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Hoogenboom
fdstools
Commits
a4a5d02e
Commit
a4a5d02e
authored
Mar 14, 2016
by
Hoogenboom, Jerry
Browse files
Fix TSSV tool outputting Other sequences and No data for same marker.
parent
e30c0408
Changes
1
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Inline
Side-by-side
fdstools/tools/tssv.py
View file @
a4a5d02e
...
...
@@ -87,6 +87,11 @@ def run_tssv_lite(infile, outfile, reportfile, is_fastq, library, seqformat,
library
.
get
(
"expected_length"
,
{}).
get
(
marker
))}
for
marker
in
sequences
}
# Add aggregate rows if the user requested so.
if
aggregate_filtered
:
for
marker
in
aggregates
:
sequences
[
marker
][
"Other sequences"
]
=
aggregates
[
marker
]
# Check presence of all markers.
if
missing_marker_action
!=
"exclude"
:
for
marker
in
library
[
"flanks"
]:
...
...
@@ -96,11 +101,6 @@ def run_tssv_lite(infile, outfile, reportfile, is_fastq, library, seqformat,
else
:
raise
ValueError
(
"Marker %s was not detected!"
%
marker
)
# Add aggregate rows if the user requested so.
if
aggregate_filtered
:
for
marker
in
aggregates
:
sequences
[
marker
][
"Other sequences"
]
=
aggregates
[
marker
]
column_names
,
tables
=
make_sequence_tables
(
sequences
,
0
)
# Convert sequences to the desired format.
...
...
@@ -108,8 +108,6 @@ def run_tssv_lite(infile, outfile, reportfile, is_fastq, library, seqformat,
if
seqformat
!=
"raw"
:
for
marker
in
tables
:
for
line
in
tables
[
marker
]:
if
line
[
colid_sequence
]
==
"No Data"
:
continue
line
[
colid_sequence
]
=
ensure_sequence_format
(
line
[
colid_sequence
],
seqformat
,
library
=
library
,
marker
=
marker
)
...
...
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