Discussion :

[loula427]

Je me permet un petit post dans cette section car j'ai un script de bio-info que je souhaiterais optimiser mais je suis a court de ressource.

J'ai un programme capable de lire des fichiers STOCKHOLM et de les convertir en differents autres formats (par exemple fasta... )

Je souhaite implementer une sous routine qui permette au programme de filtrer les donnees STOKHOLM grace aux valeurs PP et PP_cons presentent dans le fichier STOCKHOLM.

De la facon suivante :
- Si une position n'est pas conserve (PP_cons) je supprime la colonne dans tous les alignements.

- Si une position n'est pas conserve dans une sequence je remplace l'amino acide present a cette position par "-" dans la dite sequence.

Pour savoir quelles collones supprimer je cree un petit tableau @$columnToRemove contenant les positions ou PP_cons est inferieur au seuil souhaite.

Je travaille avec des PirObjects AlignedSeq :

Code :

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0  PirObject::AlignedSeq=HASH(0x17b9978)
   'PP' => '.................................................8764............................................................................................689**********************************************************************************************************************************************************************************************************************************99998......677889***********................................................*..*...*****......*******************..*.....****************************.***********************************..****************.****......**.****************...................................**********....*..**.*......................................*.**..............********.*******************........*****.......**...***************99999...887655.....22222.......................................................................................2.68999*************..***98...66.377.8.8999998666555..55...............44444.........222........1..2333333.........................................................................33333333332..2221111......................................1................................111111111111.11..1111.111.................1111........................................1111.................................11.......................................1....111...1110.11111..1...11..1...111111..1..................................1.2..23444444.....444.......44.4433......222...............................................................2333.......3....3332...2211......11111...................................................................................................................................11.1111111...........00.....1122...2.2.222211.......................112222111...11.111.1..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................111..1111....111111.111.111111..11........111111.1111...1234..67899*******.*******.*.....*********.........................*..****.........***********************************...***********.**************************755.....566666666515678................................................................99**************************************************999****************.****....***.................................................................................................*****************..*************************************************99988554444.................................43333330...............................................3445555666666777777777777777777778888888999999***********............................................................................................................................................................................................................................................................'
   'seqId' => 'Zygnema_circumcarinatum@AAX45864'
   'sequence' => '-------------------------------------------------MAEL--------------------------------------------------------------------------------------------KNRIFYNQVMDKSAIKQLIIRLVACLGRVCTAHILDQLKTLGFQYSTQTGISLGIDDLLASPLKNWILQDAENEANVSQEYCRHGYIHAVERLRQIVETWHTTSEFLKREMTVSFNILDGFNPVHMMSFSGARGNVSQVHQLVGMRGLISDPQGNIIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAIRTADAGYLTRRLVEVAQHVVIRNVDCNTYEGIILRSIRTRQGNA------YLTQENRIIGRVLARPL------------------------------------------------Y--F---GKRCI------AVRNQDIGPDLAAKLSIIS--P-----QAILVRSPITCKTTDWVCQLCYGWGVNQ-GKMVSLGEAIGVVAGQSIGEPGTQLTLRTFHTGGV--FTGDIANHLRAPFNGI-AHFE------TH-NCKPTRNRHGRLVWKC-----------------------------------LQDLTITVIG----Q--GK-K--------------------------------------H-SL--------------NVPSQSLL-LINNNQYVESKQVIAEVRA--------SIAPI-------KE---KVQRNIYSYLQGEVVHTRSA---LRLSNA-----FSGTI---------------------------------------------------------------------------------------L-LIHHNPNTGHLWIWSGKL--YQLSG---QQ-ASS-I-YTSEDFIQTNITV--AN---------------KRYLK---------FDT--------H--KISNKKV-------------------------------------------------------------------------LKSVLIGKFTR--FKQVKSI--------------