def __call__(self, track, slice=None):
fn = os.path.join(
DATADIR,
"replicated_intervals/%(track)s.peakshape.gz.matrix_%(slice)s.gz" %
locals())
if not os.path.exists(fn):
return
x = IOTools.openFile(fn)
matrix, rownames, colnames = IOTools.readMatrix(x)
nrows = len(rownames)
if nrows == 0:
return
if nrows > self.scale:
take = numpy.array(numpy.floor(
numpy.arange(0, nrows,
float(nrows + 1) / self.scale)),
dtype=int)
rownames = [rownames[x] for x in take]
matrix = matrix[take]
return odict(
(('matrix', matrix), ('rows', rownames), ('columns', colnames)))
def buildPFAMDomains( infiles, outfile ):
'''map PFAM domains onto current sequence collection.
The mapping is done by ID lookup.'''
infile = infiles[0]
with IOTools.openFile( "nrdb50.fasta.tsv") as inf:
reader = csv.DictReader( inf, dialect='excel-tab' )
map_id2nid = {}
for row in reader:
map_id2nid[row['repid']] = row['nid']
rx = re.compile( "(\S+)\/(\d+)-(\d+)\s+(\S+);(.*);" )
c = E.Counter()
outf = IOTools.openFile( outfile, "w" )
with IOTools.openFile( infile ) as inf:
for entry in FastaIterator.iterate( inf ):
c.input += 1
pid, start, end, pfam_id, description = rx.match( entry.title ).groups()
try:
outf.write( "%s\t%i\t%i\t%s\n" % (map_id2nid[pid], int(start)-1, int(end), pfam_id ) )
except KeyError:
c.missed += 1
continue
c.output += 1
outf.close()
E.info( c )
def __call__(self, track, slice=None):
fn = "ortholog_pairs_with_feature.matrix2"
if not os.path.exists(fn):
return
x = IOTools.openFile(fn)
matrix, rownames, colnames = IOTools.readMatrix(x)
return odict((("matrix", matrix), ("rows", rownames), ("columns", colnames)))
def __call__(self, track, slice=None):
fn = "ortholog_pairs_with_feature.matrix2"
if not os.path.exists(fn):
return
x = IOTools.openFile(fn)
matrix, rownames, colnames = IOTools.readMatrix(x)
return odict(
(('matrix', matrix), ('rows', rownames), ('columns', colnames)))
def __call__(self, track, slice = None):
c_transcript = []
c_gene = []
for transcript in GTF.transcript_iterator(GTF.iterator(IOTools.openFile(self.getFilename(track)))):
c_transcript.append(len(transcript))
for gene in GTF.flat_gene_iterator(GTF.iterator(IOTools.openFile(self.getFilename(track)))):
c_gene.append(len(gene))
return odict( ( ("transcript", np.mean(c_transcript)), ("gene",np.mean(c_gene) )) )
def configToDictionary( config ):
p = {}
for section in config.sections():
for key,value in config.items( section ):
v = IOTools.convertValue( value )
p["%s_%s" % (section,key)] = v
if section in ( "general", "DEFAULT" ):
p["%s" % (key)] = v
for key, value in config.defaults().iteritems():
p["%s" % (key)] = IOTools.convertValue( value )
return p
def __call__(self, track, slice = None):
if slice == "transcript":
lengths_transcripts = []
for transcript in GTF.transcript_iterator(GTF.iterator(IOTools.openFile(self.getFilename(track)))):
length = sum([gtf.end - gtf.start for gtf in transcript])
lengths_transcripts.append(length)
return np.mean(lengths_transcripts)
elif slice == "gene":
lengths_genes = []
for gene in GTF.flat_gene_iterator(GTF.iterator(IOTools.openFile(self.getFilename(track)))):
length = sum([gtf.end - gtf.start for gtf in gene])
lengths_genes.append(length)
return np.mean(lengths_genes)
def buildSummaryCalledDMRs( infiles, outfile ):
'''build summary of differentially methylated regions.'''
dbh = connect()
cc = dbh.cursor()
outf = IOTools.openFile( outfile, "w" )
outf.write( "metatrack\ttest\tntested\tnok\tnsignificant\tn2fold\n" )
for track in TRACKS:
tables = [x[0] for x in cc.execute( """SELECT name FROM medip_%s.sqlite_master
WHERE type='table' and sql LIKE '%%control_mean%%' and sql LIKE '%%treatment_mean%%'""" % track
).fetchall()]
for table in tables:
statement = """SELECT
COUNT(*) as ntested,
SUM(CASE WHEN status='OK' THEN 1 ELSE 0 END) AS nok,
SUM(CASE WHEN significant THEN 1 ELSE 0 END) AS nsignificant,
SUM(CASE WHEN significant AND (l2fold < -1 OR l2fold > 1) THEN 1 ELSE 0 END) as n2fold
FROM medip_%(track)s.%(table)s"""
ntested, nok, nsignificant, n2fold = cc.execute( statement % locals() ).fetchone()
outf.write( "\t".join( map(str, (track, table, ntested, nok, nsignificant, n2fold )))+ "\n" )
outf.close()
def buildSummaryMapping( infiles, outfile ):
dbh = connect()
cc = dbh.cursor()
outf = IOTools.openFile( outfile, "w" )
table = "bam_stats"
colnames = None
for track in TRACKS:
statement = """SELECT *
FROM medip_%(track)s.%(table)s"""
data = cc.execute( statement % locals() ).fetchall()
_colnames = [x[0] for x in cc.description]
if not colnames:
colnames = _colnames
outf.write( "\t".join( ["metatrack"] + colnames,) + "\n" )
assert colnames == _colnames
for row in data:
outf.write( "\t".join( map(str, (track,) + row))+ "\n" )
outf.close()
def getParameters(filename="pipeline.ini"):
'''read a config file and return as a dictionary.
Sections and keys are combined with an underscore. If
a key without section does not exist, it will be added
plain.
For example::
[general]
input=input1.file
[special]
input=input2.file
will be entered as { 'general_input' : "input1.file",
'input: "input1.file", 'special_input' : "input2.file" }
This function also updates the module-wide parameter map.
'''
p = {}
config = ConfigParser.ConfigParser()
config.readfp(open(filename), "r")
for section in config.sections():
for key, value in config.items(section):
v = IOTools.convertValue(value)
if key not in p: p[key] = v
p["%s_%s" % (section, key)] = v
PARAMS.update(p)
return p
def buildSummaryCpGCoverage(infiles, outfile):
'''build summary of differentially methylated regions.'''
dbh = connect()
cc = dbh.cursor()
outf = IOTools.openFile(outfile, "w")
outf.write("metatrack\ttrack\tcoverage\tncovered\tpcovered\n")
for track in TRACKS:
tables = [x[0] for x in cc.execute( """SELECT name FROM medip_%s.sqlite_master
WHERE type='table' and name LIKE '%%coveredpos%%' """ % track
).fetchall()]
for table in tables:
statement = """SELECT '%(track)s' as metatrack,
'%(table)s' as track,
coverage, ncovered, pcovered FROM medip_%(track)s.%(table)s"""
for x in cc.execute(statement % locals()):
outf.write("\t".join(map(str, x)) + "\n")
outf.close()
def buildSummaryCalledDMRs(infiles, outfile):
'''build summary of differentially methylated regions.'''
