From a6e7f5a04ebba86cf0ff8d7fe49d14e5715801d8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9my=20Dernat?= <remy.dernat@umontpellier.fr>
Date: Thu, 7 Nov 2019 17:34:28 +0100
Subject: [PATCH] adding a normalize option
---
orthofinder/orthofinder.py | 26 +++++++++++++++++++-------
1 file changed, 19 insertions(+), 7 deletions(-)
diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
index 2e5067b..b95b83f 100755
--- a/orthofinder/orthofinder.py
+++ b/orthofinder/orthofinder.py
@@ -923,6 +923,7 @@ class Options(object):#
self.speciesXMLInfoFN = None
self.speciesTreeFN = None
self.mclInflation = g_mclInflation
+ self.qNormalize = False # score normalization from Blast results
def what(self):
for k, v in self.__dict__.items():
@@ -932,17 +933,18 @@ class Options(object):#
def ProcessArgs(prog_caller):
"""
Workflow
- | 1. Fasta Files | 2. Prepare files | 3. Blast | 4. Orthogroups | 5. Gene Trees | 6. Reconciliations/Orthologues |
+ | 1. Fasta Files | 2. Prepare files | 3.a Blast | 3.b Normalize Blast scores | 4. Orthogroups | 5. Gene Trees | 6. Reconciliations/Orthologues |
Options
Start from:
-f: 1,2,..,6 (start from fasta files, --fasta)
-b: 4,5,6 (start from blast results, --blast)
- -fg: 5,6 (start from orthogroups/do orthologue workflow, --from-groups)
- -ft: 6 (start from gene tree/do reconciliation, --from-trees)
+ -N: 3b (start from blast results, --normalize)
+ -fg: 5,6 (start from orthogroups/do orthologue workflow, --from-groups)
+ -ft: 6 (start from gene tree/do reconciliation, --from-trees)
Stop at:
- -op: 2 (only prepare, --only-prepare)
- -og: 4 (orthogroups, --only-groups)
+ -op: 2 (only prepare, --only-prepare)
+ -og: 4 (orthogroups, --only-groups)
"""
if len(sys.argv) == 1 or sys.argv[1] == "--help" or sys.argv[1] == "help" or sys.argv[1] == "-h":
PrintHelp(prog_caller)
@@ -977,6 +979,11 @@ def ProcessArgs(prog_caller):
util.Fail()
options.qStartFromBlast = True
continuationDir = GetDirectoryArgument(arg, args)
+ elif arg == "-N" or arg == "--Normalize":
+ if options.qNormalize:
+ print("Repeated argument: -n/--normalize\n")
+ util.Fail()
+ options.qNormalize = True
elif arg == "-fg" or arg == "--from-groups":
if options.qStartFromGroups:
print("Repeated argument: -fg/--from-groups\n")
@@ -1200,8 +1207,8 @@ def ProcessArgs(prog_caller):
if options.qPhyldog and (not options.speciesTreeFN):
print("ERROR: Phyldog currently needs a species tree to be provided")
- util.Fail()
-
+ util.Fail()
+
if resultsDir_nonDefault != None and ((not options.qStartFromFasta) or options.qStartFromBlast):
print("ERROR: Incompatible arguments, -o (non-default output directory) can only be used with a new OrthoFinder run using option '-f'")
util.Fail()
@@ -1209,6 +1216,11 @@ def ProcessArgs(prog_caller):
if options.search_program not in (prog_caller.ListSearchMethods() + ['blast']):
print("ERROR: Search program (%s) not configured in config.json file" % options.search_program)
util.Fail()
+
+ if options.qNormalize and options.qStartFromFasta:
+ # not a failure/exit, just a warning
+ print("ERROR: Normalize option is not needed when starting from fasta")
+ util.Fail()
util.PrintTime("Starting OrthoFinder")
print("%d thread(s) for highly parallel tasks (BLAST searches etc.)" % options.nBlast)
--
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