Mercurial > repos > bgruening > split_file_to_collection
diff split_file_to_collection.py @ 6:d57735dd27b0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit 387787f65d3c245cd3e7449d92c5b8b511bc60f0"
| author | bgruening |
|---|---|
| date | Tue, 30 Jun 2020 15:10:54 -0400 |
| parents | e77b954f0da5 |
| children | 0046692724f9 |
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--- a/split_file_to_collection.py Fri Oct 11 18:24:43 2019 -0400 +++ b/split_file_to_collection.py Tue Jun 30 15:10:54 2020 -0400 @@ -92,12 +92,6 @@ 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 @@ -166,7 +160,7 @@ new_file_base = [custom_new_file_name, custom_new_file_ext] newfiles = [ - open(os.path.join(out_dir, "%s_%06d%s" % (new_file_base[0], count, new_file_base[1])) , "w") + "%s_%06d%s" % (new_file_base[0], count, new_file_base[1]) for count in range(0, numnew) ] # bunch o' counters @@ -201,13 +195,15 @@ else: # if is in fresh_files, write header and drop from freshFiles if new_file_counter in fresh_files: - newfiles[new_file_counter].write(header) + with open(newfiles[new_file_counter], "a+") as handle: + handle.write(header) fresh_files.remove(new_file_counter) if sep_at_end: record += line # write record to file - newfiles[new_file_counter].write(record) + with open(newfiles[new_file_counter], "a+") as handle: + handle.write(record) if not sep_at_end: record = line else: @@ -231,10 +227,8 @@ else: record += line # after loop, write final record to file - newfiles[new_file_counter].write(record) - - # close new files - close_files(newfiles) + with open(newfiles[new_file_counter], "a+") as handle: + handle.write(record) def split_by_column(args, in_file, out_dir, top): @@ -276,17 +270,17 @@ # write if out_file_name not in new_files.keys(): # open file (new, so not already open) - current_new_file = open(out_file_path, "w") - current_new_file.write(header) - current_new_file.write(line) + with open(out_file_path, "a+") as handle: + #current_new_file = open(out_file_path, "w") + handle.write(header) + handle.write(line) # add to dict - new_files[out_file_name] = current_new_file + new_files[out_file_name] = out_file_path else: # file is already open, so just write to it - new_files[out_file_name].write(line) - - # finally, close all files - close_files(new_files.values()) + #new_files[out_file_name].write(line) + with open(new_files[out_file_name], "a") as handle: + handle.write(line) if __name__ == "__main__":