dbh = connect()
cc = dbh.cursor()
outf = IOTools.openFile(outfile, "w")
outf.write("metatrack\ttest\tntested\tnok\tnsignificant\tn2fold\n")
for track in TRACKS:
tables = [x[0] for x in cc.execute( """SELECT name FROM medip_%s.sqlite_master
WHERE type='table' and sql LIKE '%%control_mean%%' and sql LIKE '%%treatment_mean%%'""" % track
).fetchall()]
for table in tables:
statement = """SELECT
COUNT(*) as ntested,
SUM(CASE WHEN status='OK' THEN 1 ELSE 0 END) AS nok,
SUM(CASE WHEN significant THEN 1 ELSE 0 END) AS nsignificant,
SUM(CASE WHEN significant AND (l2fold < -1 OR l2fold > 1) THEN 1 ELSE 0 END) as n2fold
FROM medip_%(track)s.%(table)s"""
ntested, nok, nsignificant, n2fold = cc.execute(
statement % locals()).fetchone()
outf.write(
"\t".join(map(str, (track, table, ntested, nok, nsignificant, n2fold))) + "\n")
outf.close()
def buildSummaryMapping(infiles, outfile):
dbh = connect()
cc = dbh.cursor()
outf = IOTools.openFile(outfile, "w")
table = "bam_stats"
colnames = None
for track in TRACKS:
statement = """SELECT *
FROM medip_%(track)s.%(table)s"""
data = cc.execute(statement % locals()).fetchall()
_colnames = [x[0] for x in cc.description]
if not colnames:
colnames = _colnames
outf.write("\t".join(["metatrack"] + colnames,) + "\n")
assert colnames == _colnames
for row in data:
outf.write("\t".join(map(str, (track,) + row)) + "\n")
outf.close()
def buildSummaryCpGCoverage( infiles, outfile ):
'''build summary of differentially methylated regions.'''
dbh = connect()
cc = dbh.cursor()
outf = IOTools.openFile( outfile, "w" )
outf.write("metatrack\ttrack\tcoverage\tncovered\tpcovered\n" )
for track in TRACKS:
tables = [x[0] for x in cc.execute( """SELECT name FROM medip_%s.sqlite_master
WHERE type='table' and name LIKE '%%coveredpos%%' """ % track
).fetchall()]
for table in tables:
statement = """SELECT '%(track)s' as metatrack,
'%(table)s' as track,
coverage, ncovered, pcovered FROM medip_%(track)s.%(table)s"""
for x in cc.execute(statement % locals()):
outf.write( "\t".join(map(str,x))+ "\n" )
outf.close()
def getParameters( filename = "pipeline.ini" ):
'''read a config file and return as a dictionary.
Sections and keys are combined with an underscore. If
a key without section does not exist, it will be added
plain.
For example::
[general]
input=input1.file
[special]
input=input2.file
will be entered as { 'general_input' : "input1.file",
'input: "input1.file", 'special_input' : "input2.file" }
This function also updates the module-wide parameter map.
'''
p = {}
config = ConfigParser.ConfigParser()
config.readfp(open(filename),"r")
for section in config.sections():
for key,value in config.items( section ):
v = IOTools.convertValue( value )
if key not in p: p[key] = v
p["%s_%s" % (section,key)] = v
PARAMS.update( p )
return p
def __call__(self, track, slice = None):
classes = ["antisense"
, "antisense_upstream"
, "antisense_downstream"
, "sense_upstream"
, "sense_downstream"
, "intergenic"
, "sense_intronic"
, "antisense_intronic"]
coding_set = {}
for gtf in GTF.iterator(IOTools.openFile("gtfs/lncrna_filtered.class.gtf.gz")):
coding_set[gtf.transcript_id] = gtf.source
result = {"noncoding": {}, "coding":collections.defaultdict(int)}
total_nc = float(self.getValue("SELECT COUNT(*) FROM %(track)s_cpc_result WHERE C_NC = 'noncoding'"))
for c in classes:
result["noncoding"][c] = (float(self.getValue("""SELECT COUNT(*) FROM lncrna_final_class as a, %s_cpc_result as b WHERE a.class = '%s'
AND b.C_NC = 'noncoding'
AND a.transcript_id = b.transcript_id""" % (track,c)))/total_nc)*100
total_c = len(coding_set.keys())
for c in classes:
ids = self.getValues("SELECT transcript_id FROM %(track)s_cpc_result WHERE C_NC = 'coding'")
for i in ids:
if i in coding_set.keys():
if coding_set[i] == c:
result["coding"][c] += 1
for x, y in result["coding"].iteritems():
result["coding"][x] = (float(y)/total_c)*100
return result
def __call__(self, track, slice = None):
fn = os.path.join( DATADIR, "%(track)s.peakshape.tsv.gz.matrix_%(slice)s.gz" % locals() )
if not os.path.exists( fn ):
return
matrix, rownames, colnames = IOTools.readMatrix( IOTools.openFile( fn ))
nrows = len(rownames)
if nrows == 0: return
if nrows > 1000:
take = numpy.array( numpy.floor( numpy.arange( 0, nrows, nrows / 1000 ) ), dtype = int )
rownames = [ rownames[x] for x in take ]
matrix = matrix[ take ]
return odict( (('matrix', matrix),
('rows', rownames),
('columns', colnames)) )
def getReferenceLincRNA(self, reference_gtf):
lincs = []
for entry in GTF.iterator(IOTools.openFile(reference_gtf)):
if entry.source == "lincRNA":
if entry.gene_id not in lincs:
lincs.append(entry.gene_id)
return len(lincs)
def getReferenceLincRNA(self, reference_gtf):
lincs = []
for entry in GTF.iterator(IOTools.openFile(reference_gtf)):
if entry.source == "lincRNA":
if entry.gene_id not in lincs:
lincs.append(entry.gene_id)
return len(lincs)
def __call__(self,track, slice = None):
transcript_counts = collections.defaultdict( set )
counts = []
for gtf in GTF.iterator(IOTools.openFile(self.getFilename(track))):
transcript_counts[gtf.gene_id].add(gtf.transcript_id)
for gene, transcripts in transcript_counts.iteritems():
counts.append(len(transcripts))
return counts
def checkBlastRuns( infiles, outfile ):
'''check if output files are complete.