------------------------Q--------------------------------TGTVRSVLIQKP-DT--LRMV-VLS-----------------SVDQ----------------------------------------LEIT---------------------------------MH---------------------------------------K----TPY---IMEP-LLTQK--I---SN--N---ILNLTS--Y----------------------------------P-K--SSTLISKQ-----KNT-------VS-SFAS------IHI---------------------------------------------------------------KRPT-------I----GFQF---QLPI------VPKIR-----------------------------------------------------------------------------------------------------------------------------------CY-SLGLLGK-----------LQ-----RPLQ---Y-N-LVLSSP-----------------------TQPIFIDRY---YN-TFT-N----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WCY--LNEH----GNSYNL-YGL-QMIVLD--KK--------LYNNNS-ISGL---FNTY--RNIPKIGQLICK-GTFVQQT-T-----QLSESGKIV-------------------------S--IFKH---------KIVLRLSQPYLLAPGTFIHPDCYDVINRGDIVITM---MYEQLRTTDII-QGLPKAEQLLEARSFNEVVLKLENDFVML-----TERIARQLRSLSRSY----------------------------------------------------------------MLSTKESTKHSQIDLVNRIQTVYLSQGVRIVDKHIEIIVRQMSSKVMLVENGDPHTFLPRELVELTRAQKI-NYVI----QNP-------------------------------------------------------------------------------------------------VAYKPVLLGITKASLNT--NSFISEASFQQTARVLSKSAIKNRVDWIRGLQENVLFGRMIPAGTGCREISSQLQYGNIF---------------------------------QKKWAQHT-----------------------------------------------KWKLFVNSFGLNLSCLQIYLHFQAYCLESTNEQPQSNLHVHNSRIFPFTTICSILKS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'
1  PirObject::AlignedSeq=HASH(0x17b99f0)
   'PP' => '....................................................6...............................................................................................7**************************************************************************************************************************************************************************************************************************************.......****************................................................*..*...*****......******************...9.....****************************.***********************************..****************.****......*******************...................................*********9....8..66.5......................................5.545............5********.******************9.......788889.......99...********************...999887.........................................................................................3.....678.9*****************..*****...**..**.*.*************..***......***..*******9........66552..........................................................................................23344444433...........................22..22......034.5.6.8................................9999********.**..****.***.................******..*********...***.....**********.**.*****86....................4567.99***.***...*******...*****......***...******.***....***...**********..*...**..**********..****...****************.**.....**.**.*..********.....***.......**.****......***.*.......**........****..........................*...*99..98.7*****.......*....****...****.**.**********...........................................................................................................*.**.****...*****.*..**.*******........*****.....****...*.*.******888......5534..33778888888887776......8**.*****...*....*****.........**99999...999888654......6.7888999999...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................**************.********.****..****99998864.4433...........................................................................................................................................................................................................................................................................................................................................35..7889999*****.*******.*.....*********.........................*..*99766.....668**********************************...***********.************************996443..322222222222....246699**********************.........**********************************************************************************.****************.****98888**.................................................................................................*****************..**************************************************9999777665554...........................43333222220...............................................222223334555666777777778888889999999999999**************.............................................................................................................................................................................................................................................................'
   'seqId' => 'Cyanothece_sp._atcc51142@ACB52835'
