def tap(iX, iY): """[点击手势] [点击屏幕上某个点坐标] Args: iX ([int]): [点击的坐标x] iY ([int]): [点击的坐标y] """ osPopen('adb %s shell input tap %d %d' % (get_devices_str(), iX, iY)) return
def move(iStartX, iStartY, iEndX, iEndY, dura=800): """[滑动手势,从起点滑动到终点] Args: iStartX ([int]): [开始坐标x] iStartY ([int]): [开始坐标y] iEndX ([int]): [终点坐标x] iEndY ([int]): [终点坐标y] dura (int, optional): [滑动时长ms]. Defaults to 800ms. """ osPopen('adb %s shell input swipe %d %d %d %d %d' % (get_devices_str(), iStartX, iStartY, iEndX, iEndY, dura)) return
def scan_polypyrimidines(self): """ """ intronseq = self.dnasequence() co = osPopen(""" echo ">intron\n%s\n" | %s %s """ % ( intronseq,PYTHON_PATH,EXECUTABE_SCAN_POLYPYRIMIDINES ) ) gfflines = parsegfftxt( co.read(), offset=self.start ) co.close() return gfflines
def _parse_cexpander_string(fname, verbose=False): """ @attention: deprecated function, not used in any of the functions above """ command = """ cat %s | grep "\$start_values" -A 1000 | grep "\$end_values" -m 1 -B 1000 | sed 's/^.*_values$//' | sed '/^$/d' | tr -d "\\t" | tr -d "\\n" """ % fname if verbose: print command co = osPopen(command) cexpanderstring = co.read().strip() co.close() return cexpanderstring
def _parse_cexpander_string(fname,verbose=False): """ @attention: deprecated function, not used in any of the functions above """ command = """ cat %s | grep "\$start_values" -A 1000 | grep "\$end_values" -m 1 -B 1000 | sed 's/^.*_values$//' | sed '/^$/d' | tr -d "\\t" | tr -d "\\n" """ % fname if verbose: print command co = osPopen(command) cexpanderstring = co.read().strip() co.close() return cexpanderstring
def WAS_scan_branchpoint(self): """ """ intronseq = self.dnasequence() co = osPopen(""" echo ">intron\n%s\n" | %s %s """ % ( intronseq,EXECUTABE_SCAN_BRANCHPOINT, EXECUTABLE_SFM ) ) gfflines = parsegfftxt( co.read(), offset=self.start ) co.close() orderable = [ ( int(line[3]), line ) for line in gfflines ] orderable.sort() orderable.reverse() return [ gffline for pos,gffline in orderable ]
def getConnectedDevices(): """[获取当前已连接的设备] Returns: [list]: [设备列表] """ connected = [] osPopen('adb devices > t.txt') with open('t.txt') as f: lines = f.read().splitlines() lines.remove(lines[-1]) lines.remove(lines[0]) for i in lines: a = str(i).partition('\tdevic')[0] connected.append(a) osOs.remove('t.txt') print(connected) try: return connected except: return
def ligtPhone(): osPopen('adb %s shell input keyevent 224' % (get_devices_str()))
def vmSize(): sVmSize = osPopen('adb shell wm size').read() aVmSize = osRe.search(r'(\d+)x(\d+)', sVmSize) return {'w': aVmSize.group(1), 'h': aVmSize.group(2)}
def closeApp(sVal): osPopen('adb %s shell am force-stop %s' % (get_devices_str(), sVal))
def callApp(sVal): osPopen('adb %s shell am start -D -S -n %s' % (get_devices_str(), sVal))
def backKey(): """[返回键] """ osPopen('adb %s shell input keyevent 4' % (get_devices_str())) return
def keyCode(number): osPopen('adb %s shell input keyevent %d' % (get_devices_str(), number))
def closePhone(): osPopen('adb %s shell reboot -p' % (get_devices_str()))
def rebootPhone(): osPopen('adb %s reboot -p' % (get_devices_str()))
def closeScreen(): osPopen('adb %s shell input keyevent 26' % (get_devices_str()))
def screen_brightness_mod(isAuto=1): osPopen('adb %s shell settings put system screen_brightness_mode %d' % (get_devices_str(), isAuto))
