python-cogent 1.5.3-2 / usr / share / pyshared / cogent / app / uclust.py

#!/usr/bin/env python
"""Application controller for uclust version 1.1.579

Includes application controllers for uclust and
convenience wrappers for different functions of uclust including
sorting fasta files, finding clusters, converting to cd-hit format and
searching and aligning against a database. Also contains
a parser for the resulting .clstr file.

Modified from cogent.app.cd_hit.py on 1-21-10, written by Daniel McDonald.
"""

__author__ = "William Walters"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["William Walters","Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@colorado.edu"
__status__ = "Production"

from os import remove, makedirs
from os.path import split, splitext, basename, isdir, abspath, isfile
from cogent.parse.fasta import MinimalFastaParser
from cogent.app.parameters import ValuedParameter, FlagParameter
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
from cogent import DNA

class UclustParseError(Exception):
    pass

class Uclust(CommandLineApplication):
    """ Uclust ApplicationController
    
    """
    
    _command = 'uclust'
    _input_handler = '_input_as_parameters'
    _parameters = {\
        
        # Fasta input file for merge-sort function
        '--mergesort':ValuedParameter('--',Name='mergesort',Delimiter=' ',
            IsPath=True),
    
        # Output file, used by several difference functions
        '--output':ValuedParameter('--',Name='output',Delimiter=' ',
            IsPath=True),
    
        # Sets temp directory for uclust to create temp fasta file
        '--tmpdir':ValuedParameter('--',Name='tmpdir',Delimiter=' ',
            IsPath=True),
    
        # input filename, fasta format
        '--input':ValuedParameter('--',Name='input',Delimiter=' ',
            IsPath=True),
        
        # Output filename will be in uclust (.uc) format
        # Output cluster file, required parameter
        '--uc':ValuedParameter('--',Name='uc',Delimiter=' ',
            IsPath=True),
        
        # ID percent for OTU, by default is 97%
        '--id':ValuedParameter('--',Name='id',Delimiter=' ',IsPath=False),

        # Disable reverse comparison option, if norev is disabled
        # memory usage is expected to double for uclust
        '--rev':FlagParameter('--',Name='rev'),

        # 'library' file -- a reference of sequences representing pre-existing
        # clusters
        '--lib':ValuedParameter('--',Name='lib',Delimiter=' ',IsPath=True),
        
        # only compare sequences to the library file, don't add new clusters
        # for sequences which don't hit the library
        '--libonly':FlagParameter('--',Name='libonly'),
        
        # Maximum hits before quitting search (default 1, 0=infinity).
        '--maxaccepts':ValuedParameter('--',Name='maxaccepts',Delimiter=' '),
        
        # Maximum rejects before quitting search (default 8, 0=infinity). 
        '--maxrejects':ValuedParameter('--',Name='maxrejects',Delimiter=' '),
        
        # Target nr. of common words (default 8, 0=don't step)
        '--stepwords':ValuedParameter('--',Name='stepwords',Delimiter=' '),
        
        # Word length for windex (default 5 aa.s, 8 nuc.s).
        '--w':ValuedParameter('--',Name='w',Delimiter=' '),
        
        # output fp for pairwise aligned sequences
        '--fastapairs':ValuedParameter('--',Name='fastapairs',Delimiter=' ',
            IsPath=True),
        
        # input filename, .uc format
        '--uc2clstr':ValuedParameter('--', Name='uc2clstr', Delimiter=' ',
            IsPath=True),

        # Don't assume input is sorted by length (default assume sorted).
        '--usersort':FlagParameter('--',Name='usersort'),
        
        # Same as --maxrejects 0 --nowordcountreject.
        # comes with a performance hit.
        '--exact':FlagParameter('--',Name='exact'),

        # Same as --maxrejects 0 --maxaccepts 0 --nowordcountreject -- 
        # comes with a performance hit.
        '--optimal':FlagParameter('--',Name='optimal'),

