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"""Definitions for interacting with Blast related applications.
"""
from Bio import Application
from Bio.Application import _Option
class FastacmdCommandline(Application.AbstractCommandline):
"""Create a commandline for the fasta program from NCBI.
"""
def __init__(self, fastacmd = "fastacmd"):
Application.AbstractCommandline.__init__(self)
self.program_name = fastacmd
self.parameters = \
[
_Option(["-d", "database"], ["input"], None, 1,
"The database to retrieve from."),
_Option(["-s", "search_string"], ["input"], None, 1,
"The id to search for.")
]
class BlastallCommandline(Application.AbstractCommandline):
"""Create a commandline for the blastall program from NCBI.
XXX This could use more checking for valid paramters to the program.
"""
def __init__(self, blastcmd = "blastall"):
Application.AbstractCommandline.__init__(self)
self.program_name = blastcmd
self.parameters = \
[# Scoring options
_Option(["-M", "matrix"], ["input"], None, 0,
"Matrix to use"),
_Option(["-G", "gap_open"], ["input"], None, 0,
"Gap open penalty"),
_Option(["-E", "gap_extend"], ["input"], None, 0,
"Gap extension penalty"),
_Option(["-A", "window_size"], ["input"], None, 0,
"Multiple hits window size"),
_Option(["-j", "npasses"], ["input"], None, 0,
"Number of passes"),
_Option(["-p", "passes"], ["input"], None, 0,
"Hits/passes. Integer 0-2."),
# Algorithm options
_Option(["-g", "gapped"], ["input"], None, 0,
"Whether to do a gapped alignment. T/F"),
_Option(["-e", "expectation"], ["input"], None, 0,
"Expectation value cutoff."),
_Option(["-W", "wordsize"], ["input"], None, 0,
"Word size"),
_Option(["-K", "keep_hits"], ["input"], None, 0,
" Number of best hits from a region to keep."),
_Option(["-X", "xdrop"], ["input"], None, 0,
"Dropoff value (bits) for gapped alignments."),
_Option(["-f", "hit_extend"], ["input"], None, 0,
"Threshold for extending hits."),
_Option(["-L", "region_length"], ["input"], None, 0,
"Length of region used to judge hits."),
_Option(["-Z", "db_length"], ["input"], None, 0,
"Effective database length."),
_Option(["-Y", "search_length"], ["input"], None, 0,
"Effective length of search space."),
_Option(["-N", "nbits_gapping"], ["input"], None, 0,
"Number of bits to trigger gapping."),
_Option(["-c", "pseudocounts"], ["input"], None, 0,
"Pseudocounts constants for multiple passes."),
_Option(["-Z", "xdrop_final"], ["input"], None, 0,
"X dropoff for final gapped alignment."),
_Option(["-y", "xdrop_extension"], ["input"], None, 0,
"Dropoff for blast extensions."),
_Option(["-h", "model_threshold"], ["input"], None, 0,
"E-value threshold to include in multipass model."),
_Option(["-S", "required_start"], ["input"], None, 0,
"Start of required region in query."),
_Option(["-H", "required_end"], ["input"], None, 0,
"End of required region in query."),
# Processing options
_Option(["-p", "program"], ["input"], None, 1,
"The blast program to use."),
_Option(["-d", "database"], ["input"], None, 1,
"The database to BLAST against."),
_Option(["-i", "infile"], ["input", "file"], None, 1,
"The sequence to search with."),
_Option(["-F", "filter"], ["input"], None, 0,
"Filter query sequence with SEG? T/F"),
_Option(["-J", "believe_query"], ["input"], None, 0,
"Believe the query defline? T/F"),
_Option(["-a", "nprocessors"], ["input"], None, 0,
"Number of processors to use."),
# Formatting options
_Option(["-T", "html"], ["input"], None, 0,
"Produce HTML output? T/F"),
_Option(["-v", "descriptions"], ["input"], None, 0,
"Number of one-line descriptions."),
_Option(["-b", "alignments"], ["input"], None, 0,
"Number of alignments."),
_Option(["-m", "align_view"], ["input"], None, 0,
"Alignment view. Integer 0-6."),
_Option(["-I", "show_gi"], ["input"], None, 0,
"Show GI's in deflines? T/F"),
_Option(["-O", "seqalign_file"], ["output", "file"], None, 0,
"seqalign file to output."),
_Option(["-o", "align_outfile"], ["output", "file"], None, 1,
"Output file for alignment."),
_Option(["-C", "checkpoint_outfile"], ["output", "file"], None, 0,
"Output file for PSI-BLAST checkpointing."),
_Option(["-R", "restart_infile"], ["input", "file"], None, 0,
"Input file for PSI-BLAST restart."),
_Option(["-k", "hit_infile"], ["input", "file"], None, 0,
"Hit file for PHI-BLAST."),
_Option(["-Q", "matrix_outfile"], ["output", "file"], None, 0,
"Output file for PSI-BLAST matrix in ASCII."),
_Option(["-B", "align_infile"], ["input", "file"], None, 0,
"Input alignment file for PSI-BLAST restart.")
]
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