Configuration

modpipe.config – Configuration file handling

class modpipe.config.Config

A ModPipe configuration file

parse_file(fh)

Read a ModPipe configuration file

modpipe.config.read_file(fh)

Create and return a new Config, read from a configuration file

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 the modpipe.sequence module (usually FASTAFile). 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.