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December 28, 2013 16:33
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| # Copyright 2001 Brad Chapman. | |
| # Revisions copyright 2009-2010 by Peter Cock. | |
| # Revisions copyright 2010 by Phillip Garland. | |
| # All rights reserved. | |
| # This code is part of the Biopython distribution and governed by its | |
| # license. Please see the LICENSE file that should have been included | |
| # as part of this package. | |
| """Definitions for interacting with BLAST related applications. | |
| Obsolete wrappers for the old/classic NCBI BLAST tools (written in C): | |
| - FastacmdCommandline | |
| - BlastallCommandline | |
| - BlastpgpCommandline | |
| - RpsBlastCommandline | |
| Wrappers for the new NCBI BLAST+ tools (written in C++): | |
| - NcbiblastpCommandline - Protein-Protein BLAST | |
| - NcbideltablastCommandline - Protein-Protein domain enhanced lookup time accelerated blast | |
| - NcbiblastnCommandline - Nucleotide-Nucleotide BLAST | |
| - NcbiblastxCommandline - Translated Query-Protein Subject BLAST | |
| - NcbitblastnCommandline - Protein Query-Translated Subject BLAST | |
| - NcbitblastxCommandline - Translated Query-Protein Subject BLAST | |
| - NcbipsiblastCommandline - Position-Specific Initiated BLAST | |
| - NcbirpsblastCommandline - Reverse Position Specific BLAST | |
| - NcbirpstblastnCommandline - Translated Reverse Position Specific BLAST | |
| - NcbiblastformatterCommandline - Convert ASN.1 to other BLAST output formats | |
| For further details, see: | |
| Camacho et al. BLAST+: architecture and applications | |
| BMC Bioinformatics 2009, 10:421 | |
| doi:10.1186/1471-2105-10-421 | |
| """ | |
| from __future__ import print_function | |
| from Bio import BiopythonDeprecationWarning | |
| from Bio.Application import _Option, AbstractCommandline, _Switch | |
| class FastacmdCommandline(AbstractCommandline): | |
| """Create a commandline for the fasta program from NCBI (OBSOLETE). | |
| """ | |
| def __init__(self, cmd="fastacmd", **kwargs): | |
| self.parameters = [ | |
| _Option(["-d", "database"], | |
| "The database to retrieve from.", | |
| is_required=True, | |
| equate=False), | |
| _Option(["-s", "search_string"], | |
| "The id to search for.", | |
| is_required=True, | |
| equate=False) | |
| ] | |
| AbstractCommandline.__init__(self, cmd, **kwargs) | |
| class _BlastCommandLine(AbstractCommandline): | |
| """Base Commandline object for (classic) NCBI BLAST wrappers (PRIVATE). | |
| This is provided for subclassing, it deals with shared options | |
| common to all the BLAST tools (blastall, rpsblast, blastpgp). | |
| """ | |
| def __init__(self, cmd=None, **kwargs): | |
| assert cmd is not None | |
| extra_parameters = [ | |
| _Switch(["--help", "help"], | |
| "Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments."), | |
| _Option(["-d", "database"], | |
| "The database to BLAST against.", | |
| is_required=True, | |
| equate=False), | |
| _Option(["-i", "infile"], | |
| "The sequence to search with.", | |
| filename=True, | |
| is_required=True, | |
| equate=False), | |
| _Option(["-e", "expectation"], | |
| "Expectation value cutoff.", | |
| equate=False), | |
| _Option(["-m", "align_view"], | |
| "Alignment view. Integer 0-11. Use 7 for XML output.", | |
| equate=False), | |
| _Option(["-o", "align_outfile", "outfile"], | |
| "Output file for alignment.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-y", "xdrop_extension"], | |
| "Dropoff for blast extensions.", | |
| equate=False), | |
| _Option(["-F", "filter"], | |
| "Filter query sequence with SEG? T/F", | |
| equate=False), | |
| _Option(["-X", "xdrop"], | |
| "Dropoff value (bits) for gapped alignments.", | |
| equate=False), | |
| _Option(["-I", "show_gi"], | |
| "Show GI's in deflines? T/F", | |
| equate=False), | |
| _Option(["-J", "believe_query"], | |
| "Believe the query defline? T/F", | |
| equate=False), | |
| _Option(["-Z", "xdrop_final"], | |
| "X dropoff for final gapped alignment.", | |
| equate=False), | |
| _Option(["-z", "db_length"], | |
| "Effective database length.", | |
| equate=False), | |
| _Option(["-O", "seqalign_file"], | |
| "seqalign file to output.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-v", "descriptions"], | |
| "Number of one-line descriptions.", | |
| equate=False), | |
| _Option(["-b", "alignments"], | |
| "Number of alignments.", | |
| equate=False), | |
| _Option(["-Y", "search_length"], | |
| "Effective length of search space (use zero for the " | |
| "real size).", | |
| equate=False), | |
| _Option(["-T", "html"], | |
| "Produce HTML output? T/F", | |
| equate=False), | |
| _Option(["-U", "case_filter"], | |
| "Use lower case filtering of FASTA sequence? T/F", | |
| equate=False), | |
| _Option(["-a", "nprocessors"], | |
| "Number of processors to use.", | |
| equate=False), | |
| _Option(["-g", "gapped"], | |
| "Whether to do a gapped alignment. T/F", | |
| equate=False), | |
| ] | |
| try: | |
| #Insert extra parameters - at the start just in case there | |
| #are any arguments which must come last: | |
| self.parameters = extra_parameters + self.parameters | |
| except AttributeError: | |
| #Should we raise an error? The subclass should have set this up! | |
| self.parameters = extra_parameters | |
| AbstractCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| if self.help: | |
| #Don't want to check the normally mandatory arguments like db | |
| return | |
| AbstractCommandline._validate(self) | |
| class _BlastAllOrPgpCommandLine(_BlastCommandLine): | |
| """Base Commandline object for NCBI BLAST wrappers (PRIVATE). | |
| This is provided for subclassing, it deals with shared options | |
| common to all the blastall and blastpgp tools (but not rpsblast). | |
| """ | |
| def __init__(self, cmd=None, **kwargs): | |
| assert cmd is not None | |
| extra_parameters = [ | |
| _Option(["-G", "gap_open"], | |
| "Gap open penalty", | |
| equate=False), | |
| _Option(["-E", "gap_extend"], | |
| "Gap extension penalty", | |
| equate=False), | |
| _Option(["-A", "window_size"], | |
| "Multiple hits window size", | |
| equate=False), | |
| _Option(["-f", "hit_extend"], | |
| "Threshold for extending hits.", | |
| equate=False), | |
| _Option(["-K", "keep_hits"], | |
| " Number of best hits from a region to keep.", | |
| equate=False), | |
| _Option(["-W", "wordsize"], | |
| "Word size", | |
| equate=False), | |
| _Option(["-P", "passes"], | |
| "Hits/passes. Integer 0-2. 0 for multiple hit, " | |
| "1 for single hit (does not apply to blastn)", | |
| equate=False), | |
| ] | |
| try: | |
| #Insert extra parameters - at the start just in case there | |
| #are any arguments which must come last: | |
| self.parameters = extra_parameters + self.parameters | |
| except AttributeError: | |
| #Should we raise an error? The subclass should have set this up! | |
| self.parameters = extra_parameters | |
| _BlastCommandLine.__init__(self, cmd, **kwargs) | |
