Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fixes for pairend_distro.py and l_merge.py #90

Open
wants to merge 3 commits into
base: master
Choose a base branch
from
Open

fixes for pairend_distro.py and l_merge.py #90

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
98af622
Get rid of -u in shebang header of l_merge.py.
glebkuznetsov Jul 7, 2015
a0ca2d8
Make pairend_distro.py support data of all same length.
glebkuznetsov Jul 8, 2015
63dec4d
l_merge.py preserves per-sample SU (support) in SULIST property.
glebkuznetsov Jul 8, 2015
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 14 additions & 2 deletions scripts/l_merge.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
#!/usr/bin/env python -u
#!/usr/bin/env python

from operator import add
import time
import sys
Expand Down Expand Up @@ -68,6 +69,7 @@ def print_var_line(l):
PRPOS = m['PREND']
PREND = m['PRPOS']
SNAME = m['SNAME']
SULIST = m.get('SULIST', m['SU']) # Fall back to single SU as default
EVENT = A[2]

A[4] = ALT
Expand All @@ -84,6 +86,7 @@ def print_var_line(l):
'PRPOS=' + str(PRPOS),
'PREND=' + str(PREND),
'SNAME=' + str(SNAME),
'SULIST=' + str(SULIST),
'EVENT=' + str(EVENT)])

# reconstruct the line
Expand Down Expand Up @@ -123,6 +126,7 @@ def print_var_line(l):
PRPOS = m['PREND']
PREND = m['PRPOS']
SNAME = m['SNAME']
SULIST = m.get('SULIST', m['SU']) # Fall back to single SU as default
EVENT = A[2]
SECONDARY = 'SECONDARY'
MATEID=A[2] + '_1'
Expand All @@ -141,6 +145,7 @@ def print_var_line(l):
'PRPOS=' + str(PRPOS),
'PREND=' + str(PREND),
'SNAME=' + str(SNAME),
'SULIST=' + str(SULIST),
'EVENT=' + str(EVENT),
'MATEID=' + str(MATEID)])

Expand Down Expand Up @@ -458,6 +463,8 @@ def merge(BP, sample_order, v_id, use_product):

gt_list = []

su_list = []

#for g_i in c:
for b_i in c:
#A = G[g_i].b.l.rstrip().split('\t')
Expand All @@ -481,10 +488,14 @@ def merge(BP, sample_order, v_id, use_product):

gt_list += A[9:]

su_list.append(m['SU'])

SNAME=','.join(s_name_list)

GTS = '\t'.join(gt_list)

SULIST = ','.join(su_list)

strand_types_counts = []
for strand in strand_map:
strand_types_counts.append(strand + ':' + str(strand_map[strand]))
Expand Down Expand Up @@ -516,7 +527,8 @@ def merge(BP, sample_order, v_id, use_product):
'PRPOS=' + str(PRPOS),
'PREND=' + str(PREND),
'ALG=' + str(ALG),
'SNAME=' + str(SNAME)]
'SNAME=' + str(SNAME),
'SULIST=' + str(SULIST)]

if BP[c[0]].sv_type == 'BND':
I.append('EVENT=' + str(ID))
Expand Down
8 changes: 7 additions & 1 deletion scripts/pairend_distro.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,13 @@ def unscaled_upper_mad(xs):
above the median.
"""
med = np.median(xs)
return med, np.median(xs[xs > med] - med)
if len(xs[xs > med]):
umad = np.median(xs[xs > med] - med)
else:
# When lengths are all the same, return a safe default.
# This is common with simulated data used for testing.
umad = 1
return med, umad


(options, args) = parser.parse_args()
Expand Down