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Barplot bug fixes for Outgroup Argument
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@alipirani88
alipirani88 committed Sep 27, 2019
1 parent b7f2c40 commit 0fe6fa5
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Showing 5 changed files with 20 additions and 15,901 deletions.
29 changes: 20 additions & 9 deletions modules/variant_diagnostics/core_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -661,7 +661,7 @@ def generate_paste_command_outgroup():
f4=open(paste_file, 'w+')
paste_command = "paste %s/unique_positions_file" % args.filter2_only_snp_vcf_dir
for i in vcf_filenames:
if outgroup not in i:
if "%s_filter2_final.vcf_no_proximate_snp.vcf" % outgroup not in i:
label_file = i.replace('_filter2_final.vcf_no_proximate_snp.vcf', '_filter2_final.vcf_no_proximate_snp.vcf_positions_label')
paste_command = paste_command + " " + label_file

Expand Down Expand Up @@ -865,7 +865,7 @@ def generate_indel_paste_command_outgroup():

# Generate paste command
for i in vcf_filenames:
if outgroup not in i:
if "%s_filter2_final.vcf_no_proximate_snp.vcf" % outgroup not in i:
label_file = i.replace('_filter2_final.vcf_no_proximate_snp.vcf', '_filter2_indel_final.vcf_indel_positions_label')
paste_command = paste_command + " " + label_file
# Change header awk command to exclude outgroup
Expand Down Expand Up @@ -1094,7 +1094,7 @@ def temp_generate_position_label_data_matrix_All_label():

if args.outgroup:
for i in vcf_filenames:
if outgroup not in i:
if "%s_filter2_final.vcf_no_proximate_snp.vcf" % outgroup not in i:
print_string_header = print_string_header + os.path.basename(i) + "\t"
else:
for i in vcf_filenames:
Expand All @@ -1106,13 +1106,15 @@ def temp_generate_position_label_data_matrix_All_label():
ref_var = ['reference_allele', 'VARIANT']

if args.outgroup:
print "here"
with open("%s/temp_label_final_raw_outgroup.txt" % args.filter2_only_snp_vcf_dir, 'r') as csv_file:
csv_reader = csv.reader(csv_file, delimiter='\t')
next(csv_reader, None)
for row in csv_reader:
if set(ref_var) & set(row[1:]):
if set(lll) & set(row[1:]):
if int(row[0]) not in outgroup_specific_positions:

print_string = ""
for i in row[1:]:
print_string = print_string + "\t" + i
Expand Down Expand Up @@ -1272,6 +1274,7 @@ def barplot_stats():
f_bar_perc = open("%s/bargraph_percentage.txt" % args.filter2_only_snp_vcf_dir, 'w+')
f_bar_count.write("Sample\tunmapped_positions\treference_allele\ttrue_variant\tOnly_low_FQ\tOnly_DP\tOnly_low_MQ\tother\n")
f_bar_perc.write("Sample\tunmapped_positions_perc\ttrue_variant_perc\tOnly_low_FQ_perc\tOnly_DP_perc\tOnly_low_MQ_perc\tother_perc\n")

for i in xrange(1, end, 1):
""" Bar Count Statistics: Variant Position Count Statistics """
true_variant = columns[i].count('VARIANT')
Expand All @@ -1283,8 +1286,11 @@ def barplot_stats():
low_FQ_other_parameters = columns[i].count('LowFQ_QUAL_DP_proximate_SNP') + columns[i].count('LowFQ_DP_QUAL_proximate_SNP') + columns[i].count('LowFQ_QUAL_proximate_SNP') + columns[i].count('LowFQ_DP_proximate_SNP') + columns[i].count('LowFQ_proximate_SNP') + columns[i].count('LowFQ_QUAL_DP') + columns[i].count('LowFQ_DP_QUAL') + columns[i].count('LowFQ_QUAL') + columns[i].count('LowFQ_DP')
high_FQ_other_parameters = columns[i].count('HighFQ_QUAL_DP_proximate_SNP') + columns[i].count('HighFQ_DP_QUAL_proximate_SNP') + columns[i].count('HighFQ_QUAL_proximate_SNP') + columns[i].count('HighFQ_DP_proximate_SNP') + columns[i].count('HighFQ_proximate_SNP') + columns[i].count('HighFQ_QUAL_DP') + columns[i].count('HighFQ_DP_QUAL') + columns[i].count('HighFQ_QUAL')
other = low_FQ_other_parameters + high_FQ_other_parameters

total = true_variant + unmapped_positions + reference_allele + Only_low_FQ + Only_DP + low_FQ_other_parameters + high_FQ_other_parameters + Only_low_MQ