def screen_brightness(iLen=255): osPopen('adb %s shell settings put system screen_brightness %d ' % (get_devices_str(), iLen))
def _merge_pacbporfs_by_tinyexon_and_two_introns(pacbporfD,pacbporfA, orfSetObject,queryorsbjct,verbose = False, **kwargs): """ Merge 2 PacbPORF objects by introns @attention: see pacb.connecting.merge_orfs_with_intron for **kwargs) @type pacbporfD: PacbPORF object @param pacbporfD: PacbPORF object that has to deliver PSSM donor objects @type pacbporfA: PacbPORF object @param pacbporfA: PacbPORF object that has to deliver PSSM acceptor objects @type orfSetObject: object with elegiable Orfs @param orfSetObject: object with elegiable Orfs @type queryorsbjct: string @param queryorsbjct: literal string 'query' or 'sbjct' @type verbose: Boolean @param verbose: print debugging info to STDOUT when True @rtype: list @return: list with ( intron, ExonOnOrf, intron ) on the query sequence """ # input validation IsPacbPORF(pacbporfD) IsPacbPORF(pacbporfA) # edit **kwargs dictionary for some forced attributes _update_kwargs(kwargs,KWARGS_PROJECTED_TINYEXON) MAX_TINYEXON_NT_LENGTH = 33 MIN_TINYEXON_NT_LENGTH = 6 tinyexons = [] if queryorsbjct == "query": donorOrf = pacbporfD.orfQ accepOrf = pacbporfA.orfQ prjctOrf = pacbporfD.orfS alignedDonorRange = pacbporfD.alignment_dna_range_query() alignedAccepRange = pacbporfA.alignment_dna_range_query() elif queryorsbjct == "sbjct": donorOrf = pacbporfD.orfS accepOrf = pacbporfA.orfS prjctOrf = pacbporfD.orfQ alignedDonorRange = pacbporfD.alignment_dna_range_sbjct() alignedAccepRange = pacbporfA.alignment_dna_range_sbjct() else: message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct raise InproperlyAppliedArgument, message for dObj in donorOrf._donor_sites: # do not make a projection OVER the aligned area if dObj.pos < min(alignedDonorRange): continue if queryorsbjct == "query": (dPos,dPhase) = pacbporfD.dnaposition_query(dObj.pos,forced_return=True) else: (dPos,dPhase) = pacbporfD.dnaposition_sbjct(dObj.pos,forced_return=True) try: algDobj = pacbporfD._positions[dPos] except IndexError: # site out of range of PacbPORF -> break break for aObj in accepOrf._acceptor_sites: # do not make a projection OVER the aligned area if aObj.pos > max(alignedAccepRange): continue if queryorsbjct == "query": (aPos,aPhase) = pacbporfA.dnaposition_query(aObj.pos,forced_return=True) else: (aPos,aPhase) = pacbporfA.dnaposition_sbjct(aObj.pos,forced_return=True) try: algAobj = pacbporfA._positions[aPos] except IndexError: # site out of range of PacbPORF -> break break if queryorsbjct == "query": posDsbjct = algDobj.sbjct_dna_start + dPhase posAsbjct = algAobj.sbjct_dna_start + aPhase else: posDsbjct = algDobj.query_dna_start + dPhase posAsbjct = algAobj.query_dna_start + aPhase distance = posAsbjct - posDsbjct if distance >= MAX_TINYEXON_NT_LENGTH: break if distance < MIN_TINYEXON_NT_LENGTH: continue #################################################### # generate a ScanForMatches pattern file #################################################### # example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3 query = list(prjctOrf.inputgenomicsequence[posDsbjct:posAsbjct]) # mask all non-phase0 nucleotides to N residues; # this represents the regularexpression for a specific # peptide sequence firstphasepositions = range( 3-dPhase % 3, len(query), 3) for pos in range(0,len(query)): if pos not in firstphasepositions: query[pos] = "N" # calculate a ~50% mismatch number mismatches = max([ 0, (len(query) - query.count("N"))/2 ]) # write the pattern to string and subsequently to file # example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3 if kwargs['allow_non_canonical_donor']: sfmpat = "%s...