Commit a4a5d02e authored by Hoogenboom, Jerry's avatar Hoogenboom, Jerry

Fix TSSV tool outputting Other sequences and No data for same marker.

parent e30c0408
......@@ -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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