| class BlastallCommandline(_BlastAllOrPgpCommandLine): | |
| """Create a commandline for the blastall program from NCBI (OBSOLETE). | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| are replacing blastall with separate tools blastn, blastp, blastx, tblastn | |
| and tblastx. | |
| Like blastall, this wrapper is now obsolete, and will be deprecated and | |
| removed in a future release of Biopython. | |
| >>> from Bio.Blast.Applications import BlastallCommandline | |
| >>> cline = BlastallCommandline(program="blastx", infile="m_cold.fasta", | |
| ... database="nr", expectation=0.001) | |
| >>> cline | |
| BlastallCommandline(cmd='blastall', database='nr', infile='m_cold.fasta', expectation=0.001, program='blastx') | |
| >>> print(cline) | |
| blastall -d nr -i m_cold.fasta -e 0.001 -p blastx | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| #TODO - This could use more checking for valid parameters to the program. | |
| def __init__(self, cmd="blastall",**kwargs): | |
| import warnings | |
| warnings.warn("Like blastall, this wrapper is now deprecated and will be removed in a future release of Biopython.", BiopythonDeprecationWarning) | |
| self.parameters = [ | |
| #Sorted in the same order as the output from blastall --help | |
| #which should make it easier to keep them up to date in future. | |
| #Note that some arguments are defined in the base classes (above). | |
| _Option(["-p", "program"], | |
| "The blast program to use (e.g. blastp, blastn).", | |
| is_required=True, | |
| equate=False), | |
| _Option(["-q", "nuc_mismatch"], | |
| "Penalty for a nucleotide mismatch (blastn only).", | |
| equate=False), | |
| _Option(["-r", "nuc_match"], | |
| "Reward for a nucleotide match (blastn only).", | |
| equate=False), | |
| _Option(["-Q", "query_genetic_code"], | |
| "Query Genetic code to use.", | |
| equate=False), | |
| _Option(["-D", "db_genetic_code"], | |
| "DB Genetic code (for tblast[nx] only).", | |
| equate=False), | |
| _Option(["-M", "matrix"], | |
| "Matrix to use", | |
| equate=False), | |
| _Option(["-S", "strands"], | |
| "Query strands to search against database (for blast[nx], " | |
| "and tblastx). 3 is both, 1 is top, 2 is bottom.", | |
| equate=False), | |
| _Option(["-l", "restrict_gi"], | |
| "Restrict search of database to list of GI's.", | |
| equate=False), | |
| _Option(["-R", "checkpoint"], | |
| "PSI-TBLASTN checkpoint input file.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-n", "megablast"], | |
| "MegaBlast search T/F.", | |
| equate=False), | |
| #The old name "region_length" is for consistency with our | |
| #old blastall function wrapper: | |
| _Option(["-L", "region_length", "range_restriction"], | |
| """Location on query sequence (string format start,end). | |
| In older versions of BLAST, -L set the length of region | |
| used to judge hits (see -K parameter).""", | |
| equate=False), | |
| _Option(["-w", "frame_shift_penalty"], | |
| "Frame shift penalty (OOF algorithm for blastx).", | |
| equate=False), | |
| _Option(["-t", "largest_intron"], | |
| "Length of the largest intron allowed in a translated " | |
| "nucleotide sequence when linking multiple distinct " | |
| "alignments. (0 invokes default behavior; a negative value " | |
| "disables linking.)", | |
| equate=False), | |
| _Option(["-B", "num_concatenated_queries"], | |
| "Number of concatenated queries, for blastn and tblastn.", | |
| equate=False), | |
| _Option(["-V", "oldengine"], | |
| "Force use of the legacy BLAST engine.", | |
| equate=False), | |
| _Option(["-C", "composition_based"], | |
| """Use composition-based statistics for tblastn: | |
| D or d: default (equivalent to F) | |
| 0 or F or f: no composition-based statistics | |
| 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001 | |
| 2: Composition-based score adjustment as in Bioinformatics | |
| 21:902-911, 2005, conditioned on sequence properties | |
| 3: Composition-based score adjustment as in Bioinformatics | |
| 21:902-911, 2005, unconditionally | |
| For programs other than tblastn, must either be absent or be | |
| D, F or 0.""", | |
| equate=False), | |
| _Option(["-s", "smith_waterman"], | |
| "Compute locally optimal Smith-Waterman alignments (This " | |
| "option is only available for gapped tblastn.) T/F", | |
| equate=False), | |
| ] | |
| _BlastAllOrPgpCommandLine.__init__(self, cmd, **kwargs) | |
| class BlastpgpCommandline(_BlastAllOrPgpCommandLine): | |
| """Create a commandline for the blastpgp program from NCBI (OBSOLETE). | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| are replacing blastpgp with a renamed tool psiblast. This module provides | |
| NcbipsiblastCommandline as a wrapper for the new tool psiblast. | |
| Like blastpgp (and blastall), this wrapper is now obsolete, and will be | |
| deprecated and removed in a future release of Biopython. | |
| >>> from Bio.Blast.Applications import BlastpgpCommandline | |
| >>> cline = BlastpgpCommandline(help=True) | |
| >>> cline | |
| BlastpgpCommandline(cmd='blastpgp', help=True) | |
| >>> print(cline) | |
| blastpgp --help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="blastpgp",**kwargs): | |
| import warnings | |
| warnings.warn("Like blastpgp (and blastall), this wrapper is now deprecated and will be removed in a future release of Biopython.", BiopythonDeprecationWarning) | |
| self.parameters = [ | |
| _Option(["-C", "checkpoint_outfile"], | |
| "Output file for PSI-BLAST checkpointing.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-R", "restart_infile"], | |
| "Input file for PSI-BLAST restart.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-k", "hit_infile"], | |
| "Hit file for PHI-BLAST.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-Q", "matrix_outfile"], | |
| "Output file for PSI-BLAST matrix in ASCII.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-B", "align_infile"], | |
| "Input alignment file for PSI-BLAST restart.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-S", "required_start"], | |
| "Start of required region in query.", | |
| equate=False), | |
| _Option(["-H", "required_end"], | |
| "End of required region in query.", | |
| equate=False), | |
| _Option(["-j", "npasses"], | |
| "Number of passes", | |
| equate=False), | |
| _Option(["-N", "nbits_gapping"], | |
| "Number of bits to trigger gapping.", | |
| equate=False), | |
| _Option(["-c", "pseudocounts"], | |
| "Pseudocounts constants for multiple passes.", | |
| equate=False), | |
| _Option(["-h", "model_threshold"], | |
| "E-value threshold to include in multipass model.", | |
| equate=False), | |
| #Does the old name "region_length" for -L make sense? | |
| _Option(["-L", "region_length"], | |
| "Cost to decline alignment (disabled when zero).", | |
| equate=False), | |
| _Option(["-M", "matrix"], | |
| "Matrix (string, default BLOSUM62).", | |
| equate=False), | |
| _Option(["-p", "program"], | |
| "The blast program to use (e.g blastpgp, patseedp or seedp).", | |