'''
outf = IOTools.openFile( outfile, "w" )
outf.write( "chunkid\tquery_first\tquery_last\tfound_first\tfound_last\tfound_total\tfound_results\thas_finished\tattempts\t%s\n" %\
"\t".join(Logfile.RuntimeInformation._fields))
for infile in infiles:
E.debug( "processing %s" % infile)
chunkid = P.snip( os.path.basename( infile ), ".blast.gz" )
logfile = infile + ".log"
chunkfile = P.snip( infile, ".blast.gz" ) + ".fasta"
with IOTools.openFile( infile ) as inf:
l = inf.readline()
ids = set()
total_results = 0
for l in inf:
if l.startswith("#//"): continue
ids.add( int(l.split("\t")[0] ) )
total_results += 1
found_first = min(ids)
found_last = max(ids)
found_total = len(ids)
l = IOTools.getFirstLine( chunkfile )
query_first = l[1:-1]
l2 = IOTools.getLastLine( chunkfile, nlines = 2).split("\n")
query_last = l2[0][1:]
logresults = Logfile.parse( logfile )
outf.write( "\t".join( map(str, (\
chunkid, query_first, query_last,
found_first, found_last,
found_total, total_results,
logresults[-1].has_finished,
len(logresults),
"\t".join( map(str, logresults[-1]) ) ) ) ) + "\n" )
outf.close()
def __call__(self, track, slice = None):
pattern = self.pattern
fn = os.path.join( DATADIR, "liver_vs_testes/%(track)s%(pattern)s.matrix_%(slice)s.gz" % locals() )
if not os.path.exists( fn ):
return
x = IOTools.openFile( fn )
matrix, rownames, colnames = IOTools.readMatrix( x )
nrows = len(rownames)
if nrows == 0: return
if nrows > self.scale:
take = numpy.array( numpy.floor( numpy.arange( 0, nrows, float(nrows + 1) / self.scale ) ), dtype = int )
rownames = [ rownames[x] for x in take ]
matrix = matrix[ take ]
return odict( (('matrix', matrix),
('rows', rownames),
('columns', colnames)) )
def __call__(self, track, slice = None):
if slice == "transcript":
lengths_transcripts = []
for transcript in GTF.transcript_iterator(GTF.iterator(IOTools.openFile(self.getFilename(track)))):
length = sum([gtf.end - gtf.start for gtf in transcript])
lengths_transcripts.append(length)
counts, lower, dx, _ = scipy.stats.cumfreq(lengths_transcripts, numbins=40, defaultreallimits=(0,20000))
x = np.arange(counts.size) * dx + lower
return odict( (("length", x), ("cumulative frequency", counts/len(lengths_transcripts))) )
elif slice == "gene":
lengths_genes = []
for gene in GTF.flat_gene_iterator(GTF.iterator(IOTools.openFile(self.getFilename(track)))):
length = sum([gtf.end - gtf.start for gtf in gene])
lengths_genes.append(length)
counts, lower, dx, _ = scipy.stats.cumfreq(lengths_genes, numbins=40, defaultreallimits=(0,20000))
x = np.arange(counts.size) * dx + lower
return odict( (("length", x), ("cumulative frequency", counts/len(lengths_genes))) )
def __call__(self,track, slice = None):
transcript_counts = collections.defaultdict( set )
counts = []
for gtf in GTF.iterator(IOTools.openFile(self.getFilename(track))):
transcript_counts[gtf.gene_id].add(gtf.transcript_id)
for gene, transcripts in transcript_counts.iteritems():
counts.append(len(transcripts))
count, lower, dx, _ = scipy.stats.cumfreq(counts, numbins=40, defaultreallimits=(1,15))
x = np.arange(count.size) * dx + lower
return odict( (("transcript number", x), ("cumulative frequency", count/len(counts))) )
def buildNrdb50( infile, outfile ):
'''build nrdb50
Renumber seqences.'''
outf_fasta = IOTools.openFile( outfile, "w" )
outf_table = IOTools.openFile( outfile + ".tsv", "w" )
outf_table.write("nid\tpid\thid\tdescription\tcluster_size\ttaxon\trepid\n" )
rx = re.compile( "(\S+) (.*) n=(\d+) Tax=(.*) RepID=(\S+)" )
nid = 1
for entry in FastaIterator.iterate( IOTools.openFile( infile )):
outf_fasta.write(">%i\n%s\n" % (nid, entry.sequence ) )
cluster_name, description, cluster_size, taxon, repid = rx.match( entry.title ).groups()
hid = computeHID( entry.sequence )
outf_table.write( "\t".join( (str(nid), cluster_name, hid, description, cluster_size, taxon, repid)) + "\n" )
nid += 1
outf_fasta.close()
outf_table.close()
def getNumColumns( filename ):
'''return number of fields in bed-file by looking at the first
entry.
Returns 0 if file is empty.
'''
with IOTools.openFile( filename ) as inf:
for line in inf:
if line.startswith("#"): continue
if line.startswith("track"): continue
return len(line[:-1].split("\t"))
return 0
def testMCL(self):
tab_path = Path('./tab.txt')
ival = 30
pival = 18
df_chr, sample_list = LoadInput.loadToPandas('testdata2.hdf',
'testdata2.tsv',
'A',
filter=False)
sections = [[1, 2, 3, 4, 5, 6, 7, 8, 9]]
pool = Pool(initializer=pc.mclInit,
initargs=(sample_list, tab_path, ival, pival))
IOTools.writeTab(sample_list, 'tab.txt')
clusters = pool.map(
pc.mclWorker,
[df_chr.loc[(slice(None), section), :] for section in sections],
chunksize=10)
expected = [[['A', 'B', 'C']]]
assert clusters == expected
def getNumColumns(filename):
'''return number of fields in bed-file by looking at the first
entry.
Returns 0 if file is empty.
'''
with IOTools.openFile(filename) as inf:
for line in inf:
if line.startswith("#"): continue
if line.startswith("track"): continue
return len(line[:-1].split("\t"))
return 0
def checkBlastRun( infiles, outfile ):
'''build summary stats on file.'''
