filter afa command line call is failing with TypeError #1
Description
When running the default notebook with the default values and test structures, the generate_msa() function is failing with a TypeError.
The output from the cell copied to the clipboard:
TypeError Traceback (most recent call last)
Cell In[9], line 5
2 os.chdir('/zfs/smblab/fduffy/source/repos/FRETNet-Designer/')
4 if settings['generate_MSA'] == True:
----> 5 msa.generate_msa(settings)
File /zfs/smblab/fduffy/source/repos/FRETNet-Designer/Script_Dependancies/GenerateMSA.py:49, in generate_msa(settings)
47 max_gaps = settings['max_align_gaps']
48 cmd = [command, script, output_file_name, max_gaps]
---> 49 sp.run(cmd)
File /zfs/smblab/fduffy/envs/fret_dev/lib/python3.9/subprocess.py:505, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
502 kwargs['stdout'] = PIPE
503 kwargs['stderr'] = PIPE
--> 505 with Popen(*popenargs, **kwargs) as process:
506 try:
507 stdout, stderr = process.communicate(input, timeout=timeout)
File /zfs/smblab/fduffy/envs/fret_dev/lib/python3.9/subprocess.py:951, in Popen.init(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask)
947 if self.text_mode:
948 self.stderr = io.TextIOWrapper(self.stderr,
949 encoding=encoding, errors=errors)
--> 951 self._execute_child(args, executable, preexec_fn, close_fds,
952 pass_fds, cwd, env,
953 startupinfo, creationflags, shell,
954 p2cread, p2cwrite,
955 c2pread, c2pwrite,
956 errread, errwrite,
957 restore_signals,
958 gid, gids, uid, umask,
959 start_new_session)
960 except:
961 # Cleanup if the child failed starting.
962 for f in filter(None, (self.stdin, self.stdout, self.stderr)):
File /zfs/smblab/fduffy/envs/fret_dev/lib/python3.9/subprocess.py:1754, in Popen._execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session)
1752 fds_to_keep = set(pass_fds)
1753 fds_to_keep.add(errpipe_write)
-> 1754 self.pid = _posixsubprocess.fork_exec(
1755 args, executable_list,
1756 close_fds, tuple(sorted(map(int, fds_to_keep))),
1757 cwd, env_list,
1758 p2cread, p2cwrite, c2pread, c2pwrite,
1759 errread, errwrite,
1760 errpipe_read, errpipe_write,
1761 restore_signals, start_new_session,
1762 gid, gids, uid, umask,
1763 preexec_fn)
1764 self._child_created = True
1765 finally:
1766 # be sure the FD is closed no matter what
TypeError: expected str, bytes or os.PathLike object, not int