def read_pe_values(lines):
"""read all combined p-values and e-values"""
result = []
current_index = next_pe_value_line(0, lines)
while current_index != -1:
gene = lines[current_index - 2].strip()
line = lines[current_index]
pvalue = float(util.extract_regex('P-VALUE\s+=\s+(\S+)', line))
evalue = float(util.extract_regex('E-VALUE\s+=\s+(\S+)', line))
result.append((gene, pvalue, evalue))
current_index = next_pe_value_line(current_index + 1, lines)
return result
def read_pe_values(lines):
"""read all combined p-values and e-values"""
result = []
current_index = next_pe_value_line(0, lines)
while current_index != -1:
gene = lines[current_index - 2].strip()
line = lines[current_index]
pvalue = float(util.extract_regex('P-VALUE\s+=\s+(\S+)', line))
evalue = float(util.extract_regex('E-VALUE\s+=\s+(\S+)', line))
result.append((gene, pvalue, evalue))
current_index = next_pe_value_line(current_index + 1, lines)
return result
def read_annotations(lines, genes):
"""extract annotations, genes are given as refseq ids"""
result = {}
current_index = next_pe_value_line(0, lines)
while current_index != -1:
gene = lines[current_index - 2].strip()
if gene in genes:
info_line = lines[current_index]
length = int(
util.extract_regex('LENGTH\s+=\s+(\d+)', info_line))
has_seqalign_block = True
diagram_match = re.match('^\s+DIAGRAM:\s+(\d+)$',
lines[current_index + 1])
if diagram_match is not None:
diagram = int(diagram_match.group(1))
if diagram == length:
has_seqalign_block = False
if has_seqalign_block:
# the diagram line can span several lines and the blank
# line after those can span several, so search for the
# first non-blank line after the block of blank lines
blank_index = current_index + 2
while len(lines[blank_index].strip()) > 0:
blank_index += 1
non_blank_index = blank_index + 1
while len(lines[non_blank_index].strip()) == 0:
non_blank_index += 1
result[gene] = read_seqalign_blocks(
lines, non_blank_index, length)
current_index = next_pe_value_line(current_index + 1, lines)
return result
def read_annotations(lines, genes):
"""extract annotations, genes are given as refseq ids"""
result = {}
current_index = next_pe_value_line(0, lines)
while current_index != -1:
gene = lines[current_index - 2].strip()
if gene in genes:
info_line = lines[current_index]
length = int(util.extract_regex('LENGTH\s+=\s+(\d+)', info_line))
has_seqalign_block = True
diagram_match = re.match('^\s+DIAGRAM:\s+(\d+)$',
lines[current_index + 1])
if diagram_match is not None:
diagram = int(diagram_match.group(1))
if diagram == length:
has_seqalign_block = False
if has_seqalign_block:
# the diagram line can span several lines and the blank
# line after those can span several, so search for the
# first non-blank line after the block of blank lines
blank_index = current_index + 2
while len(lines[blank_index].strip()) > 0:
blank_index += 1
non_blank_index = blank_index + 1
while len(lines[non_blank_index].strip()) == 0:
non_blank_index += 1
result[gene] = read_seqalign_blocks(lines,
non_blank_index,
length)
current_index = next_pe_value_line(current_index + 1, lines)
return result
def extract_evalue(infoline):
"""extract the e-value from the info line"""
return float(util.extract_regex('E-value =\s+\S+', infoline))
def extract_llr(infoline):
"""extract the llr value from the info line"""
return int(util.extract_regex('llr =\s+\d+', infoline))
def extract_num_sites(infoline):
"""extract the sites value from the info line"""
return int(util.extract_regex('sites =\s+\d+', infoline))
def extract_width(infoline):
"""extract the width value from the info line"""
return int(util.extract_regex('width =\s+\d+', infoline))
def extract_evalue(infoline):
"""extract the e-value from the info line"""
return float(util.extract_regex('E-value =\s+\S+', infoline))
def extract_llr(infoline):
"""extract the llr value from the info line"""
return int(util.extract_regex('llr =\s+\d+', infoline))
def extract_num_sites(infoline):
"""extract the sites value from the info line"""
return int(util.extract_regex('sites =\s+\d+', infoline))
def extract_width(infoline):
"""extract the width value from the info line"""
return int(util.extract_regex('width =\s+\d+', infoline))