| is_required=True, | |
| equate=False), | |
| ] | |
| _BlastAllOrPgpCommandLine.__init__(self, cmd, **kwargs) | |
| class RpsBlastCommandline(_BlastCommandLine): | |
| """Create a commandline for the classic rpsblast program from NCBI (OBSOLETE). | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| are replacing the old rpsblast with a new version of the same name plus a | |
| second tool rpstblastn, both taking different command line arguments. This | |
| module provides NcbirpsblastCommandline and NcbirpsblastCommandline as | |
| wrappers for the new tools. | |
| Like the old rpsblast (and blastall), this wrapper is now obsolete, and will | |
| be deprecated and removed in a future release of Biopython. | |
| >>> from Bio.Blast.Applications import RpsBlastCommandline | |
| >>> cline = RpsBlastCommandline(help=True) | |
| >>> cline | |
| RpsBlastCommandline(cmd='rpsblast', help=True) | |
| >>> print(cline) | |
| rpsblast --help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="rpsblast",**kwargs): | |
| import warnings | |
| warnings.warn("Like the old rpsblast (and blastall), this wrapper is now deprecated and will be removed in a future release of Biopython.", BiopythonDeprecationWarning) | |
| self.parameters = [ | |
| #Note -N is also in blastpgp, but not blastall | |
| _Option(["-N", "nbits_gapping"], | |
| "Number of bits to trigger gapping.", | |
| equate=False), | |
| #Note blastall and blastpgp wrappers have -P with name "passes". | |
| #If this is the same thing, we should be consistent! | |
| _Option(["-P", "multihit"], | |
| "0 for multiple hit, 1 for single hit", | |
| equate=False), | |
| _Option(["-l", "logfile"], | |
| "Logfile name.", | |
| filename=True, | |
| equate=False), | |
| _Option(["-p", "protein"], | |
| "Query sequence is protein. T/F", | |
| equate=False), | |
| _Option(["-L", "range_restriction"], | |
| "Location on query sequence (string format start,end).", | |
| equate=False), | |
| ] | |
| _BlastCommandLine.__init__(self, cmd, **kwargs) | |
| ############################################################################## | |
| # Legacy BLAST wrappers above, (new) BLAST+ wrappers below | |
| ############################################################################## | |
| class _NcbibaseblastCommandline(AbstractCommandline): | |
| """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). | |
| This is provided for subclassing, it deals with shared options | |
| common to all the BLAST tools (blastn, rpsblast, rpsblast, etc | |
| AND blast_formatter). | |
| """ | |
| def __init__(self, cmd=None, **kwargs): | |
| assert cmd is not None | |
| extra_parameters = [ | |
| #Core: | |
| _Switch(["-h", "h"], | |
| "Print USAGE and DESCRIPTION; ignore other arguments."), | |
| _Switch(["-help", "help"], | |
| "Print USAGE, DESCRIPTION and ARGUMENTS description; " | |
| "ignore other arguments."), | |
| _Switch(["-version", "version"], | |
| "Print version number; ignore other arguments."), | |
| # Output configuration options | |
| _Option(["-out", "out"], | |
| "Output file for alignment.", | |
| filename=True, | |
| equate=False), | |
| #Formatting options: | |
| _Option(["-outfmt", "outfmt"], | |
| "Alignment view. Integer 0-11. Use 5 for XML output " | |
| "(differs from classic BLAST which used 7 for XML).", | |
| equate=False), | |
| #TODO - Document and test the column options | |
| _Switch(["-show_gis", "show_gis"], | |
| "Show NCBI GIs in deflines?"), | |
| _Option(["-num_descriptions", "num_descriptions"], | |
| """Number of database sequences to show one-line descriptions for. | |
| Integer argument (at least zero). Default is 500. | |
| See also num_alignments.""", | |
| equate=False), | |
| _Option(["-num_alignments", "num_alignments"], | |
| """Number of database sequences to show num_alignments for. | |
| Integer argument (at least zero). Default is 200. | |
| See also num_alignments.""", | |
| equate=False), | |
| _Switch(["-html", "html"], | |
| "Produce HTML output? See also the outfmt option."), | |
| #Miscellaneous options | |
| _Switch(["-parse_deflines", "parse_deflines"], | |
| "Should the query and subject defline(s) be parsed?"), | |
| ] | |
| try: | |
| #Insert extra parameters - at the start just in case there | |
| #are any arguments which must come last: | |
| self.parameters = extra_parameters + self.parameters | |
| except AttributeError: | |
| #Should we raise an error? The subclass should have set this up! | |
| self.parameters = extra_parameters | |
| AbstractCommandline.__init__(self, cmd, **kwargs) | |
| def _validate_incompatibilities(self, incompatibles): | |
| """Used by the BLAST+ _validate method (PRIVATE).""" | |
| for a in incompatibles: | |
| if self._get_parameter(a): | |
| for b in incompatibles[a]: | |
| if self._get_parameter(b): | |
| raise ValueError("Options %s and %s are incompatible." | |
| % (a, b)) | |
| class _NcbiblastCommandline(_NcbibaseblastCommandline): | |
| """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). | |
| This is provided for subclassing, it deals with shared options | |
| common to all the BLAST tools (blastn, rpsblast, rpsblast, etc). | |
| """ | |
| def __init__(self, cmd=None, **kwargs): | |
| assert cmd is not None | |
| extra_parameters = [ | |
| #Input query options: | |
| _Option(["-query", "query"], | |
| "The sequence to search with.", | |
| filename=True, | |
| equate=False), # Should this be required? | |
| _Option(["-query_loc", "query_loc"], | |
| "Location on the query sequence (Format: start-stop)", | |
| equate=False), | |
| #General search options: | |
| _Option(["-db", "db"], | |
| "The database to BLAST against.", | |
| equate=False), | |
| _Option(["-evalue", "evalue"], | |
| "Expectation value cutoff.", | |
| equate=False), | |
| _Option(["-word_size", "word_size"], | |
| """Word size for wordfinder algorithm. | |
| Integer. Minimum 2.""", | |
| equate=False), | |
| #BLAST-2-Sequences options: | |
| # - see subclass | |
| #Formatting options: | |
| # - see baseclass | |
| #Query filtering options | |
| # TODO -soft_masking <Boolean>, is this a switch or an option? | |
| #_Switch(["-soft_masking", "soft_masking"], | |
| # "Apply filtering locations as soft masks?"), | |
| _Switch(["-lcase_masking", "lcase_masking"], | |
| "Use lower case filtering in query and subject sequence(s)?"), | |
| #Restrict search or results | |
| _Option(["-gilist", "gilist"], | |
| """Restrict search of database to list of GI's. | |
| Incompatible with: negative_gilist, seqidlist, remote, subject, subject_loc""", | |
| filename=True, | |
| equate=False), | |
| _Option(["-negative_gilist", "negative_gilist"], | |
| """Restrict search of database to everything except the listed GIs. | |
| Incompatible with: gilist, seqidlist, remote, subject, subject_loc""", | |
| filename=True, | |
| equate=False), | |
| _Option(["-seqidlist", "seqidlist"], | |
| """Restrict search of database to list of SeqID's. | |
| Incompatible with: gilist, negative_gilist, remote, subject, subject_loc""", | |