pairsdbfile, seqfile = infiles
nids = set()
with IOTools.openFile( seqfile ) as inf:
for r in FastaIterator.iterate( inf ):
nids.add( int(r.title) )
with IOTools.openFile( pairsdbfile ) as inf:
query_ids, sbjct_ids = set(), set()
total_results, self_links = 0, 0
for l in inf:
l = inf.readline()
if l.startswith("#//"): continue
query_id, sbjct_id = l.split("\t")[:2]
query_ids.add( int(query_id) )
sbjct_ids.add( int(sbjct_id) )
if query_id == sbjct_id: self_links += 1
total_results += 1
outf = IOTools.openFile( outfile, "w" )
outf.write( "category\tcounts\n")
outf.write( "\t".join( map(str, ('nids', len(nids)))) + "\n" )
outf.write( "\t".join( map(str, ('links', total_results))) + "\n" )
outf.write( "\t".join( map(str, ('self', self_links))) + "\n" )
outf.write( "\t".join( map(str, ('queries', len(query_ids)))) + "\n" )
outf.write( "\t".join( map(str, ('sbjcts', len(sbjct_ids)))) + "\n" )
outf.close()
outf = IOTools.openFile( outfile + '.missing_queries.gz', 'w' )
outf.write( 'nid\n' )
outf.write( "\n".join( map(str, sorted( list( nids.difference( query_ids )) ) )) + "\n" )
outf.close()
outf = IOTools.openFile( outfile + '.missing_sbjcts.gz', 'w' )
outf.write( 'nid\n' )
outf.write( "\n".join( map(str, sorted( list( nids.difference( sbjct_ids )) ) )) + "\n" )
outf.close()
def collectGenomeSizes(infile, outfile):
'''
output the genome sizes for each genome
'''
to_cluster = True
outf = open(outfile, "w")
outf.write("genome\tlength\n")
# assume single fasta entry
for fasta in FastaIterator.iterate(IOTools.openFile(infile)):
name = P.snip(os.path.basename(infile), ".fna")
length = len(list(fasta.sequence))
outf.write("%s\t%s\n" % (name, str(length)))
outf.close()
def collectGenomeSizes(infile, outfile):
'''
output the genome sizes for each genome
'''
to_cluster = True
outf = open(outfile, "w")
outf.write("genome\tlength\n")
# assume single fasta entry
for fasta in FastaIterator.iterate(IOTools.openFile(infile)):
name = P.snip(os.path.basename(infile), ".fna")
length = len(list(fasta.sequence))
outf.write("%s\t%s\n" % (name, str(length)))
outf.close()
def buildPFAMFamilies( infiles, outfile ):
outf = IOTools.openFile( outfile, "w" )
outf.write( "family\tshort\tdescription\n" )
infile = infiles[1]
family, description, short = None, None, None
c = E.Counter()
with IOTools.openFile( infile ) as inf:
for line in inf:
if line.startswith( "#=GF AC"):
if family:
outf.write( "%s\n" % "\t".join( (family,description,short)))
c.output += 1
family = re.match("#=GF AC\s+(\S+)", line[:-1]).groups()[0]
elif line.startswith( "#=GF DE"):
description = re.match("#=GF DE\s+(.+)",line[:-1]).groups()[0]
elif line.startswith( "#=GF ID"):
short = re.match("#=GF ID\s+(.+)",line[:-1]).groups()[0]
outf.write( "%s\n" % "\t".join( (family,description,short)))
c.outptut += 1
outf.close()
E.info(c)
def buildAlignmentSizes(infiles, outfile):
'''
use bed files to sum the total number of bases
that are aligned to the genomes
'''
outf = open(outfile, "w")
outf.write("genome\tsize\n")
for infile in infiles:
genome = P.snip(os.path.basename(infile), ".bed.gz")
c = 0
inf = IOTools.openFile(infile)
for bed in Bed.iterator(inf):
c += bed.end - bed.start
outf.write("%s\t%s\n" % (genome, str(c)))
outf.close()
def buildAlignmentSizes(infiles, outfile):
'''
use bed files to sum the total number of bases
that are aligned to the genomes
'''
outf = open(outfile, "w")
outf.write("genome\tsize\n")
for infile in infiles:
genome = P.snip(os.path.basename(infile), ".bed.gz")
c = 0
inf = IOTools.openFile(infile)
for bed in Bed.iterator(inf):
c += bed.end - bed.start
outf.write("%s\t%s\n" % (genome, str(c)))
outf.close()
def removeBlastUnfinished( infiles, outfile ):
'''remove aborted blast runs.'''
deleted = 0
for infile in infiles:
line = IOTools.getLastLine( infile )
if not re.search( "job finished", line ):
fn = infile[:-len(".log")]
if os.path.exists( fn ):
P.info("deleting %s" % fn )
os.unlink( fn )
deleted += 1
P.info("deleted %i files" % deleted)
def buildMatrixFromTables( infiles, column, column_header = 0, dtype = numpy.float, default = None ):
'''build a matrix from a column called *column* in a series of input files.
If column_value == None, the first column is taken as the name of the row.
The columns are given by order of the input files.
returns matrix, row_headers
'''
lists = []
for infile in infiles:
data = pandas.read_table( IOTools.openFile(infile) )
lists.append( zip( list( data[column_header] ), list(data[column]) ) )
return buildMatrixFromLists( lists, dtype = dtype, default = default )
def __call__(self, track):
length = {}
for transcript in GTF.transcript_iterator(GTF.iterator(IOTools.openFile("gtfs/lncrna_filtered.gtf.gz"))):
length[transcript[0].transcript_id] = sum([gtf.end - gtf.start for gtf in transcript])
score = {}
dbh = sqlite3.connect("csvdb")
cc = dbh.cursor()
for data in cc.execute("SELECT transcript_id, CP_score FROM lncrna_filtered_cpc_result"):
score[data[0]] = data[1]
result = {"length": [], "score": []}
for transcript, value in length.iteritems():
result["length"].append(np.log10(length[transcript]))
result["score"].append(score[transcript])
return result
def buildTrueTaxonomicRelativeAbundances(infile, outfile):
'''
get species level relative abundances for the simulateds
data. This involes creating maps between different identifiers
from the NCBI taxonomy. This is so that the results are comparable
to species level analysis from metaphlan
The gi_taxid_nucl is a huge table and therefore this function
takes an age to run - can think of optimising this somehow
'''
to_cluster = True
total = 0
rel_abundance = collections.defaultdict(int)
for fastq in Fastq.iterate(IOTools.openFile(infile)):
total += 1
gi = fastq.identifier.split("|")[1]
rel_abundance[gi] += 1
for gi, ab in rel_abundance.items():
rel_abundance[gi] = float(ab) / total
dbh = sqlite3.connect(PARAMS["database"])
cc = dbh.cursor()
result = collections.defaultdict(float)
for gi in list(rel_abundance.keys()):
E.info("processing gi %s" % gi)
taxid = cc.execute(
"""SELECT taxid FROM gi_taxid_nucl WHERE gi == '%s'""" %
gi).fetchone()[0]
species_id = cc.execute(
"""SELECT species_id FROM categories WHERE taxid == '%s'""" %
taxid).fetchone()[0]
species_name = cc.execute(
"""SELECT taxname FROM names WHERE taxid == '%s' AND description == 'scientific name'"""
% species_id).fetchone()[0]
abundance = rel_abundance[gi]
E.info("mapped gi %s to taxid: %s, species_id: %s, species_name: %s" %
(str(gi), str(taxid), str(species_id), species_name))
result[species_name] += abundance
outf = open(outfile, "w")
outf.write("species_name\trelab\n")
for species_name, abundance in result.items():
# create names consistent with metaphlan
species_name = species_name.replace(" ", "_")
outf.write("%s\t%f\n" % (species_name, abundance))
outf.close()
def buildMatrixFromTables(infiles,
column,
column_header=0,
dtype=numpy.float,
default=None):
'''build a matrix from a column called *column* in a series of input files.
If column_value == None, the first column is taken as the name of the row.
The columns are given by order of the input files.
returns matrix, row_headers
'''
lists = []
for infile in infiles:
data = pandas.read_table(IOTools.openFile(infile))
lists.append(zip(list(data[column_header]), list(data[column])))
return buildMatrixFromLists(lists, dtype=dtype, default=default)
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv: argv = sys.argv
# setup command line parser
parser = optparse.OptionParser( version = "%prog version: $Id: script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage = globals()["__doc__"] )
## add common options (-h/--help, ...) and parse command line
(options, args) = E.Start( parser, argv = argv )
coords_file=args[0]
bamfile=pysam.Samfile( args[1], 'rb' ) # bamfile
options.stdout.write( "gene_id\tcounts\tlength\n" )
iter = Bed.iterator( IOTools.openFile( coords_file ) )
for gene_id, exons in itertools.groupby( iter, lambda x: x.name ):
num_reads=0
anames=set([])
lgene = 0
for bed in exons:
lgene += bed.end - bed.start
for alignedread in bamfile.fetch(bed.contig, bed.start, bed.end):
anames.add((alignedread.qname, alignedread.is_read1))
num_reads = len(anames)
options.stdout.write( "\t".join( (gene_id,
str(num_reads),
str(lgene ) )) + "\n" )
## write footer and output benchmark information.
E.Stop()
def iterator_sorted( gff_iterator, sort_order = "gene" ):
'''sort input and yield sorted output.'''
