3Seq: no such file or directory

[ArtPoon]

This exception is currently being thrown on master branch (commit 3a59bc1ae09c7fed4af4dd077c02d5abe9e097ad):

art@Wernstrom OpenRDP % python3 -i -m openrdp tests/test_neisseria.fasta test.csv -cfg tests/test_cfg.ini -all
Starting 3Seq Analysis
[Errno 2] No such file or directory: '/Users/art/git/OpenRDP/test_neisseria.fasta.3s.rec'
Finished 3Seq Analysis

[ArtPoon]

OpenRDP/openrdp/threeseq.py

Lines 60 to 63 in 1863aca

	# Parse the output of 3Seq
	tseq_out = self.in_name + '.3s.rec'
	out_path = os.path.join(os.getcwd(), tseq_out)
	ts_results = self.parse_output(out_path)

[ArtPoon]

Well, it looks like the options being passed to 3Seq were wrong. -f is used to specify the starting (from) coordinate of sequences to analyze. We should be using -full to specify the entire input alignment for analysis.

[ArtPoon]

Ok I take that back. After reading the 3Seq documentation, it seems like -f is an overloaded option (I didn't think that was possible!) to specify both a full run and starting coordinate. There were other issues though - primarily that the file extension of the output file was missing (.csv) and the parser function was looking for tab delimited, not comma.
Was this a Windows thing?

[ArtPoon]

Fixed in dev branch.

[ArtPoon]

Gah. Did some more testing on my Linux machine:

• 3Seq produces <prefix>.3s.rec, not <prefix>.3s.rec.csv like macOS binary
• the output is tab-delimited not comma-delimited like macOS binary
  What the heck!?!?

[ArtPoon]

Ok updated code so it works for both macOS and Linux 3Seq binaries.