| filename=True, | |
| equate=False), | |
| _Option(["-entrez_query", "entrez_query"], | |
| "Restrict search with the given Entrez query (requires remote).", | |
| equate=False), | |
| _Option(["-max_target_seqs", "max_target_seqs"], | |
| """Maximum number of aligned sequences to keep. | |
| Integer argument (at least one).""", | |
| equate=False), | |
| #Statistical options | |
| _Option(["-dbsize", "dbsize"], | |
| "Effective length of the database (integer)", | |
| equate=False), | |
| _Option(["-searchsp", "searchsp"], | |
| "Effective length of the search space (integer)", | |
| equate=False), | |
| _Option(["-max_hsps_per_subject", "max_hsps_per_subject"], | |
| "Override maximum number of HSPs per subject to save for ungapped searches (integer)", | |
| equate=False), | |
| #Extension options | |
| _Option(["-xdrop_ungap", "xdrop_ungap"], | |
| "X-dropoff value (in bits) for ungapped extensions. Float.", | |
| equate=False), | |
| _Option(["-xdrop_gap", "xdrop_gap"], | |
| "X-dropoff value (in bits) for preliminary gapped extensions. Float.", | |
| equate=False), | |
| _Option(["-xdrop_gap_final", "xdrop_gap_final"], | |
| "X-dropoff value (in bits) for final gapped alignment. Float.", | |
| equate=False), | |
| _Option(["-window_size", "window_size"], | |
| "Multiple hits window size, use 0 to specify 1-hit algorithm. Integer.", | |
| equate=False), | |
| # Search strategy options | |
| _Option(["-import_search_strategy", "import_search_strategy"], | |
| """Search strategy to use. | |
| Incompatible with: export_search_strategy""", | |
| filename=True, | |
| equate=False), | |
| _Option(["-export_search_strategy", "export_search_strategy"], | |
| """File name to record the search strategy used. | |
| Incompatible with: import_search_strategy""", | |
| filename=True, | |
| equate=False), | |
| #Miscellaneous options | |
| _Option(["-num_threads", "num_threads"], | |
| """Number of threads to use in the BLAST search. | |
| Integer of at least one. Default is one. | |
| Incompatible with: remote""", | |
| equate=False), | |
| _Switch(["-remote", "remote"], | |
| """Execute search remotely? | |
| Incompatible with: gilist, negative_gilist, subject_loc, num_threads, ..."""), | |
| ] | |
| try: | |
| #Insert extra parameters - at the start just in case there | |
| #are any arguments which must come last: | |
| self.parameters = extra_parameters + self.parameters | |
| except AttributeError: | |
| #Should we raise an error? The subclass should have set this up! | |
| self.parameters = extra_parameters | |
| _NcbibaseblastCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| incompatibles = {"remote":["gilist", "negative_gilist", "num_threads"], | |
| "import_search_strategy" : ["export_search_strategy"], | |
| "gilist":["negative_gilist"], | |
| "seqidlist":["gilist", "negative_gilist", "remote"]} | |
| self._validate_incompatibilities(incompatibles) | |
| if self.entrez_query and not self.remote : | |
| raise ValueError("Option entrez_query requires remote option.") | |
| AbstractCommandline._validate(self) | |
| class _Ncbiblast2SeqCommandline(_NcbiblastCommandline): | |
| """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). | |
| This is provided for subclassing, it deals with shared options | |
| common to all the BLAST tools supporting two-sequence BLAST | |
| (blastn, psiblast, etc) but not rpsblast or rpstblastn. | |
| """ | |
| def __init__(self, cmd=None, **kwargs): | |
| assert cmd is not None | |
| extra_parameters = [ | |
| #General search options: | |
| _Option(["-gapopen", "gapopen"], | |
| "Cost to open a gap (integer).", | |
| equate=False), | |
| _Option(["-gapextend", "gapextend"], | |
| "Cost to extend a gap (integer).", | |
| equate=False), | |
| #BLAST-2-Sequences options: | |
| _Option(["-subject", "subject"], | |
| """Subject sequence(s) to search. | |
| Incompatible with: db, gilist, negative_gilist. | |
| See also subject_loc.""", | |
| filename=True, | |
| equate=False), | |
| _Option(["-subject_loc", "subject_loc"], | |
| """Location on the subject sequence (Format: start-stop) | |
| Incompatible with: db, gilist, seqidlist, negative_gilist, | |
| db_soft_mask, db_hard_mask, remote. | |
| See also subject.""", | |
| equate=False), | |
| #Restrict search or results: | |
| _Option(["-culling_limit", "culling_limit"], | |
| """Hit culling limit (integer). | |
| If the query range of a hit is enveloped by that of at | |
| least this many higher-scoring hits, delete the hit. | |
| Incompatible with: best_hit_overhang, best_hit_score_edge. | |
| """, | |
| equate=False), | |
| _Option(["-best_hit_overhang", "best_hit_overhang"], | |
| """Best Hit algorithm overhang value (recommended value: 0.1) | |
| Float between 0.0 and 0.5 inclusive. | |
| Incompatible with: culling_limit.""", | |
| equate=False), | |
| _Option(["-best_hit_score_edge", "best_hit_score_edge"], | |
| """Best Hit algorithm score edge value (recommended value: 0.1) | |
| Float between 0.0 and 0.5 inclusive. | |
| Incompatible with: culling_limit.""", | |
| equate=False), | |
| ] | |
| try: | |
| #Insert extra parameters - at the start just in case there | |
| #are any arguments which must come last: | |
| self.parameters = extra_parameters + self.parameters | |
| except AttributeError: | |
| #Should we raise an error? The subclass should have set this up! | |
| self.parameters = extra_parameters | |
| _NcbiblastCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| incompatibles = {"subject_loc":["db", "gilist", "negative_gilist", "seqidlist", "remote"], | |
| "culling_limit":["best_hit_overhang", "best_hit_score_edge"], | |
| "subject":["db", "gilist", "negative_gilist", "seqidlist"]} | |
| self._validate_incompatibilities(incompatibles) | |
| _NcbiblastCommandline._validate(self) | |
| class _NcbiblastMain2SeqCommandline(_Ncbiblast2SeqCommandline): | |
| """Base Commandline object for (new) NCBI BLAST+ wrappers (PRIVATE). | |
| This is provided for subclassing, it deals with shared options | |
| common to the main BLAST tools blastp, blastn, blastx, tblastx, tblastn | |
| but not psiblast, rpsblast or rpstblastn. | |
| """ | |
| def __init__(self, cmd=None, **kwargs): | |
| assert cmd is not None | |
| extra_parameters = [ | |
| #Restrict search or results: | |
| _Option(["-db_soft_mask", "db_soft_mask"], | |
| """Filtering algorithm for soft masking (integer). | |
| Filtering algorithm ID to apply to the BLAST database as soft masking. | |
| Incompatible with: db_hard_mask, subject, subject_loc""", | |
| equate=False), | |
| _Option(["-db_hard_mask", "db_hard_mask"], | |
| """Filtering algorithm for hard masking (integer). | |
| Filtering algorithm ID to apply to the BLAST database as hard masking. | |
| Incompatible with: db_soft_mask, subject, subject_loc""", | |
| equate=False), | |
| ] | |
| try: | |
| #Insert extra parameters - at the start just in case there | |
| #are any arguments which must come last: | |