        '--stable_sort':FlagParameter('--',Name='stable_sort'),
    }
     
    _suppress_stdout = False
    _suppress_stderr = False

    def _input_as_parameters(self,data):
        """ Set the input path (a fasta filepath)
        """
        # The list of values which can be passed on a per-run basis
        allowed_values = ['--input','--uc','--fastapairs',\
                           '--uc2clstr','--output','--mergesort']
        
        unsupported_parameters = set(data.keys()) - set(allowed_values)
        if unsupported_parameters:
            raise ApplicationError,\
             "Unsupported parameter(s) passed when calling uclust: %s" %\
              ' '.join(unsupported_parameters)
        
        for v in allowed_values:
            # turn the parameter off so subsequent runs are not
            # affected by parameter settings from previous runs
            self.Parameters[v].off()
            if v in data:
                # turn the parameter on if specified by the user
                self.Parameters[v].on(data[v])
        
        return ''
        
    def _get_result_paths(self,data):
        """ Set the result paths """
        
        result = {}
        
        result['Output'] = ResultPath(\
         Path=self.Parameters['--output'].Value,\
         IsWritten=self.Parameters['--output'].isOn())
         
        result['ClusterFile'] = ResultPath(
         Path = self.Parameters['--uc'].Value,
         IsWritten=self.Parameters['--uc'].isOn())
         
        result['PairwiseAlignments'] = ResultPath(
         Path = self.Parameters['--fastapairs'].Value,
         IsWritten=self.Parameters['--fastapairs'].isOn())
         
        return result
        
    def _accept_exit_status(self,exit_status):
        """ Test for acceptable exit status
        
            uclust can seg fault and still generate a parsable .uc file
            so we explicitly check the exit status
        
        """
        return exit_status == 0
        
    def getHelp(self):
        """Method that points to documentation"""
        help_str =\
        """
        UCLUST is hosted at:
        http://www.drive5.com/uclust/

        The following papers should be cited if this resource is used:

        Paper pending. Check with Robert Edgar who is writing the paper
        for uclust as of March 2010.  Cite the above URL for the time being.
        """
        return help_str

## Start functions for processing uclust output files
def get_next_record_type(lines,types):
    for line in lines:
        line = line.strip()
        if line and line[0] in types:
            yield line.split('\t')
    return
            
def get_next_two_fasta_records(lines):
    result = []
    for record in MinimalFastaParser(lines):
        result.append(record)
        if len(result) == 2:
            yield result
            result = []
    return

def process_uclust_pw_alignment_results(fasta_pairs_lines,uc_lines):
    """ Process results of uclust search and align """
    alignments = get_next_two_fasta_records(fasta_pairs_lines)
    for hit in get_next_record_type(uc_lines,'H'):
        matching_strand = hit[4]
        if matching_strand == '-':
            strand_id = '-'
            target_rev_match = True
        elif matching_strand == '+':
            strand_id = '+'
            target_rev_match = False
        elif matching_strand == '.':
            # protein sequence, so no strand information
            strand_id = ''
            target_rev_match = False
        else:
            raise UclustParseError, "Unknown strand type: %s" % matching_strand
        uc_query_id = hit[8]
        uc_target_id = hit[9]
        percent_id = float(hit[3])
        
        fasta_pair = alignments.next()
        
        fasta_query_id = fasta_pair[0][0]
        aligned_query = fasta_pair[0][1]
        
        if fasta_query_id != uc_query_id:
            raise UclustParseError,\
             "Order of fasta and uc files do not match."+\
             " Got query %s but expected %s." %\
              (fasta_query_id, uc_query_id)
            
        fasta_target_id = fasta_pair[1][0]
        aligned_target = fasta_pair[1][1]
            
        if fasta_target_id != uc_target_id + strand_id:
            raise UclustParseError, \
             "Order of fasta and uc files do not match."+\
             " Got target %s but expected %s." %\
              (fasta_target_id, uc_target_id + strand_id)
            