   'sequence' => '----------------------------------------------------M-----------------------------------------------------------------------------------------------TFYNQIVDKGRLKKLISWAYRNYGAARSSQVADNLKDLGFRYATKAGVSISIDDLTVPPTKRGMLDSAEKEINITEARYARGEITEVERFQKVIDTWNSTSEELKDEVVRNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMADPQGQIIDQPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREIDCGTRRGLKVTAMKDGDRVK-------IALGDRLLGRVLAEDV------------------------------------------------M--V---GDEVI------ASRNQSIDAALAAKIGKS---V-----ESVMVRSPLTCEAARSVCRCCYGWSLAT-GRPVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV--FTGEVAEQIKAPDHGT-VKWG------KGLSTRKVRTRHGEDAFQV-----------------------------------ELAGDLIWTP----T--GS-G--------------------------------------K-KMT------------YSVTPGSVL-FAADGDTVEKDKMLAEVTA-------AKSTRS-------TE---RATKDVSTDLAGEVFFANLI---AEEKTD-----------------------------------------------------------------------------------------R-----QGN-TTHIAQRGGLVWVLSGEV--YNLPP---GA--EP-V-VSNGDEVAEGTVL--AET------KLI--SVNGGVVR--------YQPQS------------------------------------------------------------------------------------------REIDIITASVL---------------------------LD--QA------EVR-K-E-S--------------------------------TGGHEQYVIYTA-DG--QRFL-LKA-----------------TPETKV--QNHAIIAEL---IDD-----RYQTTTGGML-RY-GGIEVAK--------------------GSRK-TGYEV-VQG---GTLLWVP---EETHE------VNK---DISLLV-VED----GQY---VEAGTEVVKD--I---FC--QCSGAIEVVQ--KNDI---LREIIIKPGEFHLDVD-PD-----EV-SY-K--NEDLIPPG-----TEV-------LP-GVVT------TDL-R-------QV--------EWIE--------------------------S---TEG--LG-LLLRPV-------E----EYPV---SNEP-AA-PSQGSINEEE-----------------------------------------------------------------------------------------------------------V-GR-HIEL---RSVQR-L--FY-KDGERVK--------SVDGI-----HLLS---T-Q-LVLEIETGS------EQAA--ANLAADIELKNDEEEDC------QRL-QLVIL---E----SLILR---------RDLDTDP---HGGTITTSV------L-VTDGDQIAPG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AVVAKTEIQCREEG-EVRGIRRG-LEAV--RRVLIVRDEDLE-IITL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KE--KPTVAKDDLIVA-GTEFAPG-V-----VAAESGLVV-------------------------A--VNQGEE-----GYEIKLRLARPYRVSPGAILHIADGDLVQRGDNLVLL---VYERAKTGDII-QGLPRIEELLEARKPKEACVLSRKPGVCQV--EYLEDESVDVKV----IEDDGTVSEYPILLNQNVIVSDNQRVDV---------GEHLTDGPANPHELLEVFFDYYVDKKGVYEAALIGLQAAQKFLVDQVQSVYQSQGIDISDKHIEVIVRQMTAKVRVDDGGDT-TMLPGELVELRQIEQV-NEAMAITGGAP-------------------------------------------------------------------------------------------------ARYTPVLLGITKASLNT--DSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFNAHEEMVMGTLDNGED---------------------------SLNNRYGQGER-----------------------------------------------DNNNSDKKPPNRLIGATLDEVDENMILDDNIARAYTEADPPWSVESKQEKDDDDDK-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'
2  PirObject::AlignedSeq=HASH(0x17b9af8)
   'PP' => '..............................................8876655..............................................................556667778888888888888888777.....9***************************************************************************************************************************************************************************************************************************************.......*************************************************************9988..8...*****......******************...9.....****************************.***********************************..****************.****......*******************...................................**********....*..99.98999999999.................988888877766.66..............********.****************9855.....5588888.......88...9*******************...99988765778888887766444899999999.............................................999999976655555555......689.999999999999999999..99999...88..5548.8899999999999..999......999..99888888........788888888.888..88877779999999999999999999..................................9999999986666666666655555555555..555555555.....4...44....443..3...............0333..........................345778888888888.88..8888.888.................777766..55554433......3.....7889999999.99.999999988887...6555....78999999.99999.99*...*******...*****......***...******.***....***...**********..*...**..**********..966........7889********.**.....**.**.*..********.....***.......**.****......***.*.......**........****..........................*...998..88.....88.......8....99.6...7778.89.999999****...........................................................................................................*.**.****...***99.98778.999999877...77778888.....9999...*.*.*********......**......**********86.67...78.***.*****...*....*99887777777766677777...889999999999.999.8888777766**********************************************************************************************************************************************************************************************************************************************************************************************************************************************************..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................