| self.parameters = extra_parameters + self.parameters | |
| except AttributeError: | |
| #Should we raise an error? The subclass should have set this up! | |
| self.parameters = extra_parameters | |
| _Ncbiblast2SeqCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| incompatibles = {"db_soft_mask":["db_hard_mask", "subject", "subject_loc"], | |
| "db_hard_mask":["db_soft_mask", "subject", "subject_loc"]} | |
| self._validate_incompatibilities(incompatibles) | |
| _Ncbiblast2SeqCommandline._validate(self) | |
| class NcbiblastpCommandline(_NcbiblastMain2SeqCommandline): | |
| """Create a commandline for the NCBI BLAST+ program blastp (for proteins). | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old blastall tool with separate tools for each of the searches. | |
| This wrapper therefore replaces BlastallCommandline with option -p blastp. | |
| >>> from Bio.Blast.Applications import NcbiblastpCommandline | |
| >>> cline = NcbiblastpCommandline(query="rosemary.pro", db="nr", | |
| ... evalue=0.001, remote=True, ungapped=True) | |
| >>> cline | |
| NcbiblastpCommandline(cmd='blastp', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True) | |
| >>> print(cline) | |
| blastp -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="blastp", **kwargs): | |
| self.parameters = [ | |
| #General search options: | |
| _Option(["-task", "task"], | |
| "Task to execute (string, blastp (default) or blastp-short).", | |
| checker_function=lambda value : value in ["blastp", | |
| "blastp-short"], | |
| equate=False), | |
| _Option(["-matrix", "matrix"], | |
| "Scoring matrix name (default BLOSUM62)."), | |
| _Option(["-threshold", "threshold"], | |
| "Minimum word score such that the word is added to the " | |
| "BLAST lookup table (float)", | |
| equate=False), | |
| _Option(["-comp_based_stats", "comp_based_stats"], | |
| """Use composition-based statistics (string, default 2, i.e. True). | |
| 0, F or f: no composition-based statistics | |
| 2, T or t, D or d : Composition-based score adjustment as in | |
| Bioinformatics 21:902-911, 2005, conditioned on sequence properties | |
| Note that tblastn also supports values of 1 and 3.""", | |
| checker_function=lambda value : value in "0Ft2TtDd", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Extension options: | |
| _Switch(["-ungapped", "ungapped"], | |
| "Perform ungapped alignment only?"), | |
| #Miscellaneous options: | |
| _Switch(["-use_sw_tback", "use_sw_tback"], | |
| "Compute locally optimal Smith-Waterman alignments?"), | |
| ] | |
| _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs) | |
| class NcbideltablastCommandline(_NcbiblastMain2SeqCommandline): | |
| """Create a commandline for the NCBI BLAST+ program deltablast (for proteins). | |
| This is a wrapper for the deltablast command line command included in the NCBI BLAST+ software (not present in the original BLAST) | |
| >>> from Bio.Blast.Applications import NcbideltablastCommandline | |
| >>> cline = NcbideltablastCommandline(query="rosemary.pro", db="nr", | |
| ... evalue=0.001, remote=True, ungapped=True) | |
| >>> cline | |
| NcbideltablastCommandline(cmd='deltablast', query='rosemary.pro', db='nr', evalue=0.001, remote=True, ungapped=True) | |
| >>> print(cline) | |
| deltablast -query rosemary.pro -db nr -evalue 0.001 -remote -ungapped | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="deltablast", **kwargs): | |
| self.parameters = [ | |
| #General search options: | |
| _Option(["-task", "task"], | |
| "Task to execute (string, or deltablast).", | |
| checker_function=lambda value : value in ["deltablast"], | |
| equate=False), | |
| _Option(["-matrix", "matrix"], | |
| "Scoring matrix name (default BLOSUM62)."), | |
| _Option(["-threshold", "threshold"], | |
| "Minimum word score such that the word is added to the " | |
| "BLAST lookup table (float)", | |
| equate=False), | |
| _Option(["-comp_based_stats", "comp_based_stats"], | |
| """Use composition-based statistics (string, default 2, i.e. True). | |
| 0, F or f: no composition-based statistics | |
| 2, T or t, D or d : Composition-based score adjustment as in | |
| Bioinformatics 21:902-911, 2005, conditioned on sequence properties | |
| Note that tblastn also supports values of 1 and 3.""", | |
| checker_function=lambda value : value in "0Ft2TtDd", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Extension options: | |
| _Switch(["-ungapped", "ungapped"], | |
| "Perform ungapped alignment only?"), | |
| #Miscellaneous options: FIXME: these are probably not valid args | |
| _Switch(["-use_sw_tback", "use_sw_tback"], | |
| "Compute locally optimal Smith-Waterman alignments?"), | |
| ] | |
| _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs) | |
| class NcbiblastnCommandline(_NcbiblastMain2SeqCommandline): | |
| """Wrapper for the NCBI BLAST+ program blastn (for nucleotides). | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old blastall tool with separate tools for each of the searches. | |
| This wrapper therefore replaces BlastallCommandline with option -p blastn. | |
| For example, to run a search against the "nt" nucleotide database using the | |
| FASTA nucleotide file "m_code.fasta" as the query, with an expectation value | |
| cut off of 0.001, saving the output to a file in XML format: | |
| >>> from Bio.Blast.Applications import NcbiblastnCommandline | |
| >>> cline = NcbiblastnCommandline(query="m_cold.fasta", db="nt", strand="plus", | |
| ... evalue=0.001, out="m_cold.xml", outfmt=5) | |
| >>> cline | |
| NcbiblastnCommandline(cmd='blastn', out='m_cold.xml', outfmt=5, query='m_cold.fasta', db='nt', evalue=0.001, strand='plus') | |
| >>> print(cline) | |
| blastn -out m_cold.xml -outfmt 5 -query m_cold.fasta -db nt -evalue 0.001 -strand plus | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="blastn", **kwargs): | |
| self.parameters = [ | |
| #Input query options: | |
| _Option(["-strand", "strand"], | |
| """Query strand(s) to search against database/subject. | |
| Values allowed are "both" (default), "minus", "plus".""", | |
| checker_function=lambda value : value in ["both", | |
| "minus", | |
| "plus"], | |
| equate=False), | |
| #General search options: | |
| _Option(["-task", "task"], | |
| """Task to execute (string, default 'megablast') | |
| Allowed values 'blastn', 'blastn-short', 'dc-megablast', 'megablast' | |
| (the default), or 'vecscreen'.""", | |
| checker_function=lambda value : value in ['blastn', | |
| 'blastn-short', | |
| 'dc-megablast', | |
| 'megablast', | |
| 'vecscreen'], | |
| equate=False), | |
| _Option(["-penalty", "penalty"], | |
| "Penalty for a nucleotide mismatch (integer, at most zero).", | |
| equate=False), | |
| _Option(["-reward", "reward"], | |
| "Reward for a nucleotide match (integer, at least zero).", | |
| equate=False), | |
| #TODO - Does this need an argument or is it a switch? | |
| #_Option(["-use_index", "use_index"], | |
| # "Use MegaBLAST database index (boolean).", | |
| # equate=False), | |
