Major changes #34
Major changes #34
Conversation
decontamlib/main.py
Outdated
| args.reverse_reads.close() | ||
|
|
||
| if args.reverse_reads is None: | ||
| rev_fp = str(None) |
There was a problem hiding this comment.
Recommend not converting to string here. In Python, it is most often best to use None itself to represent a null value. Later on in the decontaminate() method, you can do this:
if rev_fp is not None:
instead of:
if rev_fp != str(None):
| @@ -1,3 +1,3 @@ | |||
| #!/usr/bin/python | |||
| #!/usr/bin/env python | |||
There was a problem hiding this comment.
We should be able to remove the scripts directory, and instead have setup.py make the scripts for us. If we make this switch, Python will wire up the correct interpreter for the scripts it creates.
For an example, see the console_scripts argument here:
https://github.com/kylebittinger/unassigner/blob/master/setup.py
| # This program always returns non-zero exit status | ||
| self.args.extend(["--method", "bwa"]) | ||
| self.args.extend(["--bwa_fp", "false"]) | ||
| config_file = tempfile.NamedTemporaryFile(suffix=".json") |
There was a problem hiding this comment.
Config files are probably more trouble than they're worth. Let's not remove the config files now, but just regard this as a sign that things will be much easier once we do.
2 participants
There are four major parts in this pull request.
(1) Update the unit test codes for testing config_file as an option
(2) Add the benchmark work from Celeste
(3) Use python from the environment.
(4) Add single-end reads as an option: used for stitched paired-ends reads