def getAlignmentMotifs( sub_node, bedseq, seqalign):
for node_motif in sub_node:
if node_motif.tag.lower() == BedSeqAlignmentStatsCommStruct.MOTIF_TAG:
start = CommStruct.getAttributeAsint( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_START_ATT)
end = CommStruct.getAttributeAsint( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_END_ATT)
name = CommStruct.getAttribute( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_NAME_ATT)
motif_id = CommStruct.getAttribute( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_ID_ATT, False)
consensus = CommStruct.getAttribute( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_CONSENSUS_ATT, False)
nb_species = CommStruct.getAttributeAsint( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_NBSPECIES_ATT, False)
strand = CommStruct.getAttribute( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_STRAND_ATT, False)
offset = CommStruct.getAttributeAsint( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_OFFSET_ATT)
score = CommStruct.getAttributeAsfloat( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_SCORE_ATT)
# Retrieve the PWM of the motif
pwm_s1 = CommStruct.getAttribute( node_motif, BedSeqAlignmentStatsCommStruct.MOTIF_PWM_ATT)
if pwm_s1 != None and len( pwm_s1) > 0:
pwm_matrix = {}
pwm_s2 = pwm_s1.split(";")
for line in pwm_s2:
pwm_s3 = line.split(":")
if len( pwm_s3) > 1:
pwm_s4 = pwm_s3[1].split()
try:
length = 0
for value in pwm_s4:
length += 1
if not pwm_matrix.has_key( pwm_s3[0]):
pwm_matrix[ pwm_s3[0]]=[]
pwm_matrix[ pwm_s3[0]].append( int( value))
except ValueError, val_exce:
raise ParsingException( "BedSeqAlignmentStatsCommStruct.getAlignmentMotifs : Unable to get integer value for Motif '" + BedSeqAlignmentStatsCommStruct.MOTIF_PWM_ATT + "' attributes. From:\n\t---> " + str( val_exce))
pwm = PWM()
pwm.matrix = pwm_matrix
pwm.totalLength = length
pwm.nbSequences = nb_species
else:
pwm = None
if start != None and end != None and name != None:
motif = Motif( start, end, name, pwm)
motif.offset = offset
motif.score = score
if consensus != None:
motif.consensus = consensus
if motif_id != None:
motif.id = motif_id
if strand != None:
motif.strand = strand
seqalign.addMotif( motif)
else:
raise ParsingException( "BedSeqAlignmentStatsCommStruct.getAlignmentMotifs : The motifs of the alignment of '" + bedseq.toString() + "' is missing required attributes")
else:
raise ParsingException( "BedSeqAlignmentStatsCommStruct.getAlignmentMotifs : The motifs of the alignment of '" + bedseq.toString() + "' contains an unauthorized element : '" + node_motif.tag.lower() + "'")
def getMotif(node_motif, comm_struct):
name = CommStruct.getAttribute(
node_motif, MotifStatisticsCommStruct.MOTIF_NAME_ATT)
consensus = CommStruct.getAttribute(
node_motif, MotifStatisticsCommStruct.MOTIF_CONSENSUS_ATT, False)
if name != None:
motif = Motif(0, 0, name, None)
if consensus != None:
motif.consensus = consensus
comm_struct.addMotif(motif)
statistics = MotifStatisticsCommStruct.getMotifStatistics(
node_motif, motif)
comm_struct.addMotifStatistics(motif, statistics)
else:
raise ParsingException(
"MotifStatisticsCommStruct.getAlignmentMotifs : The motif is missing required attribute 'name'"
)