Mercurial > repos > bgruening > split_file_to_collection
diff split_file_to_collection.py @ 7:0046692724f9 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 6f78214d2c9d7786bfc9d8cbddac7d2613cd314e"
| author | bgruening |
|---|---|
| date | Fri, 10 Jul 2020 13:41:00 -0400 |
| parents | d57735dd27b0 |
| children | 6cbe2f30c2d7 |
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--- a/split_file_to_collection.py Tue Jun 30 15:10:54 2020 -0400 +++ b/split_file_to_collection.py Fri Jul 10 13:41:00 2020 -0400 @@ -92,6 +92,12 @@ return parser +def close_files(file_list): + # finally, close all files + for open_file in file_list: + open_file.close() + + def replace_mapped_chars(pattern): """ handles special escaped characters when coming from galaxy @@ -160,7 +166,7 @@ new_file_base = [custom_new_file_name, custom_new_file_ext] newfiles = [ - "%s_%06d%s" % (new_file_base[0], count, new_file_base[1]) + open(os.path.join(out_dir, "%s_%06d%s" % (new_file_base[0], count, new_file_base[1])) , "w") for count in range(0, numnew) ] # bunch o' counters @@ -195,15 +201,13 @@ else: # if is in fresh_files, write header and drop from freshFiles if new_file_counter in fresh_files: - with open(newfiles[new_file_counter], "a+") as handle: - handle.write(header) + newfiles[new_file_counter].write(header) fresh_files.remove(new_file_counter) if sep_at_end: record += line # write record to file - with open(newfiles[new_file_counter], "a+") as handle: - handle.write(record) + newfiles[new_file_counter].write(record) if not sep_at_end: record = line else: @@ -227,8 +231,10 @@ else: record += line # after loop, write final record to file - with open(newfiles[new_file_counter], "a+") as handle: - handle.write(record) + newfiles[new_file_counter].write(record) + + # close new files + close_files(newfiles) def split_by_column(args, in_file, out_dir, top): @@ -270,17 +276,17 @@ # write if out_file_name not in new_files.keys(): # open file (new, so not already open) - with open(out_file_path, "a+") as handle: - #current_new_file = open(out_file_path, "w") - handle.write(header) - handle.write(line) + current_new_file = open(out_file_path, "w") + current_new_file.write(header) + current_new_file.write(line) # add to dict - new_files[out_file_name] = out_file_path + new_files[out_file_name] = current_new_file else: # file is already open, so just write to it - #new_files[out_file_name].write(line) - with open(new_files[out_file_name], "a") as handle: - handle.write(line) + new_files[out_file_name].write(line) + + # finally, close all files + close_files(new_files.values()) if __name__ == "__main__":