| _Option(["-index_name", "index_name"], | |
| "MegaBLAST database index name.", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-dust", "dust"], | |
| """Filter query sequence with DUST (string). | |
| Format: 'yes', 'level window linker', or 'no' to disable. | |
| Default = '20 64 1'. | |
| """, | |
| equate=False), | |
| _Option(["-filtering_db", "filtering_db"], | |
| "BLAST database containing filtering elements (i.e. repeats).", | |
| equate=False), | |
| _Option(["-window_masker_taxid", "window_masker_taxid"], | |
| "Enable WindowMasker filtering using a Taxonomic ID (integer).", | |
| equate=False), | |
| _Option(["-window_masker_db", "window_masker_db"], | |
| "Enable WindowMasker filtering using this repeats database (string).", | |
| equate=False), | |
| #Restrict search or results: | |
| _Option(["-perc_identity", "perc_identity"], | |
| "Percent identity (real, 0 to 100 inclusive).", | |
| equate=False), | |
| #Discontiguous MegaBLAST options | |
| _Option(["-template_type", "template_type"], | |
| """Discontiguous MegaBLAST template type (string). | |
| Allowed values: 'coding', 'coding_and_optimal' or 'optimal' | |
| Requires: template_length.""", | |
| checker_function=lambda value : value in ['coding', 'coding_and_optimal', 'optimal'], | |
| equate=False), | |
| _Option(["-template_length", "template_length"], | |
| """Discontiguous MegaBLAST template length (integer). | |
| Allowed values: 16, 18, 21 | |
| Requires: template_type.""", | |
| checker_function=lambda value : value in [16, 18, 21, '16', '18', '21'], | |
| equate=False), | |
| #Extension options: | |
| _Switch(["-no_greedy", "no_greedy"], | |
| "Use non-greedy dynamic programming extension"), | |
| _Option(["-min_raw_gapped_score", "min_raw_gapped_score"], | |
| "Minimum raw gapped score to keep an alignment in the " | |
| "preliminary gapped and traceback stages (integer).", | |
| equate=False), | |
| _Switch(["-ungapped", "ungapped"], | |
| "Perform ungapped alignment only?"), | |
| _Option(["-off_diagonal_range", "off_diagonal_range"], | |
| """Number of off-diagonals to search for the 2nd hit (integer). | |
| Expects a positive integer, or 0 (default) to turn off. | |
| Added in BLAST 2.2.23+ | |
| """, | |
| equate=False), | |
| ] | |
| _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| if (self.template_type and not self.template_length) \ | |
| or (self.template_length and not self.template_type) : | |
| raise ValueError("Options template_type and template_type require each other.") | |
| _NcbiblastMain2SeqCommandline._validate(self) | |
| class NcbiblastxCommandline(_NcbiblastMain2SeqCommandline): | |
| """Wrapper for the NCBI BLAST+ program blastx (nucleotide query, protein database). | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old blastall tool with separate tools for each of the searches. | |
| This wrapper therefore replaces BlastallCommandline with option -p blastx. | |
| >>> from Bio.Blast.Applications import NcbiblastxCommandline | |
| >>> cline = NcbiblastxCommandline(query="m_cold.fasta", db="nr", evalue=0.001) | |
| >>> cline | |
| NcbiblastxCommandline(cmd='blastx', query='m_cold.fasta', db='nr', evalue=0.001) | |
| >>> print(cline) | |
| blastx -query m_cold.fasta -db nr -evalue 0.001 | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="blastx", **kwargs): | |
| self.parameters = [ | |
| #Input query options: | |
| _Option(["-strand", "strand"], | |
| """Query strand(s) to search against database/subject. | |
| Values allowed are "both" (default), "minus", "plus".""", | |
| checker_function=lambda value : value in ["both", "minus", "plus"], | |
| equate=False), | |
| #Input query options: | |
| _Option(["-query_gencode", "query_gencode"], | |
| """Genetic code to use to translate query | |
| Integer. Default is one.""", | |
| equate=False), | |
| #General search options: | |
| _Option(["-frame_shift_penalty", "frame_shift_penalty"], | |
| """Frame shift penalty (integer, at least 1, default ignored) (OBSOLETE). | |
| This was removed in BLAST 2.2.27+""", | |
| equate=False), | |
| _Option(["-max_intron_length", "max_intron_length"], | |
| """Maximum intron length (integer). | |
| Length of the largest intron allowed in a translated nucleotide | |
| sequence when linking multiple distinct alignments (a negative | |
| value disables linking). Default zero.""", | |
| equate=False), | |
| _Option(["-matrix", "matrix"], | |
| "Scoring matrix name (default BLOSUM62).", | |
| equate=False), | |
| _Option(["-threshold", "threshold"], | |
| "Minimum word score such that the word is added to the " | |
| "BLAST lookup table (float)", | |
| equate=False), | |
| _Option(["-comp_based_stats", "comp_based_stats"], | |
| """Use composition-based statistics for blastp, blastx, or tblastn: | |
| D or d: default (equivalent to 2 ) | |
| 0 or F or f: no composition-based statistics | |
| 1: Composition-based statistics as in NAR 29:2994-3005, 2001 | |
| 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties | |
| 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally | |
| For programs other than tblastn, must either be absent or be D, F or 0 | |
| Default = `2' | |
| """, | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Extension options: | |
| _Switch(["-ungapped", "ungapped"], | |
| "Perform ungapped alignment only?"), | |
| _Switch(["-use_sw_tback", "use_sw_tback"], | |
| "Compute locally optimal Smith-Waterman alignments?"), | |
| ] | |
| _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs) | |
| class NcbitblastnCommandline(_NcbiblastMain2SeqCommandline): | |
| """Wrapper for the NCBI BLAST+ program tblastn. | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old blastall tool with separate tools for each of the searches. | |
| This wrapper therefore replaces BlastallCommandline with option -p tblastn. | |
| >>> from Bio.Blast.Applications import NcbitblastnCommandline | |
| >>> cline = NcbitblastnCommandline(help=True) | |
| >>> cline | |
| NcbitblastnCommandline(cmd='tblastn', help=True) | |
| >>> print(cline) | |
| tblastn -help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="tblastn", **kwargs): | |
| self.parameters = [ | |
| #General search options: | |
| _Option(["-db_gencode", "db_gencode"], | |
| """Genetic code to use to translate query | |
| Integer. Default is one.""", | |
| equate=False), | |
| _Option(["-frame_shift_penalty", "frame_shift_penalty"], | |
| """Frame shift penalty (integer, at least 1, default ignored) (OBSOLETE). | |
| This was removed in BLAST 2.2.27+""", | |
| equate=False), | |
| _Option(["-max_intron_length", "max_intron_length"], | |
| """Maximum intron length (integer). | |
| Length of the largest intron allowed in a translated nucleotide | |
| sequence when linking multiple distinct alignments (a negative | |
| value disables linking). Default zero.""", | |
| equate=False), | |
| _Option(["-matrix", "matrix"], | |
| "Scoring matrix name (default BLOSUM62).", | |
| equate=False), | |
| _Option(["-threshold", "threshold"], | |
| "Minimum word score such that the word is added to the BLAST lookup table (float)", | |
| equate=False), | |
| _Option(["-comp_based_stats", "comp_based_stats"], | |
| """Use composition-based statistics (string, default 2, i.e. True). | |
| 0, F or f: no composition-based statistics | |
| 1: Composition-based statistics as in NAR 29:2994-3005, 2001 | |
| 2, T or t, D or d : Composition-based score adjustment as in | |
| Bioinformatics 21:902-911, 2005, conditioned on sequence properties | |
| 3: Composition-based score adjustment as in Bioinformatics 21:902-911, | |
| 2005, unconditionally | |
| Note that only tblastn supports values of 1 and 3.""", | |
| checker_function=lambda value : value in "0Ft12TtDd3", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Extension options: | |
| _Switch(["-ungapped", "ungapped"], | |
| "Perform ungapped alignment only?"), | |
| #Miscellaneous options: | |
| _Switch(["-use_sw_tback", "use_sw_tback"], | |
| "Compute locally optimal Smith-Waterman alignments?"), | |
| #PSI-TBLASTN options: | |
| _Option(["-in_pssm", "in_pssm"], | |
| """PSI-BLAST checkpoint file | |
| Incompatible with: remote, query""", | |
| filename=True, | |
| equate=False), | |
| ] | |
| _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs) | |
| class NcbitblastxCommandline(_NcbiblastMain2SeqCommandline): | |
| """Wrapper for the NCBI BLAST+ program tblastx. | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old blastall tool with separate tools for each of the searches. | |
| This wrapper therefore replaces BlastallCommandline with option -p tblastx. | |
| >>> from Bio.Blast.Applications import NcbitblastxCommandline | |
| >>> cline = NcbitblastxCommandline(help=True) | |
| >>> cline | |
| NcbitblastxCommandline(cmd='tblastx', help=True) | |
| >>> print(cline) | |
| tblastx -help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="tblastx", **kwargs): | |
| self.parameters = [ | |
| #Input query options: | |
| _Option(["-strand", "strand"], | |
| """Query strand(s) to search against database/subject. | |
| Values allowed are "both" (default), "minus", "plus".""", | |
| checker_function=lambda value : value in ["both", "minus", "plus"], | |
| equate=False), | |
| #Input query options: | |
| _Option(["-query_gencode", "query_gencode"], | |
| """Genetic code to use to translate query | |
| Integer. Default is one.""", | |
| equate=False), | |
| #General search options: | |
| _Option(["-db_gencode", "db_gencode"], | |
| """Genetic code to use to translate query | |
| Integer. Default is one.""", | |
| equate=False), | |
| _Option(["-max_intron_length", "max_intron_length"], | |
| """Maximum intron length (integer). | |
| Length of the largest intron allowed in a translated nucleotide | |
| sequence when linking multiple distinct alignments (a negative | |
| value disables linking). Default zero.""", | |
| equate=False), | |
| _Option(["-matrix", "matrix"], | |
| "Scoring matrix name (default BLOSUM62).", | |
| equate=False), | |
| _Option(["-threshold", "threshold"], | |
| "Minimum word score such that the word is added to the " | |
| "BLAST lookup table (float)", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| ] | |
| _NcbiblastMain2SeqCommandline.__init__(self, cmd, **kwargs) | |
| class NcbipsiblastCommandline(_Ncbiblast2SeqCommandline): | |
| """Wrapper for the NCBI BLAST+ program psiblast. | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old blastpgp tool with a similar tool psiblast. This wrapper | |
| therefore replaces BlastpgpCommandline, the wrapper for blastpgp. | |
| >>> from Bio.Blast.Applications import NcbipsiblastCommandline | |
| >>> cline = NcbipsiblastCommandline(help=True) | |
| >>> cline | |
| NcbipsiblastCommandline(cmd='psiblast', help=True) | |
| >>> print(cline) | |
| psiblast -help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="psiblast", **kwargs): | |
| self.parameters = [ | |
| #General search options: | |
| _Option(["-matrix", "matrix"], | |
| "Scoring matrix name (default BLOSUM62).", | |
| equate=False), | |
| _Option(["-threshold", "threshold"], | |
| "Minimum word score such that the word is added to the " | |
| "BLAST lookup table (float)", | |
| equate=False), | |
| _Option(["-comp_based_stats", "comp_based_stats"], | |
| """Use composition-based statistics (string, default 2, i.e. True). | |
| 0, F or f: no composition-based statistics | |
| 2, T or t, D or d : Composition-based score adjustment | |
| as in Bioinformatics 21:902-911, 2005, conditioned on | |
| sequence properties | |
| Note that tblastn also supports values of 1 and 3.""", | |
| checker_function=lambda value : value in "0Ft2TtDd", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Extension options: | |
| _Option(["-gap_trigger", "gap_trigger"], | |
| "Number of bits to trigger gapping (float, default 22)", | |
| equate=False), | |
| #Miscellaneous options: | |
| _Switch(["-use_sw_tback", "use_sw_tback"], | |
| "Compute locally optimal Smith-Waterman alignments?"), | |
| #PSI-BLAST options: | |
| _Option(["-num_iterations", "num_iterations"], | |
| """Number of iterations to perform, integer | |
| Integer of at least one. Default is one. | |
| Incompatible with: remote""", | |
| equate=False), | |
| _Option(["-out_pssm", "out_pssm"], | |
| "File name to store checkpoint file", | |
| filename=True, | |
| equate=False), | |
| _Option(["-out_ascii_pssm", "out_ascii_pssm"], | |
| "File name to store ASCII version of PSSM", | |
| filename=True, | |
| equate=False), | |
| _Option(["-in_msa", "in_msa"], | |
| """File name of multiple sequence alignment to restart | |
| PSI-BLAST | |
| Incompatible with: in_pssm, query""", | |
| filename=True, | |
| equate=False), | |
| _Option(["-msa_master_idx", "msa_master_idx"], | |
| """Index of sequence to use as master in MSA. | |
| Index (1-based) of sequence to use as the master in the | |
| multiple sequence alignment. If not specified, the first | |
| sequence is used.""", | |
| equate=False), | |
| _Option(["-in_pssm", "in_pssm"], | |
| """PSI-BLAST checkpoint file | |
| Incompatible with: in_msa, query, phi_pattern""", | |
| filename=True, | |
| equate=False), | |
| #PSSM engine options: | |
| _Option(["-pseudocount", "pseudocount"], | |
| """Pseudo-count value used when constructing PSSM | |
| Integer. Default is zero.""", | |
| equate=False), | |
| _Option(["-inclusion_ethresh", "inclusion_ethresh"], | |
| """E-value inclusion threshold for pairwise alignments | |
| Float. Default is 0.002.""", | |
| equate=False), | |
| _Switch(["-ignore_msa_master", "ignore_msa_master"], | |
| """Ignore the master sequence when creating PSSM | |
| * Requires: in_msa | |
| * Incompatible with: msa_master_idx, in_pssm, query, | |
| query_loc, phi_pattern | |
| """), | |
| #PHI-BLAST options: | |
| _Option(["-phi_pattern", "phi_pattern"], | |
| """File name containing pattern to search | |
| Incompatible with: in_pssm""", | |
| filename=True, | |
