Configuration¶
modpipe.config
– Configuration file handling¶
modpipe.filesystem
– ModPipe filesystem¶
- class modpipe.filesystem.FileSystem(top)¶
A ModPipe filesystem, rooted at top, which is either a path or a
Config
object.- add_sequence(seq, parser)¶
Add the
Sequence
object seq to the filesystem. This sets the align code for the sequence and writes it to disk using parser, which should be one of the file parsers in themodpipe.sequence
module (usuallyFASTAFile
). The ModPipe ID for the sequence is returned.
- get_alignment_dir(seqid)¶
- get_model_dir(seqid)¶
- get_selected_file(seqid)¶
- get_sequence_dir(seqid)¶
- get_sequence_file(seqid)¶
modpipe.binaries
– Locations of external binaries¶
This module provides a number of functions that return the location
of various external binaries used by ModPipe. These locations are
set by the Setup
script (see also Installing external programs). If a
given binary is not present, the corresponding function will raise
a modpipe.MissingBinaryError
.
- modpipe.binaries.get_blast(bin)¶
- modpipe.binaries.get_cd_hit()¶
- modpipe.binaries.get_ce()¶
- modpipe.binaries.get_ce_mkdb()¶
- modpipe.binaries.get_hhsuite(bin)¶
- modpipe.binaries.get_jess()¶
- modpipe.binaries.get_modpipe_script(bin)¶
- modpipe.binaries.get_seg()¶
- modpipe.binaries.get_spasm(bin)¶
- modpipe.binaries.get_tess2jess()¶
- modpipe.binaries.get_tmalign()¶
modpipe.version
– Version and copyright information¶
- modpipe.version.get()¶
Return the ModPipe version number.
- modpipe.version.message()¶
Return version and copyright information, suitable for display by a command-line program’s
--version
option.