[Bioperl-l] Problem with $seqobj->translate() when supplying parameters

[Brian Osborne]

Eric,

I took your code, unmodified, and ran it using a file in the distribution.
The output looks OK, different frames are used and I don't see "-frame" in
the output sequence (see below). This is using the latest bioperl-live -
what version Bioperl are you using?

Brian O.


269 ~/bioperl-live>./test.pl t/data/HUMBETGLOA.fa
loaded one sequence:
        display_id      HUMBETGLOA
        description     Human haplotype C4 beta-globin gene, complete cds.
translation = 
TSYLTPLITPLIVTLWVVSDFLFICIFDCIKRSLVFYLLFPKT**VTNAQSTLICIYSIFRHNLLACMSKLRKTTT
NECIYMYMYVCTYTHIYIYIFFLFLPEGFNPNKEKICLELR*SFHPFCPVSILHILETQEEIHLHIPKLNYGRQNS
STFSASTSYLCNKKIGKTIFNMLTKL*FQILRKYTCKGGCF**QFVLMVWGQEIYLRGRAEGLKSNS*ASARRAKD
RYGCHHLDLTLWSHTLGLANLLPGAGRAGARAGHKSQGRAIYCLHLLLTQLCSLATSNRHHGASDS*GEVCRYCPV
GQGERG*SWW*GