# (C) 2013 Elke Schaper
import logging
logger = logging.getLogger(__name__)
'''
Functions to check whether the exon structure and the repeat unit structure are correlated.
'''
################################### Repeat exon structure ################
[docs]def get_exon_structure(my_TR, exon_structure):
'''
Exon structure parameters:
# exon_structure = [{'Exon Chr End (bp)': '43478424', 'Exon Chr Start (bp)': '43477252', 'CDS End': '272', 'CDS Start': '1'}, {'Exon Chr End (bp)': '43476658', 'Exon Chr Start (bp)': '43476498', 'CDS End': '433', 'CDS Start': '273'}, {'Exon Chr End (bp)': '43476158', 'Exon Chr Start (bp)': '43476036', 'CDS End': '556', 'CDS Start': '434'}, {'Exon Chr End (bp)': '43475664', 'Exon Chr Start (bp)': '43475564', 'CDS End': '657', 'CDS Start': '557'}, {'Exon Chr End (bp)': '43475416', 'Exon Chr Start (bp)': '43475194', 'CDS End': '880', 'CDS Start': '658'}, {'Exon Chr End (bp)': '43475046', 'Exon Chr Start (bp)': '43474707', 'CDS End': '951', 'CDS Start': '881'}]
'''
# Extract the exon structure in protein coordinates
exon_start_aa = [int(i['CDS Start'])
for i in exon_structure if 'CDS Start' in i and i['CDS Start'] != '']
exon_end_aa = [int(i['CDS End'])
for i in exon_structure if 'CDS End' in i and i['CDS End'] != '']
if not exon_end_aa == []:
protein_length = exon_end_aa[-1]
else:
protein_length = None
# Extract the TR structure in protein coordinates
index = my_TR.begin
tr_start_aa = []
for iMSA in my_TR.msa:
unit_length = len(iMSA.replace("-", ""))
tr_start_aa.append(index)
index += unit_length
return exon_start_aa, protein_length, tr_start_aa, index
[docs]def get_exon_measures(my_TR, exon_structure):
'''
Calculate diverse exon measures
Exon structure parameters:
# exon_structure = [{'Exon Chr End (bp)': '43478424', 'Exon Chr Start (bp)': '43477252', 'CDS End': '272', 'CDS Start': '1'}, {'Exon Chr End (bp)': '43476658', 'Exon Chr Start (bp)': '43476498', 'CDS End': '433', 'CDS Start': '273'}, {'Exon Chr End (bp)': '43476158', 'Exon Chr Start (bp)': '43476036', 'CDS End': '556', 'CDS Start': '434'}, {'Exon Chr End (bp)': '43475664', 'Exon Chr Start (bp)': '43475564', 'CDS End': '657', 'CDS Start': '557'}, {'Exon Chr End (bp)': '43475416', 'Exon Chr Start (bp)': '43475194', 'CDS End': '880', 'CDS Start': '658'}, {'Exon Chr End (bp)': '43475046', 'Exon Chr Start (bp)': '43474707', 'CDS End': '951', 'CDS Start': '881'}]
'''
exon_start_aa, protein_length, tr_start_aa, exon_stop_aa = get_exon_structure(
my_TR, exon_structure)
if exon_start_aa == [] or tr_start_aa == []:
return None
nExon = len(
[i for i in exon_start_aa if i > tr_start_aa[0] and i < tr_start_aa[-1]]) + 1
nTR_in_Exon_Max = 0
for iExon_start, iExon_end in zip(exon_start_aa[:-1], exon_start_aa[1:]):
lTR_Start_in_Exon = [
iTR_start for iTR_start in tr_start_aa if iTR_start >= iExon_start and iTR_start < iExon_end]
if len(lTR_Start_in_Exon) > nTR_in_Exon_Max:
nTR_in_Exon_Max = len(lTR_Start_in_Exon)
return nExon, nTR_in_Exon_Max
[docs]def print_exon_structure(my_TR, exon_structure):
'''
Exon structure parameters:
# exon_structure = [{'Exon Chr End (bp)': '43478424', 'Exon Chr Start (bp)': '43477252', 'CDS End': '272', 'CDS Start': '1'}, {'Exon Chr End (bp)': '43476658', 'Exon Chr Start (bp)': '43476498', 'CDS End': '433', 'CDS Start': '273'}, {'Exon Chr End (bp)': '43476158', 'Exon Chr Start (bp)': '43476036', 'CDS End': '556', 'CDS Start': '434'}, {'Exon Chr End (bp)': '43475664', 'Exon Chr Start (bp)': '43475564', 'CDS End': '657', 'CDS Start': '557'}, {'Exon Chr End (bp)': '43475416', 'Exon Chr Start (bp)': '43475194', 'CDS End': '880', 'CDS Start': '658'}, {'Exon Chr End (bp)': '43475046', 'Exon Chr Start (bp)': '43474707', 'CDS End': '951', 'CDS Start': '881'}]
'''
exon_start_aa, tr_start_aa, protein_length = get_exon_structure(
my_TR, exon_structure)
if exon_start_aa == [] or tr_start_aa == []:
return ""
protein_structure = ""
for i in range(1, protein_length + 1):
if i in exon_start_aa:
if i in tr_start_aa:
protein_structure += "B"
else:
protein_structure += "E"
elif i in tr_start_aa:
protein_structure += "x"
else:
protein_structure += "_"
return protein_structure
# def main():
#
# exon_structure = [{'Exon Chr End (bp)': '43478424',
# 'Exon Chr Start (bp)': '43477252',
# 'CDS End': '272',
# 'CDS Start': '1'},
# {'Exon Chr End (bp)': '43476658',
# 'Exon Chr Start (bp)': '43476498',
# 'CDS End': '433',
# 'CDS Start': '273'},
# {'Exon Chr End (bp)': '43476158',
# 'Exon Chr Start (bp)': '43476036',
# 'CDS End': '556',
# 'CDS Start': '434'},
# {'Exon Chr End (bp)': '43475664',
# 'Exon Chr Start (bp)': '43475564',
# 'CDS End': '657',
# 'CDS Start': '557'},
# {'Exon Chr End (bp)': '43475416',
# 'Exon Chr Start (bp)': '43475194',
# 'CDS End': '880',
# 'CDS Start': '658'},
# {'Exon Chr End (bp)': '43475046',
# 'Exon Chr Start (bp)': '43474707',
# 'CDS End': '951',
# 'CDS Start': '881'}]
#
# #[{'Exon Chr End (bp)': '120068186', 'Exon Chr Start (bp)': '120067591', 'CDS End': '500', 'CDS Start': '1'}, {'Exon Chr End (bp)': '120054800', 'Exon Chr Start (bp)': '120054672', 'CDS End': '629', 'CDS Start': '501'}, {'Exon Chr End (bp)': '120053986', 'Exon Chr Start (bp)': '120053709', 'CDS End': '907', 'CDS Start': '630'}, {'Exon Chr End (bp)': '120050255', 'Exon Chr Start (bp)': '120043356', 'CDS End': '1116', 'CDS Start': '908'}]
# exon_structure = my_gene_tree['leafs']['ENSP00000295628']['exon']
# my_TR = my_TR_data['homologs']['ENSP00000295628']['TR']['HMM']
#
# exon_structure_aa = [[i['CDS Start'], i['CDS End']]
# for i in exon_structure]