entries = list(gff_iterator)
if sort_order == "gene":
entries.sort( key = lambda x: (x.gene_id, x.transcript_id, x.contig, x.start) )
elif sort_order == "gene":
entries.sort( key = lambda x: (x.gene_id, x.contig, x.start) )
elif sort_order == "contig+gene":
entries.sort( key = lambda x: (x.contig,x.gene_id,x.transcript_id,x.start) )
elif sort_order == "transcript":
entries.sort( key = lambda x: (x.transcript_id, x.contig, x.start) )
elif sort_order == "position":
entries.sort( key = lambda x: (x.contig, x.start) )
elif sort_order == "position+gene":
entries.sort( key = lambda x: (x.gene_id, x.start) )
genes = list( flat_gene_iterator(entries) )
genes.sort( key = lambda x: (x[0].contig, x[0].start) )
entries = IOTools.flatten( genes )
for entry in entries:
yield entry
def buildTrueTaxonomicRelativeAbundances(infile, outfile):
'''
get species level relative abundances for the simulateds
data. This involes creating maps between different identifiers
from the NCBI taxonomy. This is so that the results are comparable
to species level analysis from metaphlan
The gi_taxid_nucl is a huge table and therefore this function
takes an age to run - can think of optimising this somehow
'''
to_cluster = True
total = 0
rel_abundance = collections.defaultdict(int)
for fastq in Fastq.iterate(IOTools.openFile(infile)):
total += 1
gi = fastq.identifier.split("|")[1]
rel_abundance[gi] += 1
for gi, ab in rel_abundance.iteritems():
rel_abundance[gi] = float(ab)/total
dbh = sqlite3.connect(PARAMS["database"])
cc = dbh.cursor()
result = collections.defaultdict(float)
for gi in rel_abundance.keys():
E.info("processing gi %s" % gi)
taxid = cc.execute("""SELECT taxid FROM gi_taxid_nucl WHERE gi == '%s'""" % gi).fetchone()[0]
species_id = cc.execute("""SELECT species_id FROM categories WHERE taxid == '%s'""" % taxid).fetchone()[0]
species_name = cc.execute("""SELECT taxname FROM names WHERE taxid == '%s' AND description == 'scientific name'""" % species_id).fetchone()[0]
abundance = rel_abundance[gi]
E.info("mapped gi %s to taxid: %s, species_id: %s, species_name: %s" % (str(gi), str(taxid), str(species_id), species_name))
result[species_name] += abundance
outf = open(outfile, "w")
outf.write("species_name\trelab\n")
for species_name, abundance in result.iteritems():
# create names consistent with metaphlan
species_name = species_name.replace(" ", "_")
outf.write("%s\t%f\n" % (species_name, abundance))
outf.close()
def iterator_sorted(gff_iterator, sort_order="gene"):
'''sort input and yield sorted output.'''
entries = list(gff_iterator)
if sort_order == "gene":
entries.sort(
key=lambda x: (x.gene_id, x.transcript_id, x.contig, x.start))
elif sort_order == "gene":
entries.sort(key=lambda x: (x.gene_id, x.contig, x.start))
elif sort_order == "contig+gene":
entries.sort(
key=lambda x: (x.contig, x.gene_id, x.transcript_id, x.start))
elif sort_order == "transcript":
entries.sort(key=lambda x: (x.transcript_id, x.contig, x.start))
elif sort_order == "position":
entries.sort(key=lambda x: (x.contig, x.start))
elif sort_order == "position+gene":
entries.sort(key=lambda x: (x.gene_id, x.start))
genes = list(flat_gene_iterator(entries))
genes.sort(key=lambda x: (x[0].contig, x[0].start))
entries = IOTools.flatten(genes)
for entry in entries:
yield entry
#######################################################################
## retrieve structure
if options.filename_pdb:
infile = open(options.filename_pdb, "r")
pdb_lines = infile.readlines()
infile.close()
else:
pdb_lines = os.popen(param_retrieval_command %
string.lower(param_pdb_id)).readlines()
viewer = PdbTools.RasmolViewInline(pdb_lines, sys.stdout)
viewer.Command("echo %s" % message)
if options.filename_fasta:
infile = open(options.filename_fasta, "r")
description, reference_sequence = IOTools.readSequence(infile)
infile.close()
else:
reference_sequence = None
if DEBUG:
viewer.Command("echo cmdline: %s" % (string.join(sys.argv, " ")))
if not pdb_lines:
viewer.Command("echo error: structure not found in local database")
viewer.WriteScript()
sys.exit()
if reference_sequence:
map_pdb2seq, rmap_pdb2seq, rmap_seq2pdb, lstructure, first_residue, last_residue, sequence = PdbTools.buildMapPdb2Sequence(
reference_sequence, options.filename_pdb, options,
#python ..\ChromatinImagingV2\Scripts\BatchAllnew.py
import sys, os
#add path
workbookDir = os.getcwd()
sys.path.append(os.path.dirname(workbookDir) + os.sep + r'\CommonTools')
import IOTools as io
if __name__ == "__main__":
script = r'"' + workbookDir + os.sep + r'BatchSequentialSmall2colV3.py"'
str_runs = []
for i in range(10):
str_runs.append('python ' + script + ' ' + str(i))
io.batch_command(str_runs, batch_size=10)
dest="dump",
action="store_true",
help="dump output.")
parser.set_defaults(
separator="|",
dump=False,
filename_map=None,
filename_alignment="-",
filename_tree=None,
)
(options, args) = E.Start(parser)
if options.filename_map:
map_species2sp = IOTools.ReadMap(open(options.filename_map, "r"))
E.debug("species map: %s" % str(map_species2sp))
identifier_parser = IdentifierParserGPipe(map_species2sp=map_species2sp)
njtree = NJTree(identifier_parser=identifier_parser)
njtree.SetLog(options.stdlog)
njtree.SetErr(options.stderr)
if options.filename_tree:
njtree.SetSpeciesTree(options.filename_tree)
mali = Mali.Mali()
if options.filename_alignment == "-":
def main(argv=None):
parser = E.OptionParser(
version=
"%prog version: $Id: CBioPortal.py 2888 2012-06-07 15:52:00Z ians $",
usage=globals()["__doc__"])
parser.add_option(
"-o",
"--output_file",
type="string",
default=None,
help="[Optional] Filename to output results to. [default=STDOUT]")
parser.add_option(
"-u",
"--url",
type="string",
default="http://www.cbioportal.org/public-portal/webservice.do",
help="[Optional] Url to the cBioPortal webservice [default=%default]")
cqueryopts = optparse.OptionGroup(parser, "Common parameters",
"Common arguments to the query")
cqueryopts.add_option(
"-s",
"--study_id",
dest="study_id",
type="string",
default=None,
help=
"[Required/OPtional] cBioPortal ID for study [default=%default].\n This or study_name required for: getGeneticProfiles, getCaseLists, getProteinArrayInfo, getLink,getOncoprintHTML, getPercentAltered, getTotalAltered"
)
cqueryopts.add_option(
"-n",
"--study_name",
dest="study_name",
type="string",
default=None,
help=
"[Required/Optional] cBioPortal Name for study [defualt=%default].\n See above for which commands require this."
