def TpedIterator(handle):
"""
Iterates on an TPed file handler.
Returns Marker objects.
>>> import tempfile
>>> sample_Tped_file = tempfile.TemporaryFile()
>>> sample_Tped_file.write('''
... # Chromosome Marker_Id ??? position locus1_allele1 locus1_allele2 locus2_allele1
... 4 rs10000543 0 30979886 C C T C
... 4 rs10000929 0 131516474 A A A A
... 4 rs10002472 0 159087423 A G G G
... ''')
>>> sample_Tped_file.seek(0)
>>> ti = TpedIterator(sample_Tped_file)
>>> for marker in ti:
... print marker
Marker rs10000543, 2 individuals
Marker rs10000929, 2 individuals
Marker rs10002472, 2 individuals
"""
for line in handle:
# if line.strip() == "":
# debug('premature end of file?')
# return
if line.startswith('#'):
comment = line
elif line.strip() == '':
# empy line, ignore
pass
else:
tped_fields = line.split()
if len(tped_fields) < 4:
raise InvalidInputFile('line too short - check input file\n("%s")' % line.strip())
# should check that current line has the same length than the previous
# should check that characters after [4] are rigth
chromosome = tped_fields[0]
marker_name = tped_fields[1]
unknown = tped_fields[2]
position = tped_fields[3]
current_marker = Marker(marker_name)
current_marker.position = "%s - chrom %s" % (position, chromosome)
logging.debug(current_marker)
genotypes = [(tped_fields[i], tped_fields[i+1]) for i in xrange(4, len(tped_fields), 2)]
logging.debug(genotypes)
current_marker.genotypes = genotypes
yield current_marker
def hgdpgenotypesParser(handle, individuals_filter = None, markers_filter = None):
"""
Parse a genotypes file handler.
It returns a Marker object for every line of the file
>>> from StringIO import StringIO
>>> genotypes_file = StringIO(
... ''' HGDP00001 HGDP00002 HGDP00003 HGDP00004 HGDP00005 HGDP00006 HGDP00007 HGDP00008 HGDP00009 HGDP000010
... rs1112390 AA GG AG AA AA AA AA AA AA AA
... rs1112391 TT TC CC CC CC CC CC CC CC CC
... MitoA11252G AA AA AA AA AA AA AA AA AA AA
... rs11124185 TC TT TT TT TT TT TT TT TT TT
... MitoA13265G AA AA AA AA AA AA AA AA AA AA
... MitoA13264G GG AA AA AA GG AG AA AA AA AA
... MitoA13781G AA AA AA AA AA AA -- AA AA AA
... MitoA14234G AA AA AA AA AA AA AA AA AA AA
... MitoA14583G AA AA AA AA AA AA AA AA AA AA
... MitoA14906G GG GG GG GG GG GG GG GG GG GG
... MitoA15219G AA AA AA GG AA AA AA AA AA AA''')
>>> individuals_filter = ['HGDP00001', 'HGDP00004', ]
>>> markers = hgdpgenotypesParser(genotypes_file, individuals_filter)
>>> print '\t' + '\t'.join(markers[0].individuals)
HGDP00001 HGDP00004
>>> for marker in markers:
... print marker.to_geno_format() #doctest: +NORMALIZE_WHITESPACE
rs1112390 AA AA
rs1112391 TT CC
MitoA11252G AA AA
rs11124185 TC TT
MitoA13265G AA AA
MitoA13264G GG AA
MitoA13781G AA AA
MitoA14234G AA AA
MitoA14583G AA AA
MitoA14906G GG GG
MitoA15219G AA GG
"""
# initialize output var
markers = []
# read the header, containing the Individuals names
# handle.readline() # first line is empty??
header = handle.readline()
if header is None:
raise ValueError('Empty file!!')
individuals = [Individual(ind_id) for ind_id in header.split()]
if individuals_filter is None: # TODO: ugly
individuals_filter = [ind.individual_id for ind in individuals]
columns_to_filter = []
for ind in header.split():
if ind in individuals_filter:
columns_to_filter.append(1)
else:
columns_to_filter.append(0)
# Read the remaining lines of genotypes file, containin genotypes info.
for line in handle.readlines():
fields = line.split() # TODO: add more rigorous conditions
if fields is None:
break
# Initialize a Genotype object
marker = Marker(name = fields[0], individuals = individuals_filter)
markers.append(marker)
for n in range(1, len(fields)):
current_individual = individuals[n-1]
if current_individual in individuals_filter: #TODO: this consumes CPU time
# if columns_to_filter[0] == 1:
current_genotype = fields[n]
marker.add_genotype(current_genotype)
# print current_individual
else:
pass
return markers
