Merge pull request #705 from CCMS-UCSD/network-id-fix-fbmn

[FBMN] Top K sorting to make sure top hit gets in the graphml Network
CCMS-UCSD · Mar 19, 2021 · 8a0c7fa · 8a0c7fa
2 parents 2dac050 + d09904f
commit 8a0c7fa
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Showing 5 changed files with 14 additions and 5 deletions.
diff --git a/feature-based-molecular-networking/Makefile b/feature-based-molecular-networking/Makefile
@@ -3,5 +3,5 @@ include ../Makefile.deploytemplate
 
 WORKFLOW_NAME=feature-based-molecular-networking
 TOOL_FOLDER_NAME=feature-based-molecular-networking
-WORKFLOW_VERSION=release_28
+WORKFLOW_VERSION=release_28.1
 WORKFLOW_DESCRIPTION='Feature-Based Molecular Networking (FBMN) is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on GNPS. The supported tools are: MZmine, OpenMS, MS-DIAL, MetaboScape, XCMS, Progenesis QI, and the mzTab-M format. FBMN facilitates the detection of isomers that are separated by chromatographic or ion mobility separation, and provides accurate ion abundances for statistical analysis. Note that FBMN requires processing the mass spectrometry data with a feature detection and alignment tool. For rapid/qualitative analysis, we recommend using classical molecular networking that accepts unprocessed mass spectrometry files. See the FBMN documentation at https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking and refer to the "Method and Citation for Manuscripts" on the results page for citations.'
diff --git a/feature-based-molecular-networking/feature-based-molecular-networking/result.xml b/feature-based-molecular-networking/feature-based-molecular-networking/result.xml
@@ -613,7 +613,7 @@
             </parsers>
         </data>
 
-        <parameter name="URLBASE" value='https://view.qiime2.org/?src=https%3A%2F%2Fapp.cors.bridged.cc%2Fhttps%3A%2F%2Fgnps.ucsd.edu%2FProteoSAFe%2FDownloadResultFile%3Ftask%3D[task]%26file%3Dqiime2_output%252Fqiime2_emperor.qzv%26block%3Dmain'/>
+        <parameter name="URLBASE" value='https://view.qiime2.org/?src=https%3A%2F%2Fcors.bridged.cc%2Fhttps%3A%2F%2Fgnps.ucsd.edu%2FProteoSAFe%2FDownloadResultFile%3Ftask%3D[task]%26file%3Dqiime2_output%252Fqiime2_emperor.qzv%26block%3Dmain'/>
     </block>
 
     <view id="view_qiime2_emperor_biplot" label="View qiime2 Emperor Bi-Plots" group="Advanced Views - qiime2 Views">
@@ -626,7 +626,7 @@
             </parsers>
         </data>
 
-        <parameter name="URLBASE" value='https://view.qiime2.org/?src=https%3A%2F%2Fapp.cors.bridged.cc%2Fhttps%3A%2F%2Fgnps.ucsd.edu%2FProteoSAFe%2FDownloadResultFile%3Ftask%3D[task]%26file%3Dqiime2_output%252Fqiime2_biplot_emperor.qzv%26block%3Dmain'/>
+        <parameter name="URLBASE" value='https://view.qiime2.org/?src=https%3A%2F%2Fcors.bridged.cc%2Fhttps%3A%2F%2Fgnps.ucsd.edu%2FProteoSAFe%2FDownloadResultFile%3Ftask%3D[task]%26file%3Dqiime2_output%252Fqiime2_biplot_emperor.qzv%26block%3Dmain'/>
     </block>
 
     <view id="download_emperor_data" label="Download qiime2 Emperor qzv" group="Advanced Views - qiime2 Views">

diff --git a/metabolomics-snets-v2/Makefile b/metabolomics-snets-v2/Makefile
@@ -3,6 +3,6 @@ include ../Makefile.deploytemplate
 
 WORKFLOW_NAME=metabolomics-snets-v2
 TOOL_FOLDER_NAME=metabolomicsnetsv2
-WORKFLOW_VERSION=release_28
+WORKFLOW_VERSION=release_28.1
 WORKFLOW_DESCRIPTION="Molecular networks are visual displays of the chemical space present in tandem mass spectrometry (MS/MS) experiments. This visualization approach can detect sets of spectra from related molecules (molecular networks), even when the spectra themselves are not matched to any known compounds. Classical molecular networking is well suited for discovery and can be analyzed directly from raw mass spectrometry files. Feature-based Molecular Networking (FBMN) is better when quantification analysis is necessary, but requires preprocessing with feature finding tools."
 
diff --git a/metabolomics-snets-v2/metabolomics-snets-v2/result.xml b/metabolomics-snets-v2/metabolomics-snets-v2/result.xml
@@ -1636,7 +1636,7 @@
             </parsers>
         </data>
 
-        <parameter name="URLBASE" value='https://view.qiime2.org/?src=https%3A%2F%2Fapp.cors.bridged.cc%2Fhttps%3A%2F%2Fgnps.ucsd.edu%2FProteoSAFe%2FDownloadResultFile%3Ftask%3D[task]%26file%3Dqiime2_output%252Fqiime2_emperor.qzv%26block%3Dmain'/>
+        <parameter name="URLBASE" value='https://view.qiime2.org/?src=https%3A%2F%2Fcors.bridged.cc%2Fhttps%3A%2F%2Fgnps.ucsd.edu%2FProteoSAFe%2FDownloadResultFile%3Ftask%3D[task]%26file%3Dqiime2_output%252Fqiime2_emperor.qzv%26block%3Dmain'/>
     </block>
 
     <view id="download_emperor_data" label="Download qiime2 Emperor qzv" group="Advanced Views - qiime2 Views">

diff --git a/shared_code/molecular_network_filtering_library.py b/shared_code/molecular_network_filtering_library.py
@@ -10,6 +10,8 @@
 import networkx as nx
 import constants_network as CONST
 
+import pandas as pd
+
 def loading_network(filename, hasHeaders=False, edgetype="Cosine"):
     node1_list = []
     node2_list = []
@@ -239,6 +241,13 @@ def add_clusterinfo_summary_to_graph(G, cluster_info_summary_filename):
 
 def add_library_search_results_to_graph(G, library_search_filename, annotation_prefix=""):
     row_count, table_data = ming_fileio_library.parse_table_with_headers(library_search_filename)
+
+    # sort in reverse match score order
+    try:
+        table_data = sorted(table_data, key=lambda x: float(x["MQScore"]), reverse=False)
+    except:
+        pass
+
 
     for i in range(row_count):
         cluster_index = table_data["#Scan#"][i]