| equate=False), | |
| ] | |
| _Ncbiblast2SeqCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| incompatibles = {"num_iterations": ["remote"], | |
| "in_msa": ["in_pssm", "query"], | |
| "in_pssm": ["in_msa", "query", "phi_pattern"], | |
| "ignore_msa_master": ["msa_master_idx", "in_pssm", | |
| "query", "query_loc", "phi_pattern"], | |
| } | |
| self._validate_incompatibilities(incompatibles) | |
| _Ncbiblast2SeqCommandline._validate(self) | |
| class NcbirpsblastCommandline(_NcbiblastCommandline): | |
| """Wrapper for the NCBI BLAST+ program rpsblast. | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old rpsblast tool with a similar tool of the same name. This | |
| wrapper replaces RpsBlastCommandline, the wrapper for the old rpsblast. | |
| >>> from Bio.Blast.Applications import NcbirpsblastCommandline | |
| >>> cline = NcbirpsblastCommandline(help=True) | |
| >>> cline | |
| NcbirpsblastCommandline(cmd='rpsblast', help=True) | |
| >>> print(cline) | |
| rpsblast -help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="rpsblast", **kwargs): | |
| self.parameters = [ | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Restrict search or results: | |
| _Option(["-culling_limit", "culling_limit"], | |
| """Hit culling limit (integer). | |
| If the query range of a hit is enveloped by that of at | |
| least this many higher-scoring hits, delete the hit. | |
| Incompatible with: best_hit_overhang, best_hit_score_edge. | |
| """, | |
| equate=False), | |
| _Option(["-best_hit_overhang", "best_hit_overhang"], | |
| """Best Hit algorithm overhang value (recommended value: 0.1) | |
| Float between 0.0 and 0.5 inclusive. | |
| Incompatible with: culling_limit.""", | |
| equate=False), | |
| _Option(["-best_hit_score_edge", "best_hit_score_edge"], | |
| """Best Hit algorithm score edge value (recommended value: 0.1) | |
| Float between 0.0 and 0.5 inclusive. | |
| Incompatible with: culling_limit.""", | |
| equate=False), | |
| #General search options: | |
| _Option(["-comp_based_stats", "comp_based_stats"], | |
| """Use composition-based statistics. | |
| D or d: default (equivalent to 0 ) | |
| 0 or F or f: Simplified Composition-based statistics as in | |
| Bioinformatics 15:1000-1011, 1999 | |
| 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001 | |
| Default = `0' | |
| """, | |
| checker_function=lambda value : value in "Dd0Ff1Tt", | |
| equate=False), | |
| #Misc options: | |
| _Switch(["-use_sw_tback", "use_sw_tback"], | |
| "Compute locally optimal Smith-Waterman alignments?"), | |
| ] | |
| _NcbiblastCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| incompatibles = {"culling_limit":["best_hit_overhang", "best_hit_score_edge"]} | |
| self._validate_incompatibilities(incompatibles) | |
| _NcbiblastCommandline._validate(self) | |
| class NcbirpstblastnCommandline(_NcbiblastCommandline): | |
| """Wrapper for the NCBI BLAST+ program rpstblastn. | |
| With the release of BLAST+ (BLAST rewritten in C++ instead of C), the NCBI | |
| replaced the old rpsblast tool with a similar tool of the same name, and a | |
| separate tool rpstblastn for Translated Reverse Position Specific BLAST. | |
| >>> from Bio.Blast.Applications import NcbirpstblastnCommandline | |
| >>> cline = NcbirpstblastnCommandline(help=True) | |
| >>> cline | |
| NcbirpstblastnCommandline(cmd='rpstblastn', help=True) | |
| >>> print(cline) | |
| rpstblastn -help | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| """ | |
| def __init__(self, cmd="rpstblastn", **kwargs): | |
| self.parameters = [ | |
| #Input query options: | |
| _Option(["-strand", "strand"], | |
| """Query strand(s) to search against database/subject. | |
| Values allowed are "both" (default), "minus", "plus".""", | |
| checker_function=lambda value : value in ["both", | |
| "minus", | |
| "plus"], | |
| equate=False), | |
| #Input query options: | |
| _Option(["-query_gencode", "query_gencode"], | |
| """Genetic code to use to translate query | |
| Integer. Default is one.""", | |
| equate=False), | |
| #Query filtering options: | |
| _Option(["-seg", "seg"], | |
| """Filter query sequence with SEG (string). | |
| Format: "yes", "window locut hicut", or "no" to disable. | |
| Default is "12 2.2 2.5""", | |
| equate=False), | |
| #Extension options: | |
| _Switch(["-ungapped", "ungapped"], | |
| "Perform ungapped alignment only?"), | |
| ] | |
| _NcbiblastCommandline.__init__(self, cmd, **kwargs) | |
| class NcbiblastformatterCommandline(_NcbibaseblastCommandline): | |
| """Wrapper for the NCBI BLAST+ program blast_formatter. | |
| With the release of BLAST 2.2.24+ (i.e. the BLAST suite rewritten in C++ | |
| instead of C), the NCBI added the ASN.1 output format option to all the | |
| search tools, and extended the blast_formatter to support this as input. | |
| The blast_formatter command allows you to convert the ASN.1 output into | |
| the other output formats (XML, tabular, plain text, HTML). | |
| >>> from Bio.Blast.Applications import NcbiblastformatterCommandline | |
| >>> cline = NcbiblastformatterCommandline(archive="example.asn", outfmt=5, out="example.xml") | |
| >>> cline | |
| NcbiblastformatterCommandline(cmd='blast_formatter', out='example.xml', outfmt=5, archive='example.asn') | |
| >>> print(cline) | |
| blast_formatter -out example.xml -outfmt 5 -archive example.asn | |
| You would typically run the command line with cline() or via the Python | |
| subprocess module, as described in the Biopython tutorial. | |
| Note that this wrapper is for the version of blast_formatter from BLAST | |
| 2.2.24+ (or later) which is when the NCBI first announced the inclusion | |
| this tool. There was actually an early version in BLAST 2.2.23+ (and | |
| possibly in older releases) but this did not have the -archive option | |
| (instead -rid is a mandatory argument), and is not supported by this | |
| wrapper. | |
| """ | |
| def __init__(self, cmd="blast_formatter", **kwargs): | |
| self.parameters = [ | |
| # Input options | |
| _Option(["-rid", "rid"], | |
| "BLAST Request ID (RID), not compatible with archive arg", | |
| equate=False), | |
| _Option(["-archive", "archive"], | |
| "Archive file of results, not compatible with rid arg.", | |
| filename=True, | |
| equate=False), | |
| # Restrict search or results | |
| _Option(["-max_target_seqs", "max_target_seqs"], | |
| "Maximum number of aligned sequences to keep", | |
| checker_function=lambda value: value >= 1, | |
| equate=False), | |
| ] | |
| _NcbibaseblastCommandline.__init__(self, cmd, **kwargs) | |
| def _validate(self): | |
| incompatibles = {"rid":["archive"]} | |
| self._validate_incompatibilities(incompatibles) | |
| _NcbibaseblastCommandline._validate(self) | |
| def _test(): | |
| """Run the Bio.Blast.Applications module's doctests.""" | |
| import doctest | |
| doctest.testmod(verbose=1) | |
| if __name__ == "__main__": | |
| #Run the doctests | |
| _test() | |
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