diff --git a/orthofinder/orthofinder.py b/orthofinder/orthofinder.py
index d4e3ee0fdc321dbb7fc880317a4d2ae7d4744723..f04594ba00c66c46d31934975a8c903cb5cc5c4c 100755
--- a/orthofinder/orthofinder.py
+++ b/orthofinder/orthofinder.py
@@ -449,18 +449,18 @@ class WaterfallMethod:
Bi.append(Bij)
if qNormalizeAndFixZeros:
for jSpecies in range(seqsInfo.nSpecies):
- WaterfallMethod.WriteFixNewScores(seqsInfo, blastDir_list, Bi[jSpecies], seqsInfo.speciesToUse[iSpecies], seqsInfo.speciesToUse[jSpecies], qDoubleBlast=qDoubleBlast)
+ WaterfallMethod.WriteFixNewScores(seqsInfo, blastDir_list, seqsInfo.speciesToUse[iSpecies], seqsInfo.speciesToUse[jSpecies], qDoubleBlast=qDoubleBlast)
matrices.DumpMatrixArray("B", Bi, iSpecies)
BH = GetBH_s(Bi, seqsInfo, iSpecies)
matrices.DumpMatrixArray("BH", BH, iSpecies)
util.PrintTime("Initial processing of species %d complete" % iSpecies)
@staticmethod
- def Worker_ProcessBlastHits(cmd_queue, qDoubleBlast, qNormalize=False):
+ def Worker_ProcessBlastHits(cmd_queue, qDoubleBlast, qNormalize=False, qNormalizeAndFixZeros=False):
while True:
try:
args = cmd_queue.get(True, 1)
- WaterfallMethod.ProcessBlastHits(*args, qDoubleBlast=qDoubleBlast, qNormalize=qNormalize)
+ WaterfallMethod.ProcessBlastHits(*args, qDoubleBlast=qDoubleBlast, qNormalize=qNormalize, qNormalizeAndFixZeros=qNormalizeAndFixZeros)
except queue.Empty:
return
@@ -472,11 +472,10 @@ class WaterfallMethod:
blast_file_processor.WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, qDoubleBlast=qDoubleBlast)
@staticmethod
- def WriteFixNewScores(seqsInfo, blastDir_list, B, iSpecies, jSpecies, qDoubleBlast):
+ def WriteFixNewScores(seqsInfo, blastDir_list, iSpecies, jSpecies, qDoubleBlast):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
- # process up to the best hits for each species; Bi is a list of matrices
- blast_file_processor.WriteFixNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, qDoubleBlast=qDoubleBlast)
+ blast_file_processor.WriteFixNormalizedBlastFile(blastDir_list, iSpecies, jSpecies, qDoubleBlast=qDoubleBlast)
@staticmethod
def ConnectCognates(seqsInfo, iSpecies):
@@ -1149,7 +1148,7 @@ def ProcessArgs(prog_caller):
# check argument combinations
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'.")
+ print("ERROR: Please specify the input directory for OrthoFinder using one of the options: '-f', '-b', '-N', '-NF', '-fg' or '-ft'.")
