mapping on first input
'''
if len(set([r[-1]
for r in id1])) == 1 and len(set([r[-1]
for r in id2])) == 1:
# if this case is true you have to edit also all pos,etc,desc indices such that the plotting works correctly
# again .. maybe it is also neccessary to test for the last two characters
cut_last_char = lambda x: x[:-1]
binary1.index = list(map(cut_last_char, binary1.index))
binary2.index = list(map(cut_last_char, binary2.index))
pos.index = list(map(cut_last_char, pos.index))
pos2.index = list(map(cut_last_char, pos2.index))
read_details.index = list(map(cut_last_char, read_details.index))
read_details2.index = list(map(cut_last_char, read_details2.index))
binary_p, binary_mis, binary_un = ht.create_paired_matrix(
binary1, binary2)
if binary_p.shape[0] < len(id1) * 0.1:
print((
"\nWARNING: Less than 10%% of reads could be paired. Consider an appropriate unpaired_weight setting "
"in your config file (currently %.3f), because you may need to resort to using unpaired reads."
) % unpaired_weight)
if unpaired_weight > 0:
if use_discordant:
binary = pd.concat([binary_p, binary_un, binary_mis])
else:
binary = pd.concat([binary_p, binary_un])
else:
binary = binary_p
paired-end
2) if not test if the intersection of ID-binary1 and ID-binary2 has at least 10% of the former read
number -> do paired-end
3) if nothing worked ( perhaps pair-end ID was in the middle or something) raise flag and do single-end
mapping on first input
'''
if len(set([r[-1] for r in id1])) == 1 and len(set([r[-1] for r in id2])) == 1:
#if this case is true you have to edit also all pos,etc,desc indixes such that the plotting works correctly
# again .. maybe it is also neccessary to test for the last two characters
binary1.index = map(lambda x: x[:-1], binary1.index)
binary2.index = map(lambda x: x[:-1], binary2.index)
pos.index = map(lambda x: x[:-1], pos.index)
pos2.index = map(lambda x: x[:-1], pos2.index)
etc.index = map(lambda x: x[:-1], etc.index)
etc2.index = map(lambda x: x[:-1], etc2.index)
binary = ht.create_paired_matrix(binary1, binary2)
else:
nof_reads1 = float(len(id1))*0.1
if float(len(id1.intersection(id2))) >= nof_reads1:
binary = ht.create_paired_matrix(binary1, binary2)
else:
print "\nCould not match paired-end pairs. Switching to single-end pipeline."
binary = binary1
is_paired = False
else:
pos, etc, desc = ht.sam_to_hdf(out_dir+"/"+date+"_0.sam", verbosity=args.verbose)
binary = pos.applymap(bool).applymap(int)
#dimensionality reduction and typing
alleles_to_keep = filter(is_frequent, binary.columns)
number -> do paired-end
3) if nothing worked ( perhaps pair-end ID was in the middle or something) raise flag and do single-end
mapping on first input
'''
if len(set([r[-1]
for r in id1])) == 1 and len(set([r[-1]
for r in id2])) == 1:
#if this case is true you have to edit also all pos,etc,desc indixes such that the plotting works correctly
# again .. maybe it is also neccessary to test for the last two characters
binary1.index = map(lambda x: x[:-1], binary1.index)
binary2.index = map(lambda x: x[:-1], binary2.index)
pos.index = map(lambda x: x[:-1], pos.index)
pos2.index = map(lambda x: x[:-1], pos2.index)
etc.index = map(lambda x: x[:-1], etc.index)
etc2.index = map(lambda x: x[:-1], etc2.index)
binary = ht.create_paired_matrix(binary1, binary2)
else:
nof_reads1 = float(len(id1)) * 0.1
if float(len(id1.intersection(id2))) >= nof_reads1:
binary = ht.create_paired_matrix(binary1, binary2)
else:
print "\nCould not match paired-end pairs. Switching to single-end pipeline."
binary = binary1
is_paired = False
else:
pos, etc, desc = ht.sam_to_hdf(out_dir + "/" + date + "_0.sam",
verbosity=args.verbose)
binary = pos.applymap(bool).applymap(int)
#dimensionality reduction and typing
number -> do paired-end
3) if nothing worked ( perhaps pair-end ID was in the middle or something) raise flag and do single-end
mapping on first input
'''
if len(set([r[-1] for r in id1])) == 1 and len(set([r[-1] for r in id2])) == 1:
# if this case is true you have to edit also all pos,etc,desc indices such that the plotting works correctly
# again .. maybe it is also neccessary to test for the last two characters
cut_last_char = lambda x: x[:-1]
binary1.index = list(map(cut_last_char, binary1.index))
binary2.index = list(map(cut_last_char, binary2.index))
pos.index = list(map(cut_last_char, pos.index))
pos2.index = list(map(cut_last_char, pos2.index))
read_details.index = list(map(cut_last_char, read_details.index))
read_details2.index = list(map(cut_last_char, read_details2.index))
binary_p, binary_mis, binary_un = ht.create_paired_matrix(binary1, binary2)
if binary_p.shape[0] < len(id1) * 0.1:
print(("\nWARNING: Less than 10%% of reads could be paired. Consider an appropriate unpaired_weight setting "
"in your config file (currently %.3f), because you may need to resort to using unpaired reads.") % unpaired_weight)
if unpaired_weight > 0:
if use_discordant:
binary = pd.concat([binary_p, binary_un, binary_mis])
else:
binary = pd.concat([binary_p, binary_un])
else:
binary = binary_p
else:
pos, read_details = ht.pysam_to_hdf(bam_paths[0])