        if target_rev_match:
            query_id = uc_query_id + ' RC'
            aligned_query = DNA.rc(aligned_query)
            target_id = uc_target_id
            aligned_target = DNA.rc(aligned_target)
        else:
            query_id = uc_query_id
            aligned_query = aligned_query
            target_id = uc_target_id
            aligned_target = aligned_target
            
        yield (query_id, target_id, aligned_query, aligned_target, percent_id)

def clusters_from_uc_file(uc_lines):
    """ Given an open .uc file, return lists (clusters, failures, new_seeds)
    
        uc_lines: open .uc file, or similar object -- this is the output
         generated by uclust's -uc parameter
         
        This function processes all hit (H), seed (S), and no hit (N) lines
         to return all clusters, failures, and new_seeds generated in
         a uclust run. failures should only arise when users have passed
         --lib and --libonly, and a sequence doesn't cluster to any existing
         reference database sequences.
    
    """
    clusters = {}
    failures = []
    seeds = []
    # the types of hit lines we're interested in here
    # are hit (H), seed (S), library seed (L) and no hit (N) 
    hit_types={}.fromkeys(list('HSNL'))
    for record in get_next_record_type(uc_lines,hit_types):
        hit_type = record[0]
        # sequence identifiers from the fasta header lines only 
        # (no comment data) are stored to identify a sequence in 
        # a cluster -- strip off any comments here as this value
        # is used in several places
        query_id = record[8].split()[0]
        target_cluster = record[9].split()[0]
        if hit_type == 'H':
            # add the hit to it's existing cluster (either library
            # or new cluster)
            clusters[target_cluster].append(query_id)
        elif hit_type == 'S':
            # a new seed was identified -- create a cluster with this 
            # sequence as the first instance
            if query_id in clusters:
                raise UclustParseError,\
                 ("A seq id was provided as a seed, but that seq id already "
                  "represents a cluster. Are there overlapping seq ids in your "
                  "reference and input files or repeated seq ids in either? "
                  "Offending seq id is %s" % query_id)
            clusters[query_id] = [query_id]
            seeds.append(query_id)
        elif hit_type == 'L':
            # a library seed was identified -- create a cluster with this 
            # id as the index, but don't give it any instances yet bc the hit
            # line will be specified separately. note we need to handle these
            # lines separately from the H lines to detect overlapping seq ids 
            # between the reference and the input fasta files
            if query_id in clusters:
                raise UclustParseError,\
                 ("A seq id was provided as a seed, but that seq id already "
                  "represents a cluster. Are there overlapping seq ids in your "
                  "reference and input files or repeated seq ids in either? "
                  "Offending seq id is %s" % query_id)
            clusters[query_id] = []
        elif hit_type == 'N':
            # a failure was identified -- add it to the failures list
            failures.append(query_id)
        else:
            # shouldn't be possible to get here, but provided for 
            # clarity
            raise UclustParseError,\
             "Unexpected result parsing line:\n%s" % '\t'.join(record)
    
    # will need to return the full clusters dict, I think, to support
    # useful identifiers in reference database clustering
    #return  clusters.values(), failures, seeds
    return  clusters, failures, seeds

## End functions for processing uclust output files


## Start uclust convenience functions
def uclust_fasta_sort_from_filepath(
    fasta_filepath,
    output_filepath=None,
    HALT_EXEC=False):
    """Generates sorted fasta file via uclust --mergesort."""
    output_filepath = output_filepath or \
     get_tmp_filename(prefix='uclust_fasta_sort', suffix='.fasta')
    tmp_working_dir = split(output_filepath)[0]
    
    app = Uclust(params={'--tmpdir':tmp_working_dir},HALT_EXEC=HALT_EXEC)
    
    app_result = app(data={'--mergesort':fasta_filepath,\
                           '--output':output_filepath})
    
    return app_result

def uclust_search_and_align_from_fasta_filepath(
    query_fasta_filepath,
    subject_fasta_filepath,
    percent_ID=0.75,
    enable_rev_strand_matching=True,
    max_accepts=8,
    max_rejects=32,
    HALT_EXEC=False):
    """ query seqs against subject fasta using uclust, 
    
       return global pw alignment of best match
    """
     