%s AG %s[%s,0,0] G (T | C) %s...%s" % ( AUSO,AUSO,"".join(query),mismatches,DDSO,DDSO) else: sfmpat = "%s...%s AG %s[%s,0,0] GT %s...%s" % ( AUSO,AUSO,"".join(query),mismatches,DDSO,DDSO) #################################################### if verbose: print (pacbporfD.orfQ.id,pacbporfA.orfQ.id), print distance, dObj, aObj print sfmpat #################################################### fname = "sfmpat_tinyexon_%s_%s_%s_%s" % ( donorOrf.id, accepOrf.id, posDsbjct, posAsbjct, ) fh = open(fname,'w') fh.write(sfmpat+"\n") fh.close() #################################################### # run ScanForMatches #################################################### command = """echo ">myseq\n%s" | %s %s | tr "[,]" "\t\t#" | """ +\ """tr -d "\n " | sed "s/>/\\n>/g" | tr "#" "\t" | """ +\ """awk -F'\t' '{ if (NF==4 && $2>%s && $3<%s) """ +\ """{ print $1"["$2","$3"]\\n"$4 } }' """ command = command % ( donorOrf.inputgenomicsequence, EXECUTABLE_SFM,fname, dObj.pos+(kwargs['min_intron_nt_length']-3), aObj.pos-(kwargs['min_intron_nt_length']-3) ) co = osPopen(command) matches = parseFasta(co.readlines()) co.close() # filter matches for: # (1) correct donor & acceptor phase # (2) high enough donor & acceptor site scores for hdr,seqmatch in matches.iteritems(): startQ,stopQ = [ int(item) for item in hdr.split(":")[1][1:-1].split(",") ] exonQstart = startQ + AUSO + 2 - 1 exonQstop = stopQ - DDSO - 2 #################################### # get Orf object of tinyexon #################################### tinyexonorf = None # select the Orf on which the tinyexon is located for orfObj in orfSetObject.get_elegiable_orfs( max_orf_start=exonQstart,min_orf_end=exonQstop): orfPhase = (exonQstart - orfObj.startPY) % 3 if orfPhase == dPhase: tinyexonorf = orfObj break else: # No tinyexonorf assigned!! Iin case a regex matched # over a STOP-codon or the regex length is smaller # then the smallest Orf, no Orf can be assigned continue # filter for donor & acceptor score dScore = _score_splice_site(seqmatch[-9:],splicetype='donor') aScore = _score_splice_site(seqmatch[0:11],splicetype='acceptor') if dScore < kwargs['min_donor_pssm_score']: continue if aScore < kwargs['min_acceptor_pssm_score']: continue # scan Orf for splicesites tinyexonorf.scan_orf_for_pssm_splice_sites( splicetype="donor", min_pssm_score=kwargs['min_donor_pssm_score'], allow_non_canonical=kwargs['allow_non_canonical_donor'], non_canonical_min_pssm_score=kwargs['non_canonical_min_donor_pssm_score']) tinyexonorf.scan_orf_for_pssm_splice_sites( splicetype="acceptor", min_pssm_score=kwargs['min_acceptor_pssm_score'], allow_non_canonical=kwargs['allow_non_canonical_acceptor'], non_canonical_min_pssm_score=kwargs['non_canonical_min_acceptor_pssm_score']) # get 1th intron donor object intron1_aObj = None for a in tinyexonorf._acceptor_sites: if a.pos == exonQstart: intron1_aObj = a break else: # pseudo-acceptorsite as found be SFM regex # is not a valid acceptor site of high enough score # continue to next iteration of (hdr,seqmatch) pair continue # get 2th intron donor object intron2_dObj = None for d in tinyexonorf._donor_sites: if d.pos == exonQstop: intron2_dObj = d break else: # pseudo-donorsite as found be SFM regex # is not a valid acceptor site of high enough score # continue to next iteration of (hdr,seqmatch) pair continue # check if introns are of elegiable lengths if (intron1_aObj.pos-dObj.pos) > kwargs['max_intron_nt_length']: continue if (aObj.pos-intron2_dObj.pos) > kwargs['max_intron_nt_length']: continue #################################################### if True or verbose: # if here, a candidate!!! print (pacbporfD.orfQ.id,tinyexonorf.id,pacbporfA.orfQ.id), print hdr, dScore, aScore print seqmatch #################################################### # append to found tinyexons query_data = ( tinyexonorf, exonQstart, exonQstop ) sbjct_data = ( prjctOrf, posDsbjct, posAsbjct ) splicesite_data = ( dObj,intron1_aObj, intron2_dObj, aObj ) tinyexons.append( ( query_data, sbjct_data, splicesite_data ) ) # file cleanup osRemove(fname) # return - End Of Function - if no tinyexons are found if not tinyexons: return [] #################################### # select the **best** tinyexon #################################### (query_data,sbjct_data,splicesite_data) = tinyexons[0] orfQ,query_dna_start,query_dna_end = query_data orfS,sbjct_dna_start,sbjct_dna_end = sbjct_data (intron1_dObj,intron1_aObj,intron2_dObj,intron2_aObj) = splicesite_data #################################################### if verbose: print "tinyexon orf:", orfQ print "tinyexon orf:", intron1_aObj print "tinyexon orf:", intron2_dObj #################################################### #################################### # make tinyexon PacbPORF #################################### startQaa = orfQ.dnapos2aapos(query_dna_start) -1 startSaa = orfS.dnapos2aapos(sbjct_dna_start) -1 stopQaa = orfQ.dnapos2aapos(query_dna_end) +1 stopSaa = orfS.dnapos2aapos(sbjct_dna_end) +1 # check for directly leading stop codon on tinyexon while startQaa <= orfQ.protein_startPY: startQaa+=1 startSaa+=1 query_dna_start+=3 sbjct_dna_start+=3 while startSaa <= orfS.protein_startPY: startQaa+=1 startSaa+=1 query_dna_start+=3 sbjct_dna_start+=3 # check for directly tailing stop codon on tinyexon while stopQaa > orfQ.protein_endPY: stopQaa-=1 stopSaa-=1 query_dna_end-=3 sbjct_dna_end-=3 while stopSaa > orfS.protein_endPY: stopQaa-=1 stopSaa-=1 query_dna_end-=3 sbjct_dna_end-=3 # get sequences qAAseq = orfQ.getaas(abs_pos_start=startQaa,abs_pos_end=stopQaa) sAAseq = orfS.getaas(abs_pos_start=startSaa,abs_pos_end=stopSaa) #################################################### if verbose or len(qAAseq) != len(sAAseq): # if unequal lengths, error will be raised upon PacbP.__init__() print orfQ, qAAseq, startQaa, stopQaa, (stopQaa-startQaa), print (query_dna_start,query_dna_end) print orfS, sAAseq, startSaa, stopSaa, (stopSaa-startSaa), print (sbjct_dna_start,sbjct_dna_end) print orfQ.inputgenomicsequence[query_dna_start-2:query_dna_end+2] print orfS.inputgenomicsequence[sbjct_dna_start-2:sbjct_dna_end+2] #################################################### # initialize extended tinyexon PacbPORF from pacb import PacbP pacbp = PacbP(input=( qAAseq, sAAseq, startQaa, startSaa ) ) pacbp.strip_unmatched_ends() pacbporf = pacbp2pacbporf(pacbp,orfQ,orfS) pacbporf.extend_pacbporf_after_stops() pacbporf.source = 'ABGPprojectingTE' #################################### # make introns #################################### intron1 = IntronConnectingOrfs( intron1_dObj, intron1_aObj, None, donorOrf,pacbporf.orfQ ) intron2 = IntronConnectingOrfs( intron2_dObj, intron2_aObj, None, pacbporf.orfQ, accepOrf ) ################################################################ # set some meta-data properties to the intron objects ################################################################ # add distance score to intron intron1._distance = 0 intron2._distance = 0 # add Alignment Positional Periphery Score into objects if queryorsbjct == "query": succes = set_apps_intron_query(intron1,pacbporfD,pacbporf) succes = set_apps_intron_query(intron2,pacbporf,pacbporfA) else: succes = set_apps_intron_sbjct(intron1,pacbporfD,pacbporf) succes = set_apps_intron_sbjct(intron2,pacbporf,pacbporfA) # set GFF fsource attribute for recognition of intron sources intron1._gff['fsource'] = "ABGPprojectingTE" intron2._gff['fsource'] = "ABGPprojectingTE" # create _linked_to_xxx attributes intron1._linked_to_pacbporfs = [ pacbporf ] intron2._linked_to_pacbporfs = [ pacbporf ] intron1._linked_to_introns = [ intron2 ] intron2._linked_to_introns = [ intron1 ] #################################################### if verbose: print pacbporf pacbporf.print_protein_and_dna() print intron1 print intron2 if False: # printing data when this function needs to be debugged: print "" print intron1 print intron2 print "" print pacbporfD pacbporfD.print_protein_and_dna() print "" print pacbporf pacbporf.print_protein_and_dna() print "" print pacbporfA pacbporfA.print_protein_and_dna() import sys sys.exit() #################################################### # return introns and intermediate tinyexon PacbPORF return [(intron1,intron2,pacbporf)]
def _merge_pacbporfs_by_tinyexon_and_two_introns(pacbporfD, pacbporfA, orfSetObject, queryorsbjct, verbose=False, **kwargs): """ Merge 2 PacbPORF objects by introns @attention: see pacb.connecting.merge_orfs_with_intron for **kwargs) @type pacbporfD: PacbPORF object @param pacbporfD: PacbPORF object that has to deliver PSSM donor objects @type pacbporfA: PacbPORF object @param pacbporfA: PacbPORF object that has to deliver PSSM acceptor objects @type orfSetObject: object with elegiable Orfs @param orfSetObject: object with elegiable Orfs @type queryorsbjct: string @param queryorsbjct: literal string 'query' or 'sbjct' @type verbose: Boolean @param verbose: print debugging info to STDOUT when True @rtype: list @return: list with ( intron, ExonOnOrf, intron ) on the query sequence """ # input validation IsPacbPORF(pacbporfD) IsPacbPORF(pacbporfA) # edit **kwargs dictionary for some forced attributes _update_kwargs(kwargs, KWARGS_PROJECTED_TINYEXON) MAX_TINYEXON_NT_LENGTH = 33 MIN_TINYEXON_NT_LENGTH = 6 tinyexons = [] if queryorsbjct == "query": donorOrf = pacbporfD.orfQ accepOrf = pacbporfA.orfQ prjctOrf = pacbporfD.orfS alignedDonorRange = pacbporfD.alignment_dna_range_query() alignedAccepRange = pacbporfA.alignment_dna_range_query() elif queryorsbjct == "sbjct": donorOrf = pacbporfD.orfS accepOrf = pacbporfA.orfS prjctOrf = pacbporfD.orfQ alignedDonorRange = pacbporfD.alignment_dna_range_sbjct() alignedAccepRange = pacbporfA.alignment_dna_range_sbjct() else: message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct raise InproperlyAppliedArgument, message for dObj in donorOrf._donor_sites: # do not make a projection OVER the aligned area if dObj.pos < min(alignedDonorRange): continue