filename_count = i - 1

if args.outgroup:
bar_string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (os.path.basename(vcf_filenames_outgroup[filename_count].replace('_filter2_final.vcf_no_proximate_snp.vcf', '')), unmapped_positions, reference_allele, true_variant, Only_low_FQ, Only_DP, Only_low_MQ, other)
f_bar_count.write(bar_string)
Expand All @@ -1293,7 +1299,7 @@ def barplot_stats():
vcf_filenames[filename_count].replace('_filter2_final.vcf_no_proximate_snp.vcf', '')),
unmapped_positions, reference_allele, true_variant,
Only_low_FQ, Only_DP, Only_low_MQ, other)
f_bar_count.write(bar_string)
#f_bar_count.write(bar_string)
""" Bar Count Percentage Statistics: Variant Position Percentage Statistics """
try:
true_variant_perc = float((columns[i].count('VARIANT') * 100) / total)
Expand Down Expand Up @@ -1334,9 +1340,9 @@ def barplot_stats():
else:
bar_perc_string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (os.path.basename(
vcf_filenames[filename_count].replace('_filter2_final.vcf_no_proximate_snp.vcf', '')),
unmapped_positions, reference_allele, true_variant,
Only_low_FQ, Only_DP, Only_low_MQ, other)
f_bar_count.write(bar_string)
unmapped_positions_perc, reference_allele_perc, true_variant_perc,
Only_low_FQ_perc, Only_DP_perc, Only_low_MQ_perc, other_perc)
f_bar_count.write(bar_string)
f_bar_perc.write(bar_perc_string)
f_bar_count.close()
f_bar_perc.close()
Expand Down Expand Up @@ -1489,7 +1495,8 @@ def temp_generate_indel_position_label_data_matrix_All_label():
print_string_header = "\t"
if args.outgroup:
for i in vcf_filenames:
if outgroup not in i:

if "%s_filter2_final.vcf_no_proximate_snp.vcf" % outgroup not in i:
print_string_header = print_string_header + os.path.basename(i) + "\t"
else:
for i in vcf_filenames:
Expand Down Expand Up @@ -1660,6 +1667,7 @@ def barplot_indel_stats():
open('%s/temp_Only_filtered_indel_positions_for_closely_matrix.txt' % args.filter2_only_snp_vcf_dir,
'r'), delimiter='\t')
columns = list(zip(*c_reader))
print len(columns)
keep_logging('Finished reading columns...', 'Finished reading columns...', logger, 'info')
counts = 1

Expand All @@ -1668,13 +1676,15 @@ def barplot_indel_stats():
end = end - 1
else:
end = len(vcf_filenames) + 1
print end

f_bar_count = open("%s/bargraph_indel_counts.txt" % args.filter2_only_snp_vcf_dir, 'w+')
f_bar_perc = open("%s/bargraph_indel_percentage.txt" % args.filter2_only_snp_vcf_dir, 'w+')
f_bar_count.write("Sample\tunmapped_positions\treference_allele\ttrue_variant\tOnly_low_AF\tOnly_DP\tOnly_low_MQ\tother\n")
f_bar_perc.write("Sample\tunmapped_positions_perc\ttrue_variant_perc\tOnly_low_AF_perc\tOnly_DP_perc\tOnly_low_MQ_perc\tother_perc\n")
for i in xrange(1, end, 1):
""" Bar Count Statistics: Variant Position Count Statistics """
print i
true_variant = columns[i].count('VARIANT')
unmapped_positions = columns[i].count('reference_unmapped_position')
reference_allele = columns[i].count('reference_allele')
Expand All @@ -1689,6 +1699,7 @@ def barplot_indel_stats():
# bar_string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (os.path.basename(vcf_filenames_outgroup[filename_count].replace('_filter2_final.vcf_no_proximate_snp.vcf', '')), unmapped_positions, reference_allele, true_variant, Only_low_AF, Only_DP, Only_low_MQ, other)
if args.outgroup:
###

bar_string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (os.path.basename(
vcf_filenames_outgroup[filename_count].replace('_filter2_final.vcf_no_proximate_snp.vcf', '')),
unmapped_positions, reference_allele, true_variant,
Expand Down Expand Up @@ -4622,7 +4633,7 @@ def someOtherFunc(data, key):
line = args.filter2_only_snp_vcf_dir + line
vcf_filenames_temp.append(line)
if args.outgroup:
if outgroup not in line:
if "%s_filter2_final.vcf_no_proximate_snp.vcf" % outgroup not in line:
vcf_filenames_temp_outgroup.append(line)
fp.close()
vcf_filenames = sorted(vcf_filenames_temp)
Expand Down
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