def translate_image(self, image_name, x_units, y_units):
input_image = cv2.imread(image_name, 1)
file_name = "ReferenceImages/translation.jpg"
translation = Translation()
translated_image = translation.translate(input_image, y_units, x_units)
cv2.imwrite(file_name, translated_image)
rows, cols = translated_image.shape[0], translated_image.shape[1]
return file_name, rows, cols
def askTranslator(self):
useropt = Validator.isValidAnswer(self, '1', '2')
if useropt == '1':
translator_obj = self.Translator()
translated_phrase = translator_obj.translate(
ReadandWrite.readFile(self),
dest=LanguageFromCode.getLanguageCode(self))
self.data = "\n%s \n\nOriginal Language was %s" % (
translated_phrase.text, Translation.detectLanguage(self))
return self.data
elif useropt == '2':
translator_obj = self.Translator()
translated_phrase = translator_obj.translate(
User.typing(self), dest=LanguageFromCode.getLanguageCode(self))
self.data = "\n%s \n\nOriginal Language was %s" % (
translated_phrase.text, Translation.detectLanguage(self))
return self.data
def loadExonSequences(self,axisSequenceRef,exons):
numExons=len(exons)
strand=self.strand
for i in range(numExons):
exon=exons[i]
start=exon.begin
length=exon.end-start
exonSeq=axisSequenceRef[start:start+length]
if(len(exonSeq)!=length):
raise Exception("start="+str(start)+", length="+str(length)
+", but substrate "+self.substrate+
" ends at "+len(axisSequenceRef))
if(strand=="-"):
exonSeq=Translation.reverseComplement(exonSeq)
exon.sequence=exonSeq
return True
def parse_page(page, cfg):
# Get raw page values.
raw = page.get_all_values()
translationsColumnId = int(cfg["TRANSLATION_COLUMN"]) - 1
# Get list of languages.
languagesRowId = int(cfg["LANGUAGES_ROW"]) - 1
langRow = raw[languagesRowId]
languagesNb = len(langRow)
languages = []
for columnId in range(translationsColumnId, languagesNb):
languages.append(raw[languagesRowId][columnId])
translationRowId = int(cfg["TRANSLATION_ROW"]) - 1
# Comments column ids.
commentKeyColumnId = int(cfg["COMMENT_KEY_COLUMN"]) - 1
groupKeyColumnId = int(cfg["GROUP_KEY_COLUMN"]) - 1
# Key column ids.
androidKeyColumnId = int(cfg["ANDROID_KEY_COLUMN"]) - 1
iosKeyColumnId = int(cfg["IOS_KEY_COLUMN"]) - 1
# Parse translations.
group_name_var = ''
translations = []
for rowId in range(0, len(raw)):
# Skip non-translation rows.
if rowId < translationRowId:
continue
tr = Translation()
# Comment keys.
comment = raw[rowId][commentKeyColumnId]
tr.comment = comment if len(comment) else None
group_key = raw[rowId][groupKeyColumnId]
group_name_var = group_key if len(group_key) else group_name_var
# print('parsed group name {}'.format(group_name_var))
tr.group = group_name_var
# Platform keys.
androidKey = raw[rowId][androidKeyColumnId]
tr.androidKey = androidKey if len(androidKey) else None
ios_key = raw[rowId][iosKeyColumnId]