    # Explanation of parameter settings
    #  id - min percent id to count a match
    #  maxaccepts = 8 , searches for best match rather than first match 
    #                   (0 => infinite accepts, or good matches before 
    #                    quitting search)
    #  maxaccepts = 32, 
    #  libonly = True , does not add sequences to the library if they don't
    #                   match something there already. this effectively makes
    #                   uclust a search tool rather than a clustering tool
    
    params = {'--id':percent_ID,
              '--maxaccepts':max_accepts,
              '--maxrejects':max_rejects,
              '--libonly':True,
              '--lib':subject_fasta_filepath}
              
    if enable_rev_strand_matching:
        params['--rev'] = True
    
    # instantiate the application controller
    app = Uclust(params,HALT_EXEC=HALT_EXEC)
    
    # apply uclust
    alignment_filepath = \
     get_tmp_filename(prefix='uclust_alignments',suffix='.fasta')
    uc_filepath = \
     get_tmp_filename(prefix='uclust_results',suffix='.uc')
    input_data = {'--input':query_fasta_filepath,
                  '--fastapairs':alignment_filepath,
                  '--uc':uc_filepath}
    app_result = app(input_data)
    
    # yield the pairwise alignments
    for result in process_uclust_pw_alignment_results(
     app_result['PairwiseAlignments'],app_result['ClusterFile']):
        try:
            yield result
        except GeneratorExit:
            break
    
    # clean up the temp files that were generated
    app_result.cleanUp()
    
    return

def uclust_cluster_from_sorted_fasta_filepath(
    fasta_filepath,
    uc_save_filepath=None, 
    percent_ID=0.97, 
    max_accepts=1,
    max_rejects=8, 
    stepwords=8,
    word_length=8,
    optimal = False,
    exact = False,
    suppress_sort = False,
    enable_rev_strand_matching=False,
    subject_fasta_filepath=None,
    suppress_new_clusters=False,
    stable_sort=False,
    HALT_EXEC=False):
    """ Returns clustered uclust file from sorted fasta"""
    output_filepath = uc_save_filepath or \
     get_tmp_filename(prefix='uclust_clusters',suffix='.uc')
     
    
    params = {'--id':percent_ID,
              '--maxaccepts':max_accepts,
              '--maxrejects':max_rejects,
              '--stepwords':stepwords,
              '--w':word_length}
    app = Uclust(params,HALT_EXEC=HALT_EXEC)
    
    # Set any additional parameters specified by the user
    if enable_rev_strand_matching: app.Parameters['--rev'].on()
    if optimal: app.Parameters['--optimal'].on()
    if exact: app.Parameters['--exact'].on()
    if suppress_sort: app.Parameters['--usersort'].on()
    if subject_fasta_filepath: app.Parameters['--lib'].on(subject_fasta_filepath)
    if suppress_new_clusters: app.Parameters['--libonly'].on()
    if stable_sort: app.Parameters['--stable_sort'].on()
    
    app_result = app({'--input':fasta_filepath,'--uc':output_filepath})
    return app_result


def get_output_filepaths(output_dir, fasta_filepath):
    """ Returns filepaths for intermediate file to be kept """
    
    if not output_dir.endswith('/'):
        output_dir += '/'
        
    output_file_basename = "".join(basename(fasta_filepath).split('.')[0:-1])
    uc_save_filepath = '%s%s_clusters.uc' % \
     (output_dir, output_file_basename)

    return uc_save_filepath




def get_clusters_from_fasta_filepath(
    fasta_filepath,
    original_fasta_path,
    percent_ID=0.97,
    max_accepts=1,
    max_rejects=8, 
    stepwords=8,
    word_length=8,
    optimal=False,
    exact=False,
    suppress_sort=False,
    output_dir=None,
    enable_rev_strand_matching=False,
    subject_fasta_filepath=None,
    suppress_new_clusters=False,
    return_cluster_maps=False,
    stable_sort=False,
    save_uc_files=True,
    HALT_EXEC=False):
    """ Main convenience wrapper for using uclust to generate cluster files
    
