From 0ac2b1d46a35b46accb1a4c1b6378772d56dedae Mon Sep 17 00:00:00 2001
From: benpullman <bp2@icloud.com>
Date: Sun, 10 Jul 2022 22:28:56 -0700
Subject: [PATCH 1/2] updates to use generic max peptides per protein function

---
 .DS_Store                                     | Bin 10244 -> 10244 bytes
 peptide_statistics_hpp/tool.xml               |   2 +-
 .../peptide_protein_cosine.py                 |   2 ++
 3 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.DS_Store b/.DS_Store
index 4687eba419d902f83e2259569195d1fadc2055b1..1b10aca863c5addf1012c44818a29459c0bd34d0 100644
GIT binary patch
delta 233
zcmZn(XbG6$&nUDpU^hRb&}JTijf?_0>4w3{`MCuQAix;^ZE~-mfk<w?i%U{YeiBfK
zqvTwT&0F;&j!=mdtP%nR8OX*=VA$L%7{SPoY<Bpbo13o*ZDb8WHvIhj2`9M>4m$!Z
pVr3{{$Opn4hT`0Oge}-rpja2tz_7Vef{kr6yTUJ)&9{Y_nE`<=MEd{$

delta 48
zcmV-00MGw~P=rvBPXP+CP`eKS3bPClu>rHi5-0()3lyRSvkw~h1+jpL0ka1n`UJBl
G76Su_c@K90

diff --git a/peptide_statistics_hpp/tool.xml b/peptide_statistics_hpp/tool.xml
index 64ebe25..5bb4c51 100644
--- a/peptide_statistics_hpp/tool.xml
+++ b/peptide_statistics_hpp/tool.xml
@@ -187,7 +187,7 @@
           <arg option="-picked_protein_fdr_comparison"        valueRef="@picked_protein_fdr_comparison"/>
           <arg option="-filter_rows_fdr"        valueRef="@filter_rows_fdr"/>
           <arg option="-main_fdr"        valueRef="@main_fdr"/>
-          <arg option="-leftover_fdr"        valueRef="picked_leftover"/>
+          <arg option="-leftover_fdr"        value="picked_leftover"/>
           <arg option="-nextprot_releases" pathRef="nextprot_releases"/>
           <arg option="-msv_to_pxd_mapping" pathRef="msv_to_pxd_mapping"/>
           <arg option="-external_provenance"  valueRef="external_provenance"/>
diff --git a/tools/peptide_statistics_hpp/peptide_protein_cosine.py b/tools/peptide_statistics_hpp/peptide_protein_cosine.py
index db9ff2a..9e61c14 100755
--- a/tools/peptide_statistics_hpp/peptide_protein_cosine.py
+++ b/tools/peptide_statistics_hpp/peptide_protein_cosine.py
@@ -1070,6 +1070,8 @@ def get_task_name(task_id):
                 '#junction_peptides_novel':0
             })
 
+    raise Exception
+
     if args.export_explorers and args.export_explorers == 1:
         hupo_mapping = {}
         unique_mapping = {}

From 68f95e028b28b4c06ec0f292f2fb463077f0d870 Mon Sep 17 00:00:00 2001
From: benpullman <bp2@icloud.com>
Date: Mon, 11 Jul 2022 12:19:52 -0700
Subject: [PATCH 2/2] check non-nested

---
 tools/peptide_statistics_hpp/peptide_protein_cosine.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tools/peptide_statistics_hpp/peptide_protein_cosine.py b/tools/peptide_statistics_hpp/peptide_protein_cosine.py
index 9e61c14..db9ff2a 100755
--- a/tools/peptide_statistics_hpp/peptide_protein_cosine.py
+++ b/tools/peptide_statistics_hpp/peptide_protein_cosine.py
@@ -1070,8 +1070,6 @@ def get_task_name(task_id):
                 '#junction_peptides_novel':0
             })
 
-    raise Exception
-
     if args.export_explorers and args.export_explorers == 1:
         hupo_mapping = {}
         unique_mapping = {}