if queryorsbjct == "query": (dPos, dPhase) = pacbporfD.dnaposition_query(dObj.pos, forced_return=True) else: (dPos, dPhase) = pacbporfD.dnaposition_sbjct(dObj.pos, forced_return=True) try: algDobj = pacbporfD._positions[dPos] except IndexError: # site out of range of PacbPORF -> break break for aObj in accepOrf._acceptor_sites: # do not make a projection OVER the aligned area if aObj.pos > max(alignedAccepRange): continue if queryorsbjct == "query": (aPos, aPhase) = pacbporfA.dnaposition_query(aObj.pos, forced_return=True) else: (aPos, aPhase) = pacbporfA.dnaposition_sbjct(aObj.pos, forced_return=True) try: algAobj = pacbporfA._positions[aPos] except IndexError: # site out of range of PacbPORF -> break break if queryorsbjct == "query": posDsbjct = algDobj.sbjct_dna_start + dPhase posAsbjct = algAobj.sbjct_dna_start + aPhase else: posDsbjct = algDobj.query_dna_start + dPhase posAsbjct = algAobj.query_dna_start + aPhase distance = posAsbjct - posDsbjct if distance >= MAX_TINYEXON_NT_LENGTH: break if distance < MIN_TINYEXON_NT_LENGTH: continue #################################################### # generate a ScanForMatches pattern file #################################################### # example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3 query = list(prjctOrf.inputgenomicsequence[posDsbjct:posAsbjct]) # mask all non-phase0 nucleotides to N residues; # this represents the regularexpression for a specific # peptide sequence firstphasepositions = range(3 - dPhase % 3, len(query), 3) for pos in range(0, len(query)): if pos not in firstphasepositions: query[pos] = "N" # calculate a ~50% mismatch number mismatches = max([0, (len(query) - query.count("N")) / 2]) # write the pattern to string and subsequently to file # example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3 if kwargs['allow_non_canonical_donor']: sfmpat = "%s...%s AG %s[%s,0,0] G (T | C) %s...%s" % ( AUSO, AUSO, "".join(query), mismatches, DDSO, DDSO) else: sfmpat = "%s...%s AG %s[%s,0,0] GT %s...%s" % ( AUSO, AUSO, "".join(query), mismatches, DDSO, DDSO) #################################################### if verbose: print(pacbporfD.orfQ.id, pacbporfA.orfQ.id), print distance, dObj, aObj print sfmpat #################################################### fname = "sfmpat_tinyexon_%s_%s_%s_%s" % ( donorOrf.id, accepOrf.id, posDsbjct, posAsbjct, ) fh = open(fname, 'w') fh.write(sfmpat + "\n") fh.close() #################################################### # run ScanForMatches #################################################### command = """echo ">myseq\n%s" | %s %s | tr "[,]" "\t\t#" | """ +\ """tr -d "\n " | sed "s/>/\\n>/g" | tr "#" "\t" | """ +\ """awk -F'\t' '{ if (NF==4 && $2>%s && $3<%s) """ +\ """{ print $1"["$2","$3"]\\n"$4 } }' """ command = command % (donorOrf.inputgenomicsequence, EXECUTABLE_SFM, fname, dObj.pos + (kwargs['min_intron_nt_length'] - 3), aObj.pos - (kwargs['min_intron_nt_length'] - 3)) co = osPopen(command) matches = parseFasta(co.readlines()) co.close() # filter matches for: # (1) correct donor & acceptor phase # (2) high enough donor & acceptor site scores for hdr, seqmatch in matches.iteritems(): startQ, stopQ = [ int(item) for item in hdr.split(":")[1][1:-1].split(",") ] exonQstart = startQ + AUSO + 2 - 1 exonQstop = stopQ - DDSO - 2 #################################### # get Orf object of tinyexon #################################### tinyexonorf = None # select the Orf on which the tinyexon is located for orfObj in orfSetObject.get_eligible_orfs( max_orf_start=exonQstart, min_orf_end=exonQstop): orfPhase = (exonQstart - orfObj.startPY) % 3 if orfPhase == dPhase: tinyexonorf = orfObj break else: # No tinyexonorf assigned!! Iin case a regex matched # over a STOP-codon or the regex length is smaller # then the smallest Orf, no Orf can be assigned continue # filter for donor & acceptor score dScore = _score_splice_site(seqmatch[-9:], splicetype='donor') aScore = _score_splice_site(seqmatch[0:11], splicetype='acceptor') if dScore < kwargs['min_donor_pssm_score']: continue if aScore < kwargs['min_acceptor_pssm_score']: continue # scan Orf for splicesites tinyexonorf.scan_orf_for_pssm_splice_sites( splicetype="donor", min_pssm_score=kwargs['min_donor_pssm_score'], allow_non_canonical=kwargs['allow_non_canonical_donor'], non_canonical_min_pssm_score=kwargs[ 'non_canonical_min_donor_pssm_score']) tinyexonorf.scan_orf_for_pssm_splice_sites( splicetype="acceptor", min_pssm_score=kwargs['min_acceptor_pssm_score'], allow_non_canonical=kwargs['allow_non_canonical_acceptor'], non_canonical_min_pssm_score=kwargs[ 'non_canonical_min_acceptor_pssm_score']) # get 1th intron donor object intron1_aObj = None for a in tinyexonorf._acceptor_sites: if a.pos == exonQstart: intron1_aObj = a break else: # pseudo-acceptorsite as found be SFM regex # is not a valid acceptor site of high enough score # continue to next iteration of (hdr,seqmatch) pair continue # get 2th intron donor object intron2_dObj = None for d in tinyexonorf._donor_sites: if d.pos == exonQstop: intron2_dObj = d break else: # pseudo-donorsite as found be SFM regex # is not a valid acceptor site of high enough score # continue to next iteration of (hdr,seqmatch) pair continue # check if introns are of elegiable lengths if (intron1_aObj.pos - dObj.pos) > kwargs['max_intron_nt_length']: continue if (aObj.pos - intron2_dObj.pos) > kwargs['max_intron_nt_length']: continue #################################################### if True or verbose: # if here, a candidate!!! print(pacbporfD.orfQ.id, tinyexonorf.id, pacbporfA.orfQ.id), print hdr, dScore, aScore print seqmatch #################################################### # append to found tinyexons query_data = (tinyexonorf, exonQstart, exonQstop) sbjct_data = (prjctOrf, posDsbjct, posAsbjct) splicesite_data = (dObj, intron1_aObj, intron2_dObj, aObj) tinyexons.append((query_data, sbjct_data, splicesite_data)) # file cleanup osRemove(fname) # return - End Of Function - if no tinyexons are found if not tinyexons: return [] #################################### # select the **best** tinyexon #################################### (query_data, sbjct_data, splicesite_data) = tinyexons[0] orfQ, query_dna_start, query_dna_end = query_data orfS, sbjct_dna_start, sbjct_dna_end = sbjct_data (intron1_dObj, intron1_aObj, intron2_dObj, intron2_aObj) = splicesite_data #################################################### if verbose: print "tinyexon orf:", orfQ print "tinyexon orf:", intron1_aObj print "tinyexon orf:", intron2_dObj #################################################### #################################### # make tinyexon PacbPORF #################################### startQaa = orfQ.dnapos2aapos(query_dna_start) - 1 startSaa = orfS.dnapos2aapos(sbjct_dna_start) - 