Beispiel #1
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def importReference( infile, outfile ):
    '''import reference domains.
    '''

    track = re.sub("[.].*", "", os.path.basename(infile ) )

    tablename_domains = "nrdb40_%s_domains" % track
    tablename_families = "nrdb40_%s_families" % track
    filename_families = re.sub( "domains", "families", infile )

    statement = '''
    python %(scriptsdir)s/DomainsReference.py 
		--Database=%(database)s
		--domains=%(database)s.%(tablename_domains)s_src
		--families=%(database)s.%(tablename_families)s_src
		--mapped_domains=%(database)s.%(tablename_domains)s
		--mapped_families=%(database)s.%(tablename_families)s
		--input=%(infile)s
		--descriptions=%(filename_families)s
		--source=%(database)s.%(eval_tablename_adda_nids)s
	  Create UpdateDomains MakeNonRedundantClone 
    > %(outfile)s
    '''

    P.run()
Beispiel #2
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def buildOverlapTable( infiles, outfile ):
    '''calculate overlap between the different sources of domains.'''
    infiles = " ".join(infiles)
    statement = '''
    python %(scriptsdir)s/set_diff.py --add-percent %(infiles)s > %(outfile)s
    '''
    P.run()
Beispiel #3
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def indexGraph(infile, outfile):
    '''index graph and store in compressed format.'''
    cmd = "index"
    to_cluster = True
    job_options = "-l mem_free=50G"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #4
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def indexSequences(infile, outfile ):
    '''index sequence database and map to internal identifiers.
    '''
    cmd = "sequences"
    statement = ADDA_STATEMENT
    to_cluster = True
    P.run()
Beispiel #5
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def importReference(infile, outfile):
    '''import reference domains.
    '''

    track = re.sub("[.].*", "", os.path.basename(infile))

    tablename_domains = "nrdb40_%s_domains" % track
    tablename_families = "nrdb40_%s_families" % track
    filename_families = re.sub("domains", "families", infile)

    statement = '''
    python %(scriptsdir)s/DomainsReference.py 
		--Database=%(database)s
		--domains=%(database)s.%(tablename_domains)s_src
		--families=%(database)s.%(tablename_families)s_src
		--mapped_domains=%(database)s.%(tablename_domains)s
		--mapped_families=%(database)s.%(tablename_families)s
		--input=%(infile)s
		--descriptions=%(filename_families)s
		--source=%(database)s.%(eval_tablename_adda_nids)s
	  Create UpdateDomains MakeNonRedundantClone 
    > %(outfile)s
    '''

    P.run()
Beispiel #6
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def buildOverlapTable(infiles, outfile):
    '''calculate overlap between the different sources of domains.'''
    infiles = " ".join(infiles)
    statement = '''
    python %(scriptsdir)s/set_diff.py --add-percent %(infiles)s > %(outfile)s
    '''
    P.run()
Beispiel #7
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def collectADDASequences(infile, outfile):
    '''unpack adda sequences.'''

    if infile.endswith(".gz"):
        statement = '''gunzip < %(infile)s > %(outfile)s'''
    else:
        statement = '''ln -s %(infile)s %(outfile)s'''

    P.run()
Beispiel #8
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def collectADDASequences( infile, outfile ):
    '''unpack adda sequences.'''

    if infile.endswith(".gz"):
        statement = '''gunzip < %(infile)s > %(outfile)s'''
    else:
        statement = '''ln -s %(infile)s %(outfile)s'''

    P.run()
Beispiel #9
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def exportResults(infile, outfile):
    '''export Adda results.'''

    statement = '''
    tar -cvzf %(outfile)s 
          %(output_result)s
          %(output_families)s
          %(output_summary)s
    '''
    P.run()
Beispiel #10
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def exportResults( infile, outfile ):
    '''export Adda results.'''
    
    statement = '''
    tar -cvzf %(outfile)s 
          %(output_result)s
          %(output_families)s
          %(output_summary)s
    '''
    P.run()
Beispiel #11
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def reindexSequences( infile, outfile ):
    '''rebuild the adda sequence database from adda.nids.'''

    database = outfile[:-len(".fasta")]
    statement = '''
    awk '!/^nid/ { printf(">%%s\\n%%s\\n", $1, $5)};' 
    < %(infile)s
    | python %(scriptsdir)s/IndexedFasta.py %(database)s -
    > %(outfile)s.log'''

    P.run()
Beispiel #12
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def reindexSequences(infile, outfile):
    '''rebuild the adda sequence database from adda.nids.'''

    database = outfile[:-len(".fasta")]
    statement = '''
    awk '!/^nid/ { printf(">%%s\\n%%s\\n", $1, $5)};' 
    < %(infile)s
    | python %(scriptsdir)s/IndexedFasta.py %(database)s -
    > %(outfile)s.log'''

    P.run()
Beispiel #13
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def buildBlatIndex(infiles, outfile):
    '''build blat index.'''
    infiles = " ".join(infiles)

    statement = '''
    blat -dots=100 -prot 
                -makeOoc=%(outfile)s 
		-minIdentity=%(map_min_identity)i
		%(infiles)s %(outfile)s.log < /dev/null >> %(outfile)s.log
    '''

    P.run()
Beispiel #14
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def buildBlatIndex( infiles, outfile):
    '''build blat index.'''
    infiles = " ".join( infiles )

    statement = '''
    blat -dots=100 -prot 
                -makeOoc=%(outfile)s 
		-minIdentity=%(map_min_identity)i
		%(infiles)s %(outfile)s.log < /dev/null >> %(outfile)s.log
    '''

    P.run()
Beispiel #15
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def collectTargetSequences(infiles, outfile):
    '''extract new sequences from input.'''

    filename_target, filename_adda = infiles
    statement = '''
	python %(scriptsdir)s/map_fasta2fasta.py 
		--filename-reference=%(filename_adda)s
                --output-filename-pattern=target.%%s
		%(filename_target)s > %(outfile)s.log
    '''

    P.run()
Beispiel #16
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def collectTargetSequences( infiles, outfile ):
    '''extract new sequences from input.'''
        
    filename_target, filename_adda = infiles
    statement = '''
	python %(scriptsdir)s/map_fasta2fasta.py 
		--filename-reference=%(filename_adda)s
                --output-filename-pattern=target.%%s
		%(filename_target)s > %(outfile)s.log
    '''

    P.run()
Beispiel #17
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def splitSequenceFile(infile, outfiles):

    # patch ruffus bug
    if type(infile) == type(list()):
        infile = infile[0]

    statement = '''
       perl %(scriptsdir)s/split_fasta.pl 
            -a blat.dir/chunk_%%s.fasta %(map_chunksize)i
            < %(infile)s > split.log
       '''

    P.run()
Beispiel #18
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def buildIndirectDomains(infiles, outfile):
    '''collect domains mapped from domains mapped via BLAT.'''

    infiles = " ".join(infiles)
    statement = '''
	cat %(infiles)s |
	python %(scriptsdir)s/substitute_tokens.py 
		--apply=target.new2new.map
		--column=1 
		--invert \
		--filter > %(outfile)s
    '''
    P.run()
Beispiel #19
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def splitSequenceFile( infile, outfiles ):

    # patch ruffus bug
    if type(infile) == type(list()):
        infile = infile[0]

    statement = '''
       perl %(scriptsdir)s/split_fasta.pl 
            -a blat.dir/chunk_%%s.fasta %(map_chunksize)i
            < %(infile)s > split.log
       '''

    P.run()
Beispiel #20
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def exportPfam(infile, outfile):
    '''export Adda results.'''

    outdir = time.strftime("%Y_%m_%d", time.localtime(time.time()))

    statement = '''
    mkdir %(outdir)s;
    awk '!/^nid/ {printf("%%s\\n%%s\\n", $1, $5);}' < %(output_nids) > %(outdir)s/adda.fasta;
    ln -s ../adda.result %(outdir)s/adda.result;
    tar -cvzf %(outfile)s %(outdir)s;
    rm -rf %(outdir)s
    '''
    P.run()
Beispiel #21
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def exportPfam( infile, outfile ):
    '''export Adda results.'''
    
    outdir = time.strftime( "%Y_%m_%d", time.localtime(time.time()))

    statement = '''
    mkdir %(outdir)s;
    awk '!/^nid/ {printf("%%s\\n%%s\\n", $1, $5);}' < %(output_nids) > %(outdir)s/adda.fasta;
    ln -s ../adda.result %(outdir)s/adda.result;
    tar -cvzf %(outfile)s %(outdir)s;
    rm -rf %(outdir)s
    '''
    P.run()
Beispiel #22
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def buildIndirectDomains( infiles, outfile ):
    '''collect domains mapped from domains mapped via BLAT.'''
    
    infiles = " ".join(infiles)
    statement = '''
	cat %(infiles)s |
	python %(scriptsdir)s/substitute_tokens.py 
		--apply=target.new2new.map
		--column=1 
		--invert \
		--filter > %(outfile)s
    '''
    P.run()
Beispiel #23
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def buildMappingCoverage(infiles, outfile):
    '''compute coverage of target sequences with ADDA domains.'''

    filename_domains, filename_lengths = infiles

    statement = '''
    python %(scriptsdir)s/adda2coverage.py 
		--log=%(outfile)s.log 
		--filename-lengths=%(filename_lengths)s 
                --output-filename-pattern="%(outfile)s_%%s"
    < %(filename_domains)s 
    > %(outfile)s
    '''
    P.run()
Beispiel #24
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def importADDAResults( infile, outfile ):
    '''import ADDA results.'''

    statement = '''
	python %(scriptsdir)s/DomainsAdda.py 
		--Database=%(database)s
		--domains=%(database)s.nrdb40_%(tablename_adda)s_domains
		--families=%(database)s.nrdb40_%(tablename_adda)s_families
		--input=%(infile)s
		--source=%(database)s.%(eval_tablename_adda_nids)s
		Create Finalize UpdateDomains 
       > %(outfile)s
    '''
    P.run()
Beispiel #25
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def buildMappingCoverage( infiles, outfile ):
    '''compute coverage of target sequences with ADDA domains.'''
    
    filename_domains, filename_lengths = infiles

    statement = '''
    python %(scriptsdir)s/adda2coverage.py 
		--log=%(outfile)s.log 
		--filename-lengths=%(filename_lengths)s 
                --output-filename-pattern="%(outfile)s_%%s"
    < %(filename_domains)s 
    > %(outfile)s
    '''
    P.run()
Beispiel #26
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def importADDAResults(infile, outfile):
    '''import ADDA results.'''

    statement = '''
	python %(scriptsdir)s/DomainsAdda.py 
		--Database=%(database)s
		--domains=%(database)s.nrdb40_%(tablename_adda)s_domains
		--families=%(database)s.nrdb40_%(tablename_adda)s_families
		--input=%(infile)s
		--source=%(database)s.%(eval_tablename_adda_nids)s
		Create Finalize UpdateDomains 
       > %(outfile)s
    '''
    P.run()
Beispiel #27
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def mapDomains( infile, outfile ):
    '''collect blat matching stats.'''

    to_cluster= True
    job_options = "-l mem_free=4000M"
    statement = '''bsub -q normal -R"select[mem>4000] rusage[mem=4000]" -M 4000000 -o %(infile)s.out2 -I "gunzip 
        < %(infile)s 
	| python %(scriptsdir)s/map_blat2adda.py 
		--filename-domains=adda.results
		--output-filename-pattern="%(outfile)s.%%s"
		--log=%(outfile)s.log 
		--verbose=2 
        > %(outfile)s"
        '''
    P.run()
Beispiel #28
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def buildDirectDomains(infiles, outfile):
    '''collect domains that could be transfered without mapping.'''

    x, filename_domains = infiles

    statement = '''gunzip
        < %(filename_domains)s 
	| python %(scriptsdir)s/substitute_tokens.py 
		--apply=target.new2old.map 
		--invert 
		--column=1 
		--filter 
	> %(outfile)s
    '''
    P.run()
Beispiel #29
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def buildDirectDomains( infiles, outfile ):
    '''collect domains that could be transfered without mapping.'''
    
    x, filename_domains = infiles

    statement = '''gunzip
        < %(filename_domains)s 
	| python %(scriptsdir)s/substitute_tokens.py 
		--apply=target.new2old.map 
		--invert 
		--column=1 
		--filter 
	> %(outfile)s
    '''
    P.run()
Beispiel #30
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def mapDomains( infile, outfile ):
    '''collect blat matching stats.'''

    to_cluster= True
    job_options = "-l mem_free=4000M"
    statement = '''gunzip 
        < %(infile)s 
	| python %(scriptsdir)s/map_blat2adda.py 
		--filename-domains=<( gunzip < %(map_filename_domains)s)
		--output-filename-pattern="%(outfile)s.%%s" 
		--log=%(outfile)s.log 
		--verbose=2 
        > %(outfile)s
        '''
    P.run()
Beispiel #31
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def mapDomains(infile, outfile):
    '''collect blat matching stats.'''

    to_cluster = True
    job_options = "-l mem_free=4000M"
    statement = '''bsub -q normal -R"select[mem>4000] rusage[mem=4000]" -M 4000000 -o %(infile)s.out2 -I "gunzip 
        < %(infile)s 
	| python %(scriptsdir)s/map_blat2adda.py 
		--filename-domains=adda.results
		--output-filename-pattern="%(outfile)s.%%s"
		--log=%(outfile)s.log 
		--verbose=2 
        > %(outfile)s"
        '''
    P.run()
Beispiel #32
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def runBlat( infiles, outfile ):
    '''run a blat job.'''

    to_cluster = True
    infile, fasta = infiles
    statement = '''
    blat  
	  -prot
	  -ooc=5.ooc
	  -noHead
	  -minIdentity=%(map_min_identity)i 
	  %(fasta)s
	  %(infile)s
          stdout | gzip > %(outfile)s
    '''
    
    P.run()
Beispiel #33
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def runBlat( infiles, outfile ):
    '''run a blat job.'''

    to_cluster = True
    infile, fasta = infiles
    statement = '''bsub -q normal -R"select[mem>4000] rusage[mem=4000]" -M 4000000 -o %(fasta)s.out -I 
    "blat  
	  -prot
	  -ooc=5.ooc
	  -noHead
	  -minIdentity=%(map_min_identity)i 
	  %(fasta)s
	  %(infile)s
    %(infile)s.out &&
    cat %(infile)s.out | gzip > %(outfile)s"
    '''
    
    P.run()
Beispiel #34
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def runBlat(infiles, outfile):
    '''run a blat job.'''

    to_cluster = True
    infile, fasta = infiles
    statement = '''bsub -q normal -R"select[mem>4000] rusage[mem=4000]" -M 4000000 -o %(fasta)s.out -I 
    "blat  
	  -prot
	  -ooc=5.ooc
	  -noHead
	  -minIdentity=%(map_min_identity)i 
	  %(fasta)s
	  %(infile)s
    %(infile)s.out &&
    cat %(infile)s.out | gzip > %(outfile)s"
    '''

    P.run()
Beispiel #35
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def importADDAIntermediateResults( infile, outfile ):
    '''import the segmentation segments.

    Nids are translated.
    '''

    table = outfile[:-len(".import")]

    statement = '''
    python %(scriptsdir)s/adda_translate.py
       --nids=%(eval_filename_adda_nids)s
    < %(infile)s
    | python %(scriptsdir)s/csv2db.py 
        %(csv2db_options)s
        --database=%(database)s
	--table=%(table)s 
	--index=nid 
    > %(outfile)s
    '''
    
    P.run()
Beispiel #36
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def importADDAIntermediateResults(infile, outfile):
    '''import the segmentation segments.

    Nids are translated.
    '''

    table = outfile[:-len(".import")]

    statement = '''
    python %(scriptsdir)s/adda_translate.py
       --nids=%(eval_filename_adda_nids)s
    < %(infile)s
    | python %(scriptsdir)s/csv2db.py 
        %(csv2db_options)s
        --database=%(database)s
	--table=%(table)s 
	--index=nid 
    > %(outfile)s
    '''

    P.run()
Beispiel #37
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def importSequences( infile, outfile ):
    '''import sequences into database.

    This command will also create the database
    '''

    statement = '''
         mysql %(load_mysql_options)s -e "DROP DATABASE IF EXISTS %(load_database)s"
    '''
    	
    P.run()

    statement = '''
         mysql %(load_mysql_options)s -e "CREATE database %(load_database)s"
    '''
    	
    P.run()

    statement ='''
        perl -p -e "s/nid/adda_nid/; s/pid/nid/" 
        < %(infile)s 
	| python %(scriptsdir)s/csv2db.py 
        %(load_csv2db_options)s
           --database=%(load_database)s
	   --table=%(load_tablename_adda_nrdb)s 
           --map=nid:int
	   --index=nid 
        > %(outfile)s
    '''

    P.run()
Beispiel #38
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def importSequences( infile, outfile ):
    '''import sequences.

    This command will also create the database
    '''

    statement = '''
         mysql %(mysql_options)s -e "DROP DATABASE IF EXISTS %(load_database)s"
    '''
    	
    P.run()

    statement = '''
         mysql %(mysql_options)s -e "CREATE database %(load_database)s"
    '''
    	
    P.run()

    table = outfile[:-len(".import")]

    statement ='''
        perl -p -e "s/nid/adda_nid/; s/pid/nid/" 
        < %(infile)s 
	| python %(scriptsdir)s/csv2db.py 
        %(csv2db_options)s
           --database=%(database)s
	   --table=%(table)s 
	   --index=nid 
        > %(outfile)s
    '''

    P.run()
Beispiel #39
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def annotateADDA( infile, outfile ):
    '''annotate ADDA families with reference families
    '''

    track = outfile[:-len(".annotations")]

    statement = '''
        python %(scriptsdir)s/OutputStatisticsClustering.py 
                --Database=%(database)s
		--domains=%(database)s.nrdb40_%(tablename_adda)s_domains 
		--families=%(database)s.nrdb40_%(tablename_adda)s_families
		--max_family=%(eval_max_family_size)i
		--min_evidence=2 
                --min_units=2 
		--ref_domains=%(database)s.nrdb40_%(track)s_domains 
		--ref_families=%(database)s.nrdb40_%(track)s_families
	        --full-table 
		Annotation 
        > %(outfile)s
        '''
    
    P.run()

    statement = '''
        perl %(scriptsdir)s/calculate_selectivity.pl < %(outfile)s > %(outfile)s.selectivity
    '''

    P.run()

    statement = '''
        perl %(scriptsdir)s/calculate_sensitivity.pl < %(outfile)s > %(outfile)s.sensitivity
    '''

    P.run()
Beispiel #40
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def annotateADDA(infile, outfile):
    '''annotate ADDA families with reference families
    '''

    track = outfile[:-len(".annotations")]

    statement = '''
        python %(scriptsdir)s/OutputStatisticsClustering.py 
                --Database=%(database)s
		--domains=%(database)s.nrdb40_%(tablename_adda)s_domains 
		--families=%(database)s.nrdb40_%(tablename_adda)s_families
		--max_family=%(eval_max_family_size)i
		--min_evidence=2 
                --min_units=2 
		--ref_domains=%(database)s.nrdb40_%(track)s_domains 
		--ref_families=%(database)s.nrdb40_%(track)s_families
	        --full-table 
		Annotation 
        > %(outfile)s
        '''

    P.run()

    statement = '''
        perl %(scriptsdir)s/calculate_selectivity.pl < %(outfile)s > %(outfile)s.selectivity
    '''

    P.run()

    statement = '''
        perl %(scriptsdir)s/calculate_sensitivity.pl < %(outfile)s > %(outfile)s.sensitivity
    '''

    P.run()
Beispiel #41
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def importSequences(infile, outfile):
    '''import sequences.

    This command will also create the database
    '''

    statement = '''
         mysql %(mysql_options)s -e "DROP DATABASE IF EXISTS %(load_database)s"
    '''

    P.run()

    statement = '''
         mysql %(mysql_options)s -e "CREATE database %(load_database)s"
    '''

    P.run()

    table = outfile[:-len(".import")]

    statement = '''
        perl -p -e "s/nid/adda_nid/; s/pid/nid/" 
        < %(infile)s 
	| python %(scriptsdir)s/csv2db.py 
        %(csv2db_options)s
           --database=%(database)s
	   --table=%(table)s 
	   --index=nid 
        > %(outfile)s
    '''

    P.run()
Beispiel #42
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def evaluateDomains( infile, outfile ):
    '''benchmark domains.

    The domain benchmark checks if the appropriate domains have
    been selected by the optimisation method.
    '''

    track = outfile[:-len("_domains.eval")]

    statement = '''
    python %(scriptsdir)s/evaluate_domain_boundaries.py 
        --database=%(database)s
        --reference=%(database)s.nrdb40_%(track)s_domains
        --parts=%(database)s.%(eval_tablename_domains)s
        --output-filename-pattern=%(outfile)s.%%s
        --switch 
        --skip-repeats 
        --bin-size=1
    > %(outfile)s
    '''

    P.run()
Beispiel #43
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def evaluateDomains(infile, outfile):
    '''benchmark domains.

    The domain benchmark checks if the appropriate domains have
    been selected by the optimisation method.
    '''

    track = outfile[:-len("_domains.eval")]

    statement = '''
    python %(scriptsdir)s/evaluate_domain_boundaries.py 
        --database=%(database)s
        --reference=%(database)s.nrdb40_%(track)s_domains
        --parts=%(database)s.%(eval_tablename_domains)s
        --output-filename-pattern=%(outfile)s.%%s
        --switch 
        --skip-repeats 
        --bin-size=1
    > %(outfile)s
    '''

    P.run()
Beispiel #44
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def evaluateSegments(infile, outfile):
    '''evaluate ADDA segments against reference

    The tree benchmark checks whether the segmentation algorithm
    contains the appropriate reference domains.
    '''

    track = outfile[:-len("_segments.eval")]

    statement = '''
    python %(scriptsdir)s/evaluate_domain_boundaries.py 
        --database=%(database)s 
        --reference=%(database)s.nrdb40_%(track)s_domains
        --trees=%(database)s.%(eval_tablename_segments)s
        --output-filename-pattern=%(outfile)s.%%s
        --switch 
        --skip-repeats 
        --no-full-length 
        --bin-size=1
    > %(outfile)s
    '''

    P.run()
Beispiel #45
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def evaluateSegments( infile, outfile ):
    '''evaluate ADDA segments against reference

    The tree benchmark checks whether the segmentation algorithm
    contains the appropriate reference domains.
    '''

    track = outfile[:-len("_segments.eval")]

    statement = '''
    python %(scriptsdir)s/evaluate_domain_boundaries.py 
        --database=%(database)s 
        --reference=%(database)s.nrdb40_%(track)s_domains
        --trees=%(database)s.%(eval_tablename_segments)s
        --output-filename-pattern=%(outfile)s.%%s
        --switch 
        --skip-repeats 
        --no-full-length 
        --bin-size=1
    > %(outfile)s
    '''

    P.run()
Beispiel #46
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def computeParameters(infile, outfile ):
    '''pre-process graph.'''
    cmd = "fit"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #47
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def clusterDomains(infile, outfile):
    cmd = "cluster"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #48
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def buildAddaSummary(infile, outfile):
    cmd = "summary"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #49
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def buildFamilies(infile, outfile):
    cmd = "families"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #50
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for command line help.

Code
----
"""
import sys, tempfile, optparse, shutil, itertools, csv, math, random, re, glob, os, shutil
import fileinput, collections, gzip

import Adda.Experiment as E
import Adda.Pipeline as P
from ruffus import *
import csv
import sqlite3
from Adda import IndexedFasta, FastaIterator, IOTools, AddaIO

PARAMS = P.getParameters("adda.ini")


@files(PARAMS["eval_filename_alignment_graph"],
       ("alignment_graph.gz", "alignment.stats"))
def annotateAlignmentGraph(infile, outfiles):
    '''input the alignment graph and output
    a translated version of it and adding 
    reference domain information.
    '''

    outfile, outfile_stats = outfiles

    # collect benchmark domains
    E.info("reading benchmark domains")
    benchmark_domains = AddaIO.readMapNid2Domains(
Beispiel #51
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def indexGraph(infile, outfile):
    '''index graph and store in compressed format.'''
    cmd = "index"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #52
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def computeMSTComponents(infile, outfile):
    cmd = "mst-components"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #53
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def indexGraph(infile, outfile):
    '''index graph and store in compressed format.'''
    cmd = "index"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #54
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def indexSequences(infile, outfile):
    '''index sequence database and map to internal identifiers.
    '''
    cmd = "sequences"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #55
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def alignDomains(infile, outfile):
    cmd = "align"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #56
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def clusterDomains(infile, outfile):
    cmd = "cluster"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #57
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def buildFamilies(infile, outfile):
    cmd = "families"
    statement = ADDA_STATEMENT
    P.run()
Beispiel #58
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def buildAddaSummary(infile, outfile):
    cmd = "summary"
    statement = ADDA_STATEMENT
    P.run()