Merge branch 'dev' of https://github.com/rcedgar/muscle into dev

conflict

Author: rcedgar

test_results/success_list.txt

@@ -1 +1 @@
-muscle5.2.linux64[cbf158b]	2024-08-19/05:36:26
+muscle5.2.linux64[b81d621]	2024-08-19/10:13:05

test_scripts/RUN_TESTS.bash

@@ -0,0 +1,14 @@
+#!/bin/bash -e
+
+if [ ! -s ./_run_tests.bash ] ; then
+	echo "ERROR -- must run in test_scripts/ directory"
+	exit 1
+fi
+
+./_run_tests.bash
+
+if [ $? != 0 ] ; then
+	echo === FAILED ===
+fi
+
+tail ../test_output/TEST_LOG.txt

test_scripts/_run_tests.bash

@@ -24,7 +24,12 @@ echo STARTED `date` >> $log
 ./run_rdrp_seqs.bash
 ./run_rdrp_structs.bash
 
+./qscore_BB_seqs.bash
+./qscore_BB_structs.bash
+./qscore_rdrp.bash
+
 python3 ./check_logs.py
+python3 ./check_results.py
 python3 ./update_success_list.py $ver $date
 
 echo COMPLETED $date >> $log

test_scripts/check_results.py

@@ -0,0 +1,54 @@
+#!/usr/bin/python3
+
+import sys
+import re
+
+errors = 0
+def qscore(fn, Q=None, TC=None):
+	global errors
+	q = None
+	tc = None
+	lines = []
+	try:
+		for line in open(fn):
+			lines.append(line)
+
+	except:
+		print("ERROR reading file " + fn)
+		errors += 1
+		return
+	for line in lines:
+		if line.find(", TC=") > 0:
+			M = re.search(r"Q=([0-9.]*), TC=([0-9.]*)", line)
+			if not M is None:
+				q = float(M.group(1))
+				tc = float(M.group(2))
+				break
+	if q is None or tc is None:
+		print("ERROR Q= TC= not found " + fn)
+		errors += 1
+	if q < Q*0.7:
+		print("ERROR Q %.4f << %.4f %s" % (q, Q, fn))
+		errors += 1
+	if tc < TC*0.7:
+		print("ERROR T %.4f << %.4f %s" % (tc, TC, fn))
+		errors += 1
+
+qscore("../test_logs/qscore_BB_seqs_BB11001.log", Q=1, TC=1)
+qscore("../test_logs/qscore_BB_seqs_BB11002.log", Q=0.611, TC=0)
+qscore("../test_logs/qscore_BB_seqs_BB11004.log", Q=0.674, TC=0.5)
+qscore("../test_logs/qscore_BB_seqs_BB11005.log", Q=0.568, TC=0.17)
+qscore("../test_logs/qscore_BB_seqs_BB11006.log", Q=0.561, TC=0.375)
+qscore("../test_logs/qscore_BB_seqs_BB11007.log", Q=0.837, TC=0.662)
+qscore("../test_logs/qscore_BB_seqs_BB11009.log", Q=0.758, TC=0.7)
+qscore("../test_logs/qscore_BB_structs_BB11001.log", Q=0.985, TC=0.982)
+qscore("../test_logs/qscore_BB_structs_BB11002.log", Q=0.838, TC=0.353)
+qscore("../test_logs/qscore_BB_structs_BB11004.log", Q=0.812, TC=0.685)
+qscore("../test_logs/qscore_BB_structs_BB11005.log", Q=0.754, TC=0.455)
+qscore("../test_logs/qscore_BB_structs_BB11006.log", Q=0.683, TC=0.5)
+qscore("../test_logs/qscore_BB_structs_BB11007.log", Q=0.925, TC=0.768)
+qscore("../test_logs/qscore_BB_structs_BB11009.log", Q=0.764, TC=0.617)
+qscore("../test_logs/qscore_rdrp.log", Q=0.589, TC=0.155)
+
+print("check_results %d errors" % errors)
+exit(1 if errors > 0 else 0)

test_scripts/qscore_BB_seqs.bash

@@ -6,7 +6,7 @@ mkdir -p $outdir $logdir
 
 for acc in `cat ../test_data/info/BB.accs`
 do
-	muscle \
+	../bin//muscle \
 	  -qscore ../test_output/BB_seqs/$acc \
 	  -ref ../test_data/ref_alns/$acc \
 	  -log ../test_logs/qscore_BB_seqs_$acc.log

test_scripts/qscore_BB_structs.bash

@@ -6,7 +6,7 @@ mkdir -p $outdir $logdir
 
 for acc in `cat ../test_data/info/BB.accs`
 do
-	muscle \
+	../bin/muscle \
 	  -qscore ../test_output/BB_structs/$acc \
 	  -ref ../test_data/ref_alns/$acc \
 	  -bysequence \

test_scripts/qscore_rdrp.bash

@@ -1,4 +1,4 @@
-muscle \
+../bin/muscle \
   -qscore ../test_output/rdrp/rdrp_seqs.afa \
   -ref ../test_output/rdrp/rdrp_structs.afa \
   -bysequence \