util.Fail()
if options.qStartFromFasta and (options.qStartFromTrees or options.qStartFromGroups):
@@ -1192,12 +1191,12 @@ def ProcessArgs(prog_caller):
print("ERROR: Search program (%s) not configured in config.json file" % options.search_program)
util.Fail()
- if options.qNormalize and ( options.qNormalizeAndFixZeros or options.qStartFromFasta or options.qStartFromBlast or options.qStartFromGroups or options.qStartFromTrees ) :
+ if options.qNormalize and ( options.qStartFromFasta or options.qStartFromBlast or options.qStartFromGroups or options.qStartFromTrees ) :
# not a failure/exit, just a warning
print("ERROR: --normalize option is not possible with other options")
util.Fail()
- if options.qNormalizeAndFixZeros and ( options.qNormalize or options.qStartFromFasta or options.qStartFromBlast or options.qStartFromGroups or options.qStartFromTrees ) :
+ if options.qNormalizeAndFixZeros and ( options.qStartFromFasta or options.qStartFromBlast or options.qStartFromGroups or options.qStartFromTrees ) :
# not a failure/exit, just a warning
print("ERROR: --normalize-fix option is not possible with other options")
util.Fail()
diff --git a/orthofinder/scripts/blast_file_processor.py b/orthofinder/scripts/blast_file_processor.py
index 4be8c4c6b4096b0ae5badae1e6e18b791ef50f71..ea41e9fb4b23b3a327fd93b90d862fe2a400e2d6 100644
--- a/orthofinder/scripts/blast_file_processor.py
+++ b/orthofinder/scripts/blast_file_processor.py
@@ -41,6 +41,24 @@ file_read_mode = 'rb' if PY2 else 'rt'
#file_write_mode = 'wb+' if PY2 else 'wt+'
file_write_mode = 'wb+'
+def GetSpeciesOrder(iSpecies, jSpecies, qDoubleBlast):
+ # checking species order to get the right filenames
+ if not qDoubleBlast:
+ qRev = (iSpecies > jSpecies)
+ else:
+ qRev = False
+ if qRev:
+ iQ = 1
+ iH = 0
+ iSpeciesOpen = jSpecies
+ jSpeciesOpen = iSpecies
+ else:
+ iQ = 0
+ iH = 1
+ iSpeciesOpen = iSpecies
+ jSpeciesOpen = jSpecies
+ return iSpeciesOpen, jSpeciesOpen, iQ, iH
+
def GetBLAST6Scores(seqsInfo, blastDir_list, iSpecies, jSpecies, qExcludeSelfHits = True, sep = "_", qDoubleBlast=True):
qSameSpecies = iSpecies==jSpecies
qCheckForSelfHits = qExcludeSelfHits and qSameSpecies
@@ -118,46 +136,31 @@ def WriteNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, sep = "_", qD
sys.stderr.write("\t".join(map(str, row)) + "\n")
raise
-def WriteFixNormalizedBlastFile(blastDir_list, B, iSpecies, jSpecies, sep = "_", qDoubleBlast=True):
+def WriteFixNormalizedBlastFile(blastDir_list, iSpecies, jSpecies, sep = "_", qDoubleBlast=True):
iSpeciesOpen, jSpeciesOpen, iQ, iH = GetSpeciesOrder(iSpecies, jSpecies, qDoubleBlast)
row = ""
rows = []
- for d in blastDir_list:
- fn = d + "Blast%d_%d.txt" % (iSpeciesOpen, jSpeciesOpen)
- fnNorm = d + "Blast%d_%d.norm.blastout" % (iSpeciesOpen, jSpeciesOpen)
- if os.path.exists(fn) or os.path.exists(fn + ".gz"): break
- try:
- with (gzip.open(fn + ".gz", file_read_mode) if os.path.exists(fn + ".gz") else open(fn, file_read_mode)) as blastfile:
- blastreader = csv.reader(blastfile, delimiter='\t')
- tempfile = NamedTemporaryFile(mode='w', delete=False)
- blastwriter = csv.writer(tempfile, delimiter='\t')
- for row in blastreader:
- rows.append(row)
- newrows = sc.scnorm.FixZeroNormalizedScores(iSpeciesOpen, jSpeciesOpen, iQ, iH, sep, B, rows)
- for the_row in newrows:
- blastwriter.writerow(the_row)
- tempfile.flush()
- tempfile.close()
- move(tempfile.name, fnNorm)
- except Exception:
- sys.stderr.write("Malformatted line in %sBlast%d_%d.txt\nOffending line was:\n" % (d, iSpecies, jSpecies))
- sys.stderr.write("\t".join(map(str, row)) + "\n")
- raise
+ # 0.0 normalized value should only happen for self-hits
+ if iSpeciesOpen == jSpeciesOpen:
+ for d in blastDir_list:
+ fnNorm = d + "Blast%d_%d.norm.blastout" % (iSpeciesOpen, jSpeciesOpen)