)
cqueryopts.add_option(
"-c",
"--case_set_id",
dest="case_set_id",
type="string",
default=None,
help=
"[Required for some] cBioPortal case_set_id specifying the case list to use.\nRequired for getProfileData, getMutationData, getClincalData, getProteinArrayData, getPercentAltered, getTotalAltered. Default is case_set_id for case list 'All Tumours' "
)
cqueryopts.add_option(
"-g",
"--gene_list",
dest="gene_list",
type="string",
default=None,
help=
"[Required for some] Comma seperated list of HUGO gene symbols or Entrez gene IDs.\nRequired for getProfileData, getMutationData, getLink, getOncoprintHTML"
)
cqueryopts.add_option("-f",
"--gene_list_file",
dest="gene_list_file",
type="string",
default=None,
help="[Optional] Filename to read in gene_list from")
cqueryopts.add_option(
"-p",
"--profile_id",
dest="profile_id",
type="string",
help=
"[Optional] Comma seperated list of cBioPortal genetic_profile_ids. If none are specified then the list of profiles for the study where display in analysis is True is used."
)
squeryopts = optparse.OptionGroup(
parser, "Query specific parameters",
"Arguments specific to a particular query")
squeryopts.add_option(
"--protein_array_type",
dest="protein_array_type",
type="string",
default="protein_level",
help=
"[Optional] Either protein_level or phosphorylation [default=%default]"
)
squeryopts.add_option(
"--protein_array_id",
dest="protein_array_id",
type="string",
help=
"[Required for some] comma seperated list of one or more protein array IDs"
)
squeryopts.add_option(
"--array_info",
dest="protein_array_info",
type="int",
default=0,
help=
"[Optional] If 1, antibody infomation will also be exported in a getProteinArrayData query [default=%default]"
)
squeryopts.add_option(
"--report",
dest="report",
type="string",
default="full",
help=
"[Optional] Report type to display for getLink. Either full or oncoprint_html [default=%default] "
)
squeryopts.add_option(
"--threshold",
dest="threshold",
type="int",
default=2,
help=
"[Optional] Threshold for deciding if an alteration is significant for continuous metrics [default=%default]"
)
parser.add_option_group(cqueryopts)
parser.add_option_group(squeryopts)
(options, args) = E.Start(parser,
add_pipe_options=False,
add_output_options=False,
argv=argv)
portal = CBioPortal(url=options.url,
study=options.study_id,
study_name=options.study_name,
case_list_id=options.case_set_id)
results = []
if options.gene_list_file:
infile = IOTools.openFile(options.gene_list_file)
gene_list = [x.strip() for x in infile]
elif options.gene_list:
gene_list = options.gene_list.split(",")
if options.profile_id:
profile_id = options.profile_id.split(",")
else:
profile_id = None
if "getCancerStudies" in args:
results.append(portal.getCancerStudies())
if "getGeneticProfiles" in args:
results.append(portal.getGeneticProfiles())
if "getCaseLists" in args:
results.append(portal.getCaseLists())
if "getProfileData" in args:
results.append(
portal.getProfileData(gene_list=gene_list,
genetic_profile_id=profile_id))
if "getMutationData" in args:
results.append(
portal.getMutationData(gene_list=gene_list,
genetic_profile_id=profile_id))
if "getClinicalData" in args:
results.append(portal.getClinicalData())
if "getProteinArrayInfo" in args:
results.append(
portal.getProteinArrayInfo(
gene_list=gene_list,
protein_array_type=options.protein_array_type))
if "getProteinArrayData" in args:
results.append(
portal.getProteinArrayData(
protein_array_id=options.protein_array_id,
array_info=options.array_info))
if "getPercentAltered" in args:
results.append(
portal.getPercentAltered(gene_list=gene_list,
genetic_profile_id=profile_id,
threshold=options.threshold))
if "getLink" in args:
results.append(
portal.getLink(gene_list=gene_list, report=options.report))
if "getOncoprintHTML" in args:
results.append(portal.getOncoprintHTML(gene_list=gene_list))
if len(results) == 0:
sys.stderr.write("No recognised query commands provided")
sys.exit()
if options.output_file:
outf = IOTools.openFile(options.output_file, "w")
else:
outf = sys.stdout
for result in results:
try:
outf.write(tableToString(result))
except:
outf.write(result)
E.Stop()
def main(config_file_path):
#config loading
var_list = ['base_directory', 'organism', 'input_type', 'file_name', 'section_length', 'S1_iVal', 'S1_piVal', 'S2_iVal', 'S2_piVal', \
'reference', 'optimize']
config_file_path = sys.argv[1]
config = configparser.SafeConfigParser()
config.read(config_file_path)
#setup
start_time = time.time()
#Settings
try:
output_directory = Path(config.get('Settings', 'output_directory'))
input_path = Path(config.get('Settings', 'input_path'))
prefix = input_path.parts[-1].split('.')[0]
#set these according to config info
s1_params = pw.ParamWrapper()
s2_params = pw.ParamWrapper()
s1_params.setSectionLength(config.getint('Settings', 'section_length'))
s1_params.setIVal(config.getfloat('Settings', 'S1_iVal'))
s1_params.setPiVal(config.getfloat('Settings', 'S1_piVal'))
s2_params.setIVal(config.getfloat('Settings', 'S2_iVal'))
s2_params.setPiVal(config.getfloat('Settings', 'S2_piVal'))
#set stuff for autogroup
s2_params.setIMax(10)
s2_params.setIMin(2)
s2_params.setIStep(0.5)
s2_params.setPiMax(10)
s2_params.setPiMin(1)
s2_params.setPiStep(0.5)
reference = config.get('Settings', 'reference')
autogroup = bool(config.getboolean('Settings', 'autogroup'))
except:
raise RuntimeError('Error reading configuration file')
#output paths
if not output_directory.is_dir():
output_directory.mkdir()
os.chdir(output_directory)
cytoscape_path = Path("{0}.xgmml".format(prefix))
json_path = Path("{0}.json".format(prefix))
tab_network_path = Path("chromosome_paintings.tsv")
matrixout_path = Path("overall_similarity.tsv")
heatmaps_path = Path("heatmaps.pdf")
density_path = Path("density.txt")
group_path = Path("groups.txt")
tab_path = Path("tab.txt")
colorout_path = Path("colors.txt")
log_path = Path("log.txt")
nn_out_path = Path("{0}_nn.tsv".format(prefix))
hdf_path = input_path.parent / '{0}.h5'.format(prefix)
matrices_hdf_path = input_path.parent / '{0}_matrices.h5'.format(prefix)
save_state_path = input_path.parent / '{0}_savestate.json'.format(prefix)
#other variables
logger = configLogger(log_path)
#sanitize input
try:
assert (input_path.is_file())
assert (0 <= s1_params.getPiVal() <= 20)
assert (0 <= s1_params.getIVal() <= 20)
assert (0 <= s2_params.getPiVal() <= 20)
assert (0 <= s2_params.getIVal() <= 20)
except:
raise ValueError('Configuration file contains bad values')
