From 389d09347ccd792a792cb36b35cb425a835172fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dernat=20R=C3=A9my?= <remy.dernat@umontpellier.fr>
Date: Fri, 8 Nov 2019 15:46:48 +0100
Subject: [PATCH] Normalize option
---
orthofinder/orthofinder.py | 12 +++++++-----
orthofinder/scripts/files.py | 2 +-
2 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
index d7a4b59..46149b0 100755
--- a/orthofinder/orthofinder.py
+++ b/orthofinder/orthofinder.py
@@ -494,7 +494,7 @@ class WaterfallMethod:
def ProcessBlastHits(seqsInfo, blastDir_list, Lengths, iSpecies, qDoubleBlast):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
- # process up to the best hits for each species; Bi is a list of matrix
+ # process up to the best hits for each species; Bi is a list of matrices
Bi = []
for jSpecies in range(seqsInfo.nSpecies):
# getting Bit scores matrix for iSpecies on jSpecies
@@ -934,13 +934,13 @@ class Options(object):#
def ProcessArgs(prog_caller):
"""
Workflow
- | 1. Fasta Files | 2. Prepare files | 3.a Blast | 3.b Normalize Blast scores | 4. Orthogroups | 5. Gene Trees | 6. Reconciliations/Orthologues |
+ | 1. Fasta Files | 2. Prepare files | 3 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)
- -N: 3b (start from blast results, --normalize)
+ -N: 3.b (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:
@@ -985,6 +985,7 @@ def ProcessArgs(prog_caller):
print("Repeated argument: -N/--normalize\n")
util.Fail()
options.qNormalize = True
+ continuationDir = GetDirectoryArgument(arg, args)
elif arg == "-fg" or arg == "--from-groups":
if options.qStartFromGroups:
print("Repeated argument: -fg/--from-groups\n")
@@ -1174,8 +1175,8 @@ def ProcessArgs(prog_caller):
util.Fail()
# check argument combinations
- if not (options.qStartFromFasta or options.qStartFromBlast or options.qStartFromGroups or options.qStartFromTrees):
- print("ERROR: Please specify the input directory for OrthoFinder using one of the options: '-f', '-b', '-fg' or '-ft'.")
+ if not (options.qStartFromFasta or options.qStartFromBlast or options.qStartFromGroups or options.qStartFromTrees or options.qNormalize):
+ print("ERROR: Please specify the input directory for OrthoFinder using one of the options: '-f', '-b', '-N', '-fg' or '-ft'.")
util.Fail()
if options.qStartFromFasta and (options.qStartFromTrees or options.qStartFromGroups):
@@ -1379,6 +1380,7 @@ def DoNormalize(options, speciesInfoObj, seqsInfo):
"""
DoNormalize is a lighweigth version of the DoOrthogroups function
It will just normalize scores from a blast output
+ and write back blast results to *.norm.txt.gz
"""
# Run Algorithm, cluster and output cluster files with original accessions
util.PrintUnderline("Running OrthoFinder algorithm")
diff --git a/orthofinder/scripts/files.py b/orthofinder/scripts/files.py
index e7c7994..e527af0 100644
--- a/orthofinder/scripts/files.py
+++ b/orthofinder/scripts/files.py
@@ -589,7 +589,7 @@ class PreviousFilesLocator_new(PreviousFilesLocator):
Get all relevant data from log file.
Checks the paths ssaved do exist still
Should work with relevant paths to allow directory to move
- Other methods can then check that the data required for a particualr run is available
+ Other methods can then check that the data required for a particular run is available
"""
with open(logFN, 'r') as infile:
for line in infile:
--
GitLab