*******************************************************************************************************************************************************************************************************************************************************************************************************************************************************999966777777777777.77655555.5555..677778888888.8887...............44444433.................3443304444444555555556666666666677777777777777778888888888888888888888889999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999*****************99****..**....**...*..........****.......******..****....*99997.5...889999..**........*****9.9999...5777..99**********.***9876.55566699*******.........................*..****.........***********************************...***********.**************************8......67*********.****................................................................******************************************************.****************.***99..88**.................................................................................................*****************..**********************************************75....................................................................................................68...................................................................................................................................................................................................................................................................................................................'
   'seqId' => 'Stigeoclonium_helveticum@YP_764414'
   'sequence' => '----------------------------------------------MNIFSDF--------------------------------------------------------------SLYSLSPKKKTSLTDNKIVSFATKDFP-----QVFWNLSFNKGSLKNFVFWCFVNYGQRETIKILEKLQIIGFGYATKAGISLSIDDLKIPPTKAILLADADKSIEAGFLSYKKSQLTGLERFQRIIETWHKTSESLKDEMITNFRQTDSLNPVYMMAFSGARGNVSQVRQLVAMRGLMSDPQGKILDFPIRSNFREGLTLTEYVISCYGARKGVVDTALRTANAGYLTRRLVDVAQHVIVLNFDCGTKKGFYLTEMKKFNKTL-------YPLRQRLLGRVLAANLYNVNPFHLKKRIEIGEKEKNLSSLPSSKGKMEFFPSFPQASLAGKASCF--P---EPQIV------AFRNQEISEPLAEKISKI---T-----NKVFIRSPLTCDTPRLVCQLCYGWSLSE-GYLVSIGEAVGIIAAQSIGEPGTQLTMRTFHTGGV--FAGEMFDQLMAPYDGI-VQYS------SSIPGTLVRTTQGKIAFLT-----------------------------------KVEGKLSVFE----K--NN-STFLSNSNNGD-----------------NHSLISHTISHK-SF--------------KLPAYTLL-FIRNNETISKDQLIAELAFL-----SSKGKKK-------GE---IAEFIVKSEIEGQLYSGSVN---ILEKYTDYNDIMTKSIDWGSVWILSGKICQLP---------------------------------------------VNSSFFALPGDLVDENAI------LSQ-IQWVVPMKSLLDTNSLIK--PNLKK---EI--YFDF-SLNQTKWFQKRNL--ENL------NTL--FNLKFGIE--------KKNRTKKRV-LSQ--EKKSDFLNPSFSHSSRNYLYFSLPSK----------------------------------KTFSYYPFAYFSKIKEKNGGRETKSSFAMSG--WGKKSLSFF-----P---SL----ASD--V---------------PKLL--------------------------SDFYPTSKKRNFKSF-EK--KELK-LSS-----------------FSQTIF--FNQDKSLL------L-----KMKIKIQTIS-DF-TKVSSKMITSRE---LKKN----GMEKGKNG-EKENS-SLQ---RTFFSQG---AKAPA------FPE---LFSFFS-SRL----FPI---LPFKSSLVSS--T---FS--HNSQLCTIRR--QNK--------LVLSGNSNQFEN-FA-----YL-KD-K--ITINLPLI-----FLC-------ID-NIYY------KKI-G-------YF--------FSLF--------------------------P---PES--KI-----PR-------E----KF-L---PEEE-GF-SPPSFGRTFK-----------------------------------------------------------------------------------------------------------N-KN-LAKL---KDVFF-VPKLL-EQRNIISTK---KKNSFKKN-----NQIS---N-Q-LLHWFPKSY------LT------MKGGICVYRLTH-DF---FC-QYI-NFHSS---S----FLFEKKRGTLICNVDGEMNKP---VSSNILGRICWV-NQD-YKKTKLYTLKFFSYSKFIQQLTDRTKRLQRQIKREKKIGQADFFQTVLSMSQAKEKSSLQRTFFSQGAKSRKKVPPKTLLSGEMPIFSLSPSLCGLKPAKRSEKEKIWVKGEKAELFSLSNAFHQPQHSKKHKYSSFSLNFYKNLTSYCLKNKDKSVANCFSEKKKRQFLFFSEPKLSLFPDFLFSKSEKNIFYNANKKKYSFFYLKKTNSSKKSLTNNSIMNGFIYKPKDVVSAISLHKKFFLPGQKIIDDLSFDNFLIYVECIPEDNLSSLSETLYKSRFDKKICFNLKKLITNKMPRFIKIPTLLSTIPFAFLKSEFKEQNEKIAQRKADRQKNNKKSEAFFFKSNTLVSDFD--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SPFLSHLVVLITKVIEYPLYKPNHYKKALYNRQKTSEQSFFHYSCKVKSKMLNKIFKNNYHSNVLNKQTSSLRLLDKFPNTDLVLALKCKGIQKDLMENFLKNPLNLNLYVKLGKQKSFGKEKDKTFSVSQPFFKSSAFKKEKKSNSFSQAKAFDFNLTSKKSRKKANKLVENLANGKKSRAFPASKACGKLGKNYIFPLEERKNGKKERAKASSFPGLLSFSHLAFPIFFRKSFSKFFCMKFFSKSSIQLLELVLVGVQKNSVNNKIIGITVFNFFQKNKLKEEEKKRQEEKEIFRSLSLSPLFLSHLTRKKNSDFFSVSKSEALEKKKLQLLFFSHAAFPLKEISKNYSSKASFLSFFH-FLDKKIKK-QTRR--QANFVVSAFEKS-DFSF---------------DPNINRKK-----------------KYFSNKAFNYENIKIMNNNISQSILQPNFYFNYYQKYPFGYYLINNINVFAPSSFSFSSLFSRNTANFKNYFLFYQLLSMFNRPNFQLHKSMEENLLQVYEQSTSYFSLISCFFQQPCFDAFFTQQVSFGFNEVKNVNHYSKNLTFSKKIGKRREFYLSPFLRSKIYFKKNSFSEQGEIALTQYLSPFMGEILNH--EN----YY---W----------SQNT-------QKNRYL--LLTK----KDQISF-L---STNYNT--QK--------ESINNS-SFFI---LKNK--KNTPNLGEFLTK-GDCCFIS-KSQNSIISSESGLIV-------------------------H--SNKS---------KITLRKAQSFFLSPNCIFHYSHGDLVEKNKSILSL---PYEQLKTGDIV-QGIPKVEQLLEARSTFKGKEEEDNLHK------LLKYAFELYKT-KFSL----------------------------------------------------------------KLSVRKSFSFIQLILVNSVQRIYRSQGVSISDKHLEVIVKQMTSKVQITSRGDS-SFFRGEHVDLYIVETW-NALHP--QLKK-------------------------------------------------------------------------------------------------ICYKPILLGISRSSLEV--NSFLSAASFQHTKKVLSRSAFKTNIDFLNGLKENVIIGNLISAGTGNL----------------------------------------------------------------------------------------------------NN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------'