    A source fasta file is required for the fasta_filepath.  This will be 
    sorted to be in order of longest to shortest length sequences.  Following
    this, the sorted fasta file is used to generate a cluster file in the
    uclust (.uc) format.  Next the .uc file is converted to cd-hit format
    (.clstr).  Finally this file is parsed and returned as a list of lists, 
    where each sublist a cluster of sequences.  If an output_dir is
    specified, the intermediate files will be preserved, otherwise all
    files created are temporary and will be deleted at the end of this 
    function
    
    The percent_ID parameter specifies the percent identity for a clusters,
    i.e., if 99% were the parameter, all sequences that were 99% identical
    would be grouped as a cluster.
    """
    


    # Create readable intermediate filenames if they are to be kept
    
    fasta_output_filepath = None
    uc_output_filepath = None
    cd_hit_filepath = None
    
    if output_dir and not output_dir.endswith('/'):
        output_dir += '/'
    
    
    if save_uc_files:
        uc_save_filepath = get_output_filepaths(output_dir, original_fasta_path)
    else:
        uc_save_filepath = None
    
    sorted_fasta_filepath = ""
    uc_filepath = ""
    clstr_filepath = ""


    # Error check in case any app controller fails
    files_to_remove = []
    try:
        if not suppress_sort:
            # Sort fasta input file from largest to smallest sequence 
            sort_fasta = uclust_fasta_sort_from_filepath(fasta_filepath, \
            output_filepath=fasta_output_filepath)
            
            # Get sorted fasta name from application wrapper
            sorted_fasta_filepath = sort_fasta['Output'].name
            files_to_remove.append(sorted_fasta_filepath)
            
        else:
            sort_fasta = None
            sorted_fasta_filepath = fasta_filepath
        
        # Generate uclust cluster file (.uc format)
        uclust_cluster = uclust_cluster_from_sorted_fasta_filepath(
         sorted_fasta_filepath,
         uc_save_filepath, 
         percent_ID=percent_ID,
         max_accepts=max_accepts,
         max_rejects=max_rejects, 
         stepwords=stepwords,
         word_length=word_length,
         optimal=optimal, 
         exact=exact, 
         suppress_sort=suppress_sort,
         enable_rev_strand_matching=enable_rev_strand_matching,
         subject_fasta_filepath=subject_fasta_filepath,
         suppress_new_clusters=suppress_new_clusters,
         stable_sort=stable_sort,
         HALT_EXEC=HALT_EXEC)
        # Get cluster file name from application wrapper
        remove_files(files_to_remove)
    except ApplicationError:
        remove_files(files_to_remove)
        raise ApplicationError, ('Error running uclust. Possible causes are '
         'unsupported version (current supported version is v1.2.22) is installed or '
         'improperly formatted input file was provided')
    except ApplicationNotFoundError:
        remove_files(files_to_remove)
        raise ApplicationNotFoundError('uclust not found, is it properly '+\
         'installed?')

    # Get list of lists for each cluster
    clusters, failures, seeds = \
     clusters_from_uc_file(uclust_cluster['ClusterFile'])
    
    # Remove temp files unless user specifies output filepath
    if not save_uc_files:
        uclust_cluster.cleanUp()
    
    if return_cluster_maps:
        return clusters, failures, seeds
    else:
        return clusters.values(), failures, seeds

## End uclust convenience functions