(header): header.append(field) #try to find identity columns in the files, to use to join if possible_identity_headers is None: possible_identity_headers = set(reader.fieldnames) #winnow down the shared columns in each file by whether they're present in all, and all their values are unique in each file and not null #because these are the most likely to be shared keys possible_identity_headers = possible_identity_headers.intersection(filter(lambda f: len(set([r[f] for r in rows])) == len(rows) and all([r[f] is not None for r in rows]), reader.fieldnames)) items.extend(rows) # if len(possible_identity_headers) > 1: # #if there's more than one, we need to check that joining on any one of them produces the same results # #finally # possible_identity_headers = set((possible_identity_headers.pop(), )) #if we found an identity column, then try to join rows if possible_identity_headers: key_column = possible_identity_headers.pop() keys = set([r[key_column] for r in items]) merged_rows = [] for key in sorted(keys): new_row = {} for row in filter(lambda r: r[key_column] == key, items): new_row.update(row) merged_rows.append(new_row) items = merged_rows wr = csv.DictWriter(sys.stdout, delimiter='\t', dialect='excel-tab', fieldnames=header) wr.writeheader() wr.writerows(items) if __name__ == '__main__': main(sys.argv[1:])