Commit c29d1c85 authored by BIOPZ-Schmidt Ralf's avatar BIOPZ-Schmidt Ralf

bugfixed indent problem in...

bugfixed indent problem in PAQR/scripts/deNovo-used-sites-and-usage-inference.single_distal_included.py
parent e58b36c0
......@@ -1647,35 +1647,35 @@ def get_relative_usages(used_sites,
for cvg in bp_coverages_dict[cond]:
cvg_counter += 1
if strand == "+":
start_idx = region.index( exon_structure[2] )
if used_sites[0][1].start - read_length - min_coverage_region < exon_structure[2]:
start_idx = region.index( exon_structure[2] - add_us_extension[cond][cvg_counter] )
if strand == "+":
start_idx = region.index( exon_structure[2] )
if used_sites[0][1].start - read_length - min_coverage_region < exon_structure[2]:
start_idx = region.index( exon_structure[2] - add_us_extension[cond][cvg_counter] )
try:
end_idx = region.index( used_sites[0][1].start - read_length )
end_idx = region.index( used_sites[0][1].start - read_length )
except ValueError:
end_idx = region.index( exon_structure[2] - add_us_extension[cond][cvg_counter] + 1)
if end_idx - start_idx < min_coverage_region:
syserr(("[INFO] Distance from proximal site to exon start of exon %s cond %s sample #%i " +
"is very small despite upstream extension (%i nt). For relative usage inference, " +
"the read length is not excluded from the upstream region of the proximal site\n")
% (exon_id, cond, cvg_counter, add_us_extension[cond][cvg_counter]))
end_idx = region.index( used_sites[0][1].start )
else:
if used_sites[0][1].end + read_length + min_coverage_region > exon_structure[3]:
if end_idx - start_idx < min_coverage_region:
syserr(("[INFO] Distance from proximal site to exon start of exon %s cond %s sample #%i " +
"is very small despite upstream extension (%i nt). For relative usage inference, " +
"the read length is not excluded from the upstream region of the proximal site\n")
% (exon_id, cond, cvg_counter, add_us_extension[cond][cvg_counter]))
end_idx = region.index( used_sites[0][1].start )
else:
if used_sites[0][1].end + read_length + min_coverage_region > exon_structure[3]:
end_idx = region.index( exon_structure[3] + add_us_extension[cond][cvg_counter] - 1) + 1
else:
end_idx = region.index( exon_structure[3] - 1) + 1
else:
end_idx = region.index( exon_structure[3] - 1) + 1
try:
start_idx = region.index( used_sites[0][1].end + read_length)
start_idx = region.index( used_sites[0][1].end + read_length)
except ValueError:
start_idx = end_idx = region.index( exon_structure[3] + add_us_extension[cond][cvg_counter] - 2) + 1
if end_idx - start_idx < min_coverage_region:
syserr(("[INFO] Distance from proximal site to exon start of exon %s cond %s sample #%i " +
"is very small despite upstream extension (%i nt). For relative usage inference, " +
"the read length is not excluded from the upstream region of the proximal site\n")
% (exon_id, cond, cvg_counter, add_us_extension[cond][cvg_counter]))
start_idx = region.index( used_sites[0][1].end )
if end_idx - start_idx < min_coverage_region:
syserr(("[INFO] Distance from proximal site to exon start of exon %s cond %s sample #%i " +
"is very small despite upstream extension (%i nt). For relative usage inference, " +
"the read length is not excluded from the upstream region of the proximal site\n")
% (exon_id, cond, cvg_counter, add_us_extension[cond][cvg_counter]))
start_idx = region.index( used_sites[0][1].end )
region_means[cond].append([])
relative_usages[cond].append([])
......
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