ensuite je passe a travers le PirObject MultAlign (qui contient les objet AlignedSeq) et traite chaque sequence.
Je commence par m'occuper des probabilites par sequence definies par "PP" puis je continue dans la meme boucle par enlever les collones definies par "PP_cons".

J'ai essaye de faire les choses de differentes facons :
en utilisant un splice pour supprimer les collones, avec un remplacement de caractere puis une substitution...

Dans l'absolue mon algo fonctionne je souhaite gagner du temps a l'execution car c'est actuellement trop lent.
Pour un fichier contenant 104 sequences de 4938aa le programme met un peu moins de 2min a rouler.

Sachant que dans la partie la du code :

Code :

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        foreach my $alignedSeq (@$alignedSeqs) {
            my $PP  = $alignedSeq->get_PP();
            my $Seq = $alignedSeq->get_sequence();
            #Treat LOCALPERCENT
            my @aPP  = split(//,$PP);
            my @aSeq = split(//,$Seq);
            for (my $i = @aSeq - 1; $i >= 0 ; $i--) {
                my $PP_val = $aPP[$i];
                $PP_val    =  0  if $PP_val eq ".";
                $PP_val    = 10  if $PP_val eq "*";
                $aSeq[$i]  = "-" if $PP_val < $LocalPercent;
                $aSeq[$i]  = "=" if grep($_ == $i, @$columnToRemove)
            }

Il met 1 seconde par sequence... je ne sais pas comment reduire le temps
d'execution.

Je met ci-dessous le code de ma sous routine de filtration.

Code :

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sub FilteringStockholm {
    my $ma = shift;
 
    my $PP_cons     = $ma->get_PP_cons();
    die "Can't use option -F no line 'PP_cons' found in $INFILE\n" 
        if $PP_cons eq "" && $FILTERING == 1;
    my $alignedSeqs = $ma->get_alignedSeqs();
 
    #Make array with pos to remove use GLOBALPERCENT
    print "\n Make column to Remove :".strftime("\%H:\%M:\%S", gmtime(time));
    my $GlobalPercent = $GLOBALPERCENT;
       $GlobalPercent = 10 if $GLOBALPERCENT eq "*";
       $GlobalPercent = 0  if $GLOBALPERCENT eq ".";
    my @aPP_cons = split(//,$PP_cons);
    my $columnToRemove = ();
 
    for ( my $i = 0 ; $i < @aPP_cons ; $i++) {
        my $PP_val = $aPP_cons[$i];
        $PP_val    =  0 if $PP_val eq ".";
        $PP_val    = 10 if $PP_val eq "*";
        push(@$columnToRemove,$i) if $PP_val < $GlobalPercent;
    }
 
    #Treat each Seq with LOCALPERCENT and GLOBALPERCENT
    my $LocalPercent = $LOCALPERCENT;
       $LocalPercent = 10 if $LOCALPERCENT eq "*";
       $LocalPercent = 0  if $LOCALPERCENT eq ".";
    foreach my $alignedSeq (@$alignedSeqs) {
        my $PP  = $alignedSeq->get_PP();
        my $Seq = $alignedSeq->get_sequence();
        #Treat LOCALPERCENT
        my @aPP  = split(//,$PP);
        my @aSeq = split(//,$Seq);
        for (my $i = @aSeq - 1; $i >= 0 ; $i--) {
            my $PP_val = $aPP[$i];
            $PP_val    =  0  if $PP_val eq ".";
            $PP_val    = 10  if $PP_val eq "*";
            $aSeq[$i]  = "-" if $PP_val < $LocalPercent;
            $aSeq[$i]  = "=" if grep($_ == $i, @$columnToRemove)
        }
 
        $Seq = join('',@aSeq);
        $Seq =~ s/=//g;
        $alignedSeq->set_sequence($Seq);
    }
}

Si vous avez besoin d'autre information n'hesite pas a me demander.

Merci de m'avoir lu jusqu'ici

Loula

[loula427]

Voila mon probleme est resolu.

Au final la partie qui etait inneficace etait celle contenant le grep.

Voici ma nouvelle boucle :

Code :

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    #Treat each Seq with LOCALPERCENT and GLOBALPERCENT
    my $LocalPercent = $LOCALPERCENT;
       $LocalPercent = 10 if $LOCALPERCENT eq "*";
       $LocalPercent = 0  if $LOCALPERCENT eq ".";
    my %cols_to_remove = map { $_ => 1 } @$columnToRemove;
    foreach my $alignedSeq (@$alignedSeqs) {
        my $PP  = $alignedSeq->get_PP();
        my $Seq = $alignedSeq->get_sequence();
        #Treat LOCALPERCENT
        for (my $i = length($Seq) - 1; $i >= 0 ; $i--) {
            my $PP_val = substr($PP,$i,1);
            $PP_val    =  0  if $PP_val eq ".";
            $PP_val    = 10  if $PP_val eq "*";
            substr($Seq,$i,1) = "-" if $PP_val < $LocalPercent;
            substr($Seq,$i,1) = ""  if $cols_to_remove{$i};
        }
        $alignedSeq->set_sequence($Seq);
    }

Peut etre que ca servira a quelqu'un un jour, je l'espere en tous cas moi je garde ca en memoire .