#let's log some params used later
logger.info('config loaded')
#Input Processing
#true means need to cluster
if not io.checkPrimaryClustering(s1_params, save_state_path):
logger.info('Primary Clustering exists, loading existing matrices')
save_state, matrices = io.loadSaveState(save_state_path,
matrices_hdf_path)
sample_list = save_state['sample_list']
chr_names = save_state['chr_names']
chr_breaks = save_state['chr_breaks']
io.writeTab(sample_list, tab_path)
else:
#tabular data from GTAK loaded to pandas
df, sample_list = loadToPandas(hdf_path, input_path, reference,
s1_params, True)
os.chdir(output_directory)
logger.info('Start Primary Clustering')
io.writeTab(sample_list, tab_path)
#TODO: check for whether we're skipping primary clustering
clusters, chr_names, chr_breaks = primaryCluster(
df, sample_list, s1_params, logger)
genNNData(clusters, chr_names, chr_breaks, s1_params, sample_list,
nn_out_path)
io.writePrimaryClusters(chr_names, chr_breaks, clusters,
Path('pclusters.txt'))
matrices = at.clustersToMatrix(clusters, sample_list)
logger.info('Writing Save State')
io.writeSaveState(s1_params, sample_list, chr_names, chr_breaks,
matrices, save_state_path, matrices_hdf_path)
overall_matrix = at.overallMatrix(matrices)
logger.info('Start Secondary Clustering')
group_names, overall_clusters = sc.group(overall_matrix, tab_path,
group_path, s2_params, logger,
autogroup)
color_table = at.createColorTable(group_names, overall_clusters,
sample_list)
color_table.to_csv(colorout_path)
logger.info('calculating composition')
condensed_matrices = gc.condenseToGroupMatrix(matrices, group_names,
overall_clusters,
sample_list)
composition = gc.getChromosomePaintings(condensed_matrices, chr_breaks,
overall_clusters, group_names,
sample_list)
# for the whole thing
logger.info('writing output')
io.writeTabularPainting(composition, chr_names,
s1_params.getSectionLength(), sample_list,
tab_network_path)
io.writeOverallMatrix(overall_matrix, matrixout_path)
exporter.parse(overall_matrix, color_table, composition, group_names,
overall_clusters, sample_list, prefix)
print("PopNet Completed")
print('Run time was {0} seconds'.format(time.time() - start_time))
-1] #zxy coords of chromosomes already in the right position
#Decide where to save the candidate positions of the hybe
fl_cands = analysis_folder + os.sep + file_.replace(
'.dax', '__current_cand.pkl') #file where to save candidates
fl_cor = analysis_folder + os.sep + file_.replace(
'.dax', '__drift.pkl') #file where to save drift correction
fl_cor_fls = analysis_folder + os.sep + file_.replace(
'.dax', '__driftfiles.npy')
print fl_cands
candid_spot = {}
#load data (pseudo-memory mapping)
daxs_signal, names_signal, daxs_beads, names_beads = io.get_ims_fov_daxmap(
folders_keep, file_, col_tags=None, pad=10)
#compute the drift for the field of view
if len(daxs_beads) > 1:
txyz_both, _ = ft.get_STD_beaddrift_v2(daxs_beads,
sz_ex=sz_ex,
hseed=hseed_beads,
nseed=nbeads,
ref=None,
force=force_drift,
save_file=fl_cor)
txyz = np.mean(txyz_both, 1)
txyz = np.array(txyz) - [txyz[ref]]
np.save(fl_cor_fls, np.array(folders_keep))
#repeat for colors
#num_col = int(len(daxs_signal)/len(daxs_beads))
#iterate through folders
headers, titles, sets = [], [], []
if options.headers:
if options.headers == "-":
headers = args
else:
headers = options.headers.split(",")
if len(headers) != len(args):
raise ValueError(
"please supply the same number of headers as there are filenames."
)
for f in args:
if options.with_title:
title, data = IOTools.readList(open(f, "r"),
with_title=options.with_title)
titles.append(title)
else:
data = IOTools.readList(open(f, "r"))
sets.append(set(data))
if not headers and titles:
headers = titles
else:
headers = args
for x in range(len(sets) - 1):
set1 = sets[x]
for y in range(x + 1, len(sets)):
set2 = sets[y]
def buildSCOPDomains( infiles, outfile ):
'''reconcile mapped domains into a single domain file.
* fragments are removed - a domain must map at least 90%
of its length.
* domains overlapping on the same sequence with the same
superfamily classification are merged.
'''
linksfile, fastafile = infiles
# filtering criteria
min_coverage = 0.9
# only take first four fold classes
classes = 'abcd'
rx = re.compile('(\S+)\s(\S+)\s(.*)' )
id2class = {}
with IOTools.openFile( fastafile ) as inf:
for x in FastaIterator.iterate( inf ):
pid, cls, description = rx.match(x.title).groups()
id2class[pid] = (cls, len(x.sequence) )
E.info('read mappings for %i sequences' % len(id2class))
counter = E.Counter()
with IOTools.openFile( linksfile ) as inf:
nid2domains = collections.defaultdict( list )
ndomains = 0
for line in inf:
if line.startswith('query_nid'): continue
if line.startswith('#'): continue
counter.links += 1
domain_id, nid, evalue, domain_start, domain_end, sbjct_start, sbjct_end, \
block_sizes, domain_starts, sbjct_starts, \
bitscore, pid = line[:-1].split()
nid, domain_start, domain_end, sbjct_start, sbjct_end = map(int, \
( nid, domain_start, domain_end, sbjct_start, sbjct_end ))
family, length = id2class[domain_id]
cls, fold, superfamily, family = family.split('.')
if cls not in classes: continue
if float(domain_end - domain_start) / length < min_coverage: continue
counter.unmerged_domains += 1
superfamily = '00%c%03i%03i' % (cls, int(fold), int(superfamily))
nid2domains[nid].append( (superfamily, sbjct_start, sbjct_end ) )
counter.sequences = len(nid2domains)
E.info( 'merging %i domains in %i sequences' % (counter.unmerged_domains, counter.sequences))
outf = IOTools.openFile( outfile, 'w' )
outf.write('nid\tstart\tend\tfamily\n')
for nid, dd in sorted(nid2domains.iteritems()):
for family, domains in itertools.groupby( dd, key = lambda x: x[0] ):
unmerged_domains = [ (x[1],x[2]) for x in domains ]
merged_domains = Intervals.combine( unmerged_domains )
for start, end in merged_domains:
counter.domains += 1
outf.write( '%i\t%i\t%i\t%s\n' % (nid, start, end, family ) )
outf.close()
E.info( counter )
def testOutPut(self):
overall = pd.DataFrame([[2, 0, 2], [0, 2, 0], [2, 0, 2]],
columns=['A', 'B', 'C'],
index=['A', 'B', 'C'])
io.writeOverallMatrix(overall, 'zzz.txt')
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if not argv: argv = sys.argv
# setup command line parser
parser = E.OptionParser(
version=
"%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-f",
"--input-format",
dest="input_format",
type="choice",
choices=("bed", "bam"),
help="input file format [default=%default].")