+ fnNormFix = d + "Blast%d_%d.norm.fix.blastout" % (iSpeciesOpen, jSpeciesOpen)
+ if os.path.exists(fnNorm): break
+ try:
+ with open(fnNorm, file_read_mode) as blastfile:
+ blastreader = csv.reader(blastfile, delimiter='\t')
+ tempfile = NamedTemporaryFile(mode='w', delete=False)
+ blastwriter = csv.writer(tempfile, delimiter='\t')
+ for row in blastreader:
+ rows.append(row)
+ newrows = sc.scnorm.FixZeroNormalizedScores(iSpeciesOpen, jSpeciesOpen, rows)
+ for the_row in newrows:
+ blastwriter.writerow(the_row)
+ tempfile.flush()
+ tempfile.close()
+ move(tempfile.name, fnNormFix)
+ except Exception:
+ sys.stderr.write("Malformatted line in %sBlast%d_%d.txt\nOffending line was:\n" % (d, iSpecies, jSpecies))
+ sys.stderr.write("\t".join(map(str, row)) + "\n")
+ raise
-def GetSpeciesOrder(iSpecies, jSpecies, qDoubleBlast):
- # checking species order to get the right filenames
- if not qDoubleBlast:
- qRev = (iSpecies > jSpecies)
- else:
- qRev = False
- if qRev:
- iQ = 1
- iH = 0
- iSpeciesOpen = jSpecies
- jSpeciesOpen = iSpecies
- else:
- iQ = 0
- iH = 1
- iSpeciesOpen = iSpecies
- jSpeciesOpen = jSpecies
- return iSpeciesOpen, jSpeciesOpen, iQ, iH
diff --git a/orthofinder/scripts/scnorm.py b/orthofinder/scripts/scnorm.py
index ed4c385400f20c6886bca7e525256f44607d7a44..70bf908076f0bab11dabc21da91817ec73da2ba5 100644
--- a/orthofinder/scripts/scnorm.py
+++ b/orthofinder/scripts/scnorm.py
@@ -126,8 +126,8 @@ class scnorm:
"""
This function retrieve the Normalization Score
from Matrix B from (Seq iQ, Seq iH)
- If it is 0.0, it will try to retrieve
- a modified value from the log10 fitting curve
+ and return the csv rows modified
+ by adding normalization score as a new column
"""
newrows = []
for row in rows:
@@ -148,43 +148,35 @@ class scnorm:
return newrows
@staticmethod
- def FixZeroNormalizedScores(iSpeciesOpen, jSpeciesOpen, iQ, iH, sep, B, rows):
+ def FixZeroNormalizedScores(iSpeciesOpen, jSpeciesOpen, rows):
"""
This function retrieve the Normalization Score
- from Matrix B from (Seq iQ, Seq iH)
+ from current csv file (with Seq iQ, Seq iH)
If it is 0.0 (self-hits), it will try to retrieve
a modified value from the log10 fitting curve
"""
- NormBS = 0.0
+ selfHitNormBlastScore = "0.0"
+ NormBS = selfHitNormBlastScore
newrows = []
# retrieve value from plot https://code-examples.net/en/q/8863d1
- print(repr(iSpeciesOpen))
- print(repr(f))
- all_plots = f[0][jSpeciesOpen].get_xydata()
+ all_plots = f[jSpeciesOpen][0].get_xydata()
+ print(repr(all_plots))
+ line = 0
for row in rows:
- # Get hit and query IDs
- try:
- sequence1ID = int(row[iQ].split(sep, 2)[1])
- sequence2ID = int(row[iH].split(sep, 2)[1])
- except (IndexError, ValueError):
- sys.stderr.write("\nERROR: Query or hit sequence ID in BLAST results file was missing or incorrectly formatted.\n")
- raise
try:
- newscore = B[sequence1ID, sequence2ID]
- if newscore == 0.0:
- #sys.stderr.write("\nWARNING: 0.0 value detected in seq position %d %d for Blast species %d %d!\n" % (sequence1ID, sequence2ID, iSpeciesOpen, jSpeciesOpen))
+ if row[12] == selfHitNormBlastScore:
try:
x = float(row[11])
for index, values in all_plots:
if values == x:
NormBS = index
break
- row.append(NormBS)
+ row[12] = NormBS
except (IndexError, ValueError):
sys.stderr.write("\nERROR: 12th field in BLAST results file line should be the bit-score for the hit\n")
- row.append(newscore)
except IndexError as e:
- sys.stderr.write("\nERROR: Matrix index on Blast species %d %d, sequences B[%d, %d] : %s \n" % (iSpeciesOpen, jSpeciesOpen, sequence1ID, sequence2ID, e))
+ sys.stderr.write("\nERROR: csv values on Blast species %d %d file, line %d : %s \n" % (iSpeciesOpen, jSpeciesOpen, line, e))
pass
newrows.append(row)
+ line+=1
return newrows