tr.iosKey = ios_key if len(ios_key) else None
# Get translations.
for columnId in range(translationsColumnId, languagesNb):
tr.translations.append(raw[rowId][columnId])
translations.append(tr)
return languages, translations
def translate(body, vector):
from Translation import Translation
return Translation(body, vector)
## check the gnome background dir for Xdg
if not os.path.exists(gstyle_backgrounds_data_dir):
os.makedirs(gstyle_backgrounds_data_dir, 0700)
print "Gstyle Config ok"
## arg debug levels
LEVELS = {
'debug': logging.DEBUG,
'info': logging.INFO,
'warning': logging.WARNING,
'error': logging.ERROR,
'critical': logging.CRITICAL
}
if len(sys.argv) > 1:
level_name = sys.argv[1]
level = LEVELS.get(level_name, logging.NOTSET)
logging.basicConfig(level=level)
## LOCALISATION
source_lang = "en"
rep_trad = "/usr/share/locale"
traduction = Translation(APP_NAME, source_lang, rep_trad)
gettext.install(APP_NAME)
gtk.glade.bindtextdomain(APP_NAME, rep_trad)
gettext.textdomain(APP_NAME)
_ = traduction.gettext
def get_translation(word):
translation = Translation("proba", "test", 0)
return translation
#filename="/home/bmajoros/1000G/assembly/BRCA1-NA19782.fasta";
filename="/Users/bmajoros/python/test/data/subset.fasta"
print(FastaReader.getSize(filename))
[defline,seq]=FastaReader.firstSequence(filename)
print(len(seq))
#filename="/home/bmajoros/1000G/assembly/test.fasta"
filename="/Users/bmajoros/python/test/data/subset.fasta"
hash=FastaReader.readAllAndKeepDefs(filename)
for key in hash.keys():
[defline,seq]=hash[key]
print(defline)
[id,attrs]=FastaReader.parseDefline(defline)
print("id="+id)
for key,value in attrs.items():
print(key+"="+value)
writer=FastaWriter()
writer.writeFasta(">ABCD","ATCGATCGTAGCTAGTCTGCGCGTATCGTCAGTCTCTATCGATCGTACTGCGATCTAGCTAGCTGATCGTAGCTTCTATGACTGCTAGTCATCTAGCTAGCTGATCGTAGCTGCGCGCGATATATTGCATCTATGCTATCATTGCATGCTAGCTCTAGCTAGTCGATGCTATCTTAGCTAC","test1.fasta")
writer.appendToFasta(">XYZ","GATTACA","test1.fasta")
print(Translation.translate(seq))
print("forward:",seq)
print("revcomp: ",Translation.reverseComplement(seq))
def trimUTR(self,axisSequenceRef):
self.adjustOrders()
stopCodons=self.stopCodons
sequence=self.sequence
strand=self.strand
numExons=self.numExons()
startCodon=self.startCodon
if(not startCodon):
raise Exception("can't trim UTR, because startCodon is not set")
for j in(numExons):
exon=self.getIthExon(j)
length=exon.getLength()
if(length<=startCodon):
self.deleteExon(j)
numExons-=1
j-=1
startCodon-=length
self.adjustOrders() ### 4/1/03
else:
if(strand=="+"):
exon.trimInitialPortion(startCodon)
self.begin=exon.begin
else:
exon.trimInitialPortion(startCodon)### ???
self.end=exon.end
exon.type="initial-exon" if numExons>1 else "single-exon"
self.startCodon=0
break
# Find in-frame stop codon
codonIterator=CodonIterator(self,axisSequenceRef,stopCodons)
stopCodonFound=False
while(True):
codon=codonIterator.nextCodon()
if(not codon): break
if(stopCodons.get(codon.triplet,None)):
exon=codon.exon
coord=codon.absoluteCoord
trimBases=0
if(strand=="+"): trimBases=exon.end-coord-3
else: trimBases=coord-exon.begin-3
if(trimBases>=0):
exon.trimFinalPortion(trimBases)
exon.type="single-exon" if exon.order==0 else "final-exon"
j=numExons-1
while(j>exon.order):
self.deleteExon(j)
j-=1
stopCodonFound=True
break
else: # codon is interrupted; trim the next exon
nextExon=self.getSuccessor(exon)
if(not nextExon):
raise Exception("exon successor not found")
nextExon.trimFinalPortion(nextExon.getLength()+trimBases)
nextExon.type="final-exon"
j=numExons-1
while(j>nextExon.order):
self.deleteExon(j)
j-=1
stopCodonFound=True
break
if(not stopCodonFound):
### sometimes the GFF coords don't include the stop codon...
numExons=self.numExons()
lastExon=self.getIthExon(numExons-1)
lastExonEnd=lastExon.getEnd()
seq=axisSequenceRef
if(strand=="+"):
stopCodonBegin=lastExonEnd
stopCodon=seq[stopCodonBegin:stopCodonBegin+3]
if(stopCodon!="TAG" and stopCodon!="TAA" and stopCodon!="TGA"):
print("Warning! No stop codon found for",
self.transcriptId,self.strand,
"strand , unable to trim UTR")
else: # strand="-"
stopCodonBegin=lastExon.getBegin()-3
stopCodon=seq[stopCodonBegin,stopCodonBegin+3]
stopCodon=Translation.reverseComplement(stopCodon)
if(stopCodon!="TAG" and stopCodon!= "TAA" and stopCodon!="TGA"):
print("Warning! No stop codon found for",
self.transcriptId,self.strand,
"strand , unable to trim UTR")
self.recomputeBoundaries()