1 stopQaa = orfQ.dnapos2aapos(query_dna_end) + 1 stopSaa = orfS.dnapos2aapos(sbjct_dna_end) + 1 # check for directly leading stop codon on tinyexon while startQaa <= orfQ.protein_startPY: startQaa += 1 startSaa += 1 query_dna_start += 3 sbjct_dna_start += 3 while startSaa <= orfS.protein_startPY: startQaa += 1 startSaa += 1 query_dna_start += 3 sbjct_dna_start += 3 # check for directly tailing stop codon on tinyexon while stopQaa > orfQ.protein_endPY: stopQaa -= 1 stopSaa -= 1 query_dna_end -= 3 sbjct_dna_end -= 3 while stopSaa > orfS.protein_endPY: stopQaa -= 1 stopSaa -= 1 query_dna_end -= 3 sbjct_dna_end -= 3 # get sequences qAAseq = orfQ.getaas(abs_pos_start=startQaa, abs_pos_end=stopQaa) sAAseq = orfS.getaas(abs_pos_start=startSaa, abs_pos_end=stopSaa) #################################################### if verbose or len(qAAseq) != len(sAAseq): # if unequal lengths, error will be raised upon PacbP.__init__() print orfQ, qAAseq, startQaa, stopQaa, (stopQaa - startQaa), print(query_dna_start, query_dna_end) print orfS, sAAseq, startSaa, stopSaa, (stopSaa - startSaa), print(sbjct_dna_start, sbjct_dna_end) print orfQ.inputgenomicsequence[query_dna_start - 2:query_dna_end + 2] print orfS.inputgenomicsequence[sbjct_dna_start - 2:sbjct_dna_end + 2] #################################################### # initialize extended tinyexon PacbPORF from pacb import PacbP pacbp = PacbP(input=(qAAseq, sAAseq, startQaa, startSaa)) pacbp.strip_unmatched_ends() pacbporf = pacbp2pacbporf(pacbp, orfQ, orfS) pacbporf.extend_pacbporf_after_stops() pacbporf.source = 'ABGPprojectingTE' #################################### # make introns #################################### intron1 = IntronConnectingOrfs(intron1_dObj, intron1_aObj, None, donorOrf, pacbporf.orfQ) intron2 = IntronConnectingOrfs(intron2_dObj, intron2_aObj, None, pacbporf.orfQ, accepOrf) ################################################################ # set some meta-data properties to the intron objects ################################################################ # add distance score to intron intron1._distance = 0 intron2._distance = 0 # add Alignment Positional Periphery Score into objects if queryorsbjct == "query": succes = set_apps_intron_query(intron1, pacbporfD, pacbporf) succes = set_apps_intron_query(intron2, pacbporf, pacbporfA) else: succes = set_apps_intron_sbjct(intron1, pacbporfD, pacbporf) succes = set_apps_intron_sbjct(intron2, pacbporf, pacbporfA) # set GFF fsource attribute for recognition of intron sources intron1._gff['fsource'] = "ABGPprojectingTE" intron2._gff['fsource'] = "ABGPprojectingTE" # create _linked_to_xxx attributes intron1._linked_to_pacbporfs = [pacbporf] intron2._linked_to_pacbporfs = [pacbporf] intron1._linked_to_introns = [intron2] intron2._linked_to_introns = [intron1] #################################################### if verbose: print pacbporf pacbporf.print_protein_and_dna() print intron1 print intron2 if False: # printing data when this function needs to be debugged: print "" print intron1 print intron2 print "" print pacbporfD pacbporfD.print_protein_and_dna() print "" print pacbporf pacbporf.print_protein_and_dna() print "" print pacbporfA pacbporfA.print_protein_and_dna() import sys sys.exit() #################################################### # return introns and intermediate tinyexon PacbPORF return [(intron1, intron2, pacbporf)]