parser.add_option("-u",
"--ucsc-genome",
dest="ucsc_genome",
type="string",
help="UCSC genome identifier [default=%default].")
parser.add_option("-g",
"--genome-file",
dest="genome_file",
type="string",
help="filename with genome [default=%default].")
parser.add_option("-e",
"--extension",
dest="extension",
type="int",
help="extension size [default=%default].")
parser.add_option("-b",
"--bin-size",
dest="bin_size",
type="int",
help="bin size of genome vector [default=%default].")
parser.add_option("-l",
"--fragment-length",
dest="fragment_length",
type="int",
help="bin size of genome vector [default=%default].")
parser.add_option(
"-s",
"--saturation-iterations",
dest="saturation_iterations",
type="int",
help="iterations for saturation analysis [default=%default].")
parser.add_option("-t",
"--toolset",
dest="toolset",
type="choice",
action="append",
choices=("saturation", "coverage", "rms", "rpm", "all"),
help="actions to perform [default=%default].")
parser.add_option(
"-w",
"--bigwig",
dest="bigwig",
action="store_true",
help=
"store wig files as bigwig files - requires a genome file [default=%default]"
)
parser.set_defaults(
input_format="bam",
ucsc_genome="hg19",
genome_file=None,
extension=400,
bin_size=50,
saturation_iterations=10,
fragment_length=700,
toolset=[],
bigwig=False,
)
## add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv, add_output_options=True)
if len(args) != 1:
raise ValueError("please specify a filename with sample data")
if options.bigwig and not options.genome_file:
raise ValueError("please provide a genome file when outputting bigwig")
if options.genome_file:
fasta = IndexedFasta.IndexedFasta(options.genome_file)
contig_sizes = fasta.getContigSizes()
filename_sample = args[0]
if len(options.toolset) == 0: options.toolset = ["all"]
do_all = "all" in options.toolset
# load MEDIPS
R.library('MEDIPS')
genome_file = 'BSgenome.Hsapiens.UCSC.%s' % options.ucsc_genome
R.library(genome_file)
tmpdir = tempfile.mkdtemp()
E.debug("temporary files are in %s" % tmpdir)
bin_size = options.bin_size
extension = options.extension
fragment_length = options.fragment_length
saturation_iterations = options.saturation_iterations
if options.input_format == "bam":
E.info("converting bam files")
filename_sample = bamToMEDIPS(filename_sample,
os.path.join(tmpdir, "sample.medips"))
elif options.input_format == "bed":
E.info("converting bed files")
filename_sample = bedToMEDIPS(filename_sample,
os.path.join(tmpdir, "sample.medips"))
E.info("loading data")
R('''CONTROL.SET = MEDIPS.readAlignedSequences(
BSgenome = "%(genome_file)s",
file = "%(filename_sample)s" ) ''' % locals())
slotnames = (("extend", "extend",
"%i"), ("distFunction", "distance_function",
"%s"), ("slope", "slope", "%f"),
("fragmentLength", "fragment_length",
"%i"), ("bin_size", "bin_size",
"%i"), ("seq_pattern", "pattern",
"%s"), ("number_regions", "nregions", "%i"),
("number_pattern", "npatterns",
"%i"), ("cali_chr", "calibration_contig",
"%s"), ("genome_name", "genome", "%s"))
E.info("computing genome vector")
R('''CONTROL.SET = MEDIPS.genomeVector(data = CONTROL.SET,
bin_size = %(bin_size)i,
extend=%(extension)i )''' % locals())
E.info("computing CpG positions")
R('''CONTROL.SET = MEDIPS.getPositions(data = CONTROL.SET, pattern = "CG")'''
)
E.info("compute coupling vector")
R('''CONTROL.SET = MEDIPS.couplingVector(data = CONTROL.SET,
fragmentLength = %(fragment_length)i,
func = "count")''' % locals())
E.info("compute calibration curve")
R('''CONTROL.SET = MEDIPS.calibrationCurve(data = CONTROL.SET)''')
E.info("normalizing")
R('''CONTROL.SET = MEDIPS.normalize(data = CONTROL.SET)''')
outfile = IOTools.openFile(E.getOutputFile("summary.tsv.gz"), "w")
outfile.write("category\tvalue\n")
if "saturation" in options.toolset or do_all:
E.info("saturation analysis")
R('''sr.control = MEDIPS.saturationAnalysis(data = CONTROL.SET,
bin_size = %(bin_size)i,
extend = %(extension)i,
no_iterations = %(saturation_iterations)i,
no_random_iterations = 1)''' % locals())
R.png(E.getOutputFile("saturation.png"))
R('''MEDIPS.plotSaturation(sr.control)''')
R('''dev.off()''')
R('''write.csv( sr.control$estimation, file ='%s' )''' %
E.getOutputFile("saturation_estimation.csv"))
outfile.write("estimated_correlation\t%f\n" %
R('''sr.control$maxEstCor''')[1])
outfile.write("true_correlation\t%f\n" %
R('''sr.control$maxTruCor''')[1])
if "coverage" in options.toolset or do_all:
E.info("CpG coverage analysis")
R('''cr.control = MEDIPS.coverageAnalysis(data = CONTROL.SET,
extend = %(extension)i,
no_iterations = 10)''' % locals())
R.png(E.getOutputFile("cpg_coverage.png"))
R('''MEDIPS.plotCoverage(cr.control)''')
R('''dev.off()''')
# three rows
R('''write.csv( cr.control$coveredPos, file ='%s' )''' %
E.getOutputFile("saturation_coveredpos.csv"))
# coverage threshold
# number of CpG covered
# percentage of CpG covered
R('''write.csv( cr.control$matrix, file ='%s' )''' %
E.getOutputFile("saturation_matrix.csv"))
# R('''er.control = MEDIPS.CpGenrich(data = CONTROL.SET)''')
if "calibration" in options.toolset or do_all:
E.info("plotting calibration")
R.png(E.getOutputFile("calibration.png"))
R('''MEDIPS.plotCalibrationPlot(data = CONTROL.SET, linearFit = T, xrange=250)'''
)
R('''dev.off()''')
for slotname, label, pattern in slotnames:
value = tuple(R('''CONTROL.SET@%s''' % slotname))
if len(value) == 0: continue
outfile.write(
"%s\t%s\n" %
(label, pattern % tuple(R('''CONTROL.SET@%s''' % slotname))[0]))
outfile.close()
if "rpm" in options.toolset or do_all:
outputfile = E.getOutputFile("rpm.wig")
R('''MEDIPS.exportWIG(file = '%(outputfile)s', data = CONTROL.SET, raw = T, descr = "rpm")'''
% locals())
if options.bigwig:
bigwig(outputfile, contig_sizes)
else:
compress(outputfile)
if "rms" in options.toolset or do_all:
outputfile = E.getOutputFile("rms.wig")
R('''MEDIPS.exportWIG(file = '%(outputfile)s', data = CONTROL.SET, raw = F, descr = "rms")'''
% locals())
if options.bigwig:
bigwig(outputfile, contig_sizes)
else:
compress(outputfile)
shutil.rmtree(tmpdir)
## write footer and output benchmark information.
E.Stop()
