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[Library Search] Adding error handling #730

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[Library Search] Adding error handling #730

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84320d9
adding error handling
mwang87 May 14, 2021
a29b7fb
bump version
mwang87 May 14, 2021
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2 changes: 1 addition & 1 deletion molecular-librarysearch-v2/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@ include ../Makefile.deploytemplate

WORKFLOW_NAME=molecular-librarysearch-v2
TOOL_FOLDER_NAME=molecularsearch
WORKFLOW_VERSION=release_28
WORKFLOW_VERSION=release_29
WORKFLOW_DESCRIPTION="One of the major limitations in discovering new chemical entities is determining which metabolites are known compounds within complex biological samples. A way to overcome this limitation is to compare the MS2 spectra of the unknown metabolite with a library of MS/MS spectra generated from structurally characterized metabolites. Herein, this comparison is based upon the similarity cosine scoring of MS/MS spectra."
13 changes: 10 additions & 3 deletions molecular-librarysearch-v2/tools/molecularsearch/group_results_by_annotation.py
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Expand Up @@ -15,6 +15,7 @@ def main():
input_filename = sys.argv[1]
output_tsv = sys.argv[2]

# Loading annotations
results_list = ming_fileio_library.parse_table_with_headers_object_list(input_filename)
results_by_compound_name = defaultdict(list)
for result in results_list:
Expand All @@ -26,9 +27,15 @@ def main():
for compound_name in results_by_compound_name:
best_result = sorted(results_by_compound_name[compound_name], key=lambda result: float(result["MQScore"]), reverse=True)[0]

all_RTs = [float(result["RT_Query"]) for result in results_by_compound_name[compound_name]]
all_MZs = [float(result["SpecMZ"]) for result in results_by_compound_name[compound_name]]
all_MZ_ppmerror = [float(result["MZErrorPPM"]) for result in results_by_compound_name[compound_name]]
# Calculating errors, handling errors
try:
all_RTs = [float(result["RT_Query"]) for result in results_by_compound_name[compound_name]]
all_MZs = [float(result["SpecMZ"]) for result in results_by_compound_name[compound_name]]
all_MZ_ppmerror = [float(result["MZErrorPPM"]) for result in results_by_compound_name[compound_name]]
except:
all_RTs = [-1]
all_MZs = [-1]
all_MZ_ppmerror = [-1]

rt_mean = statistics.mean(all_RTs)
rt_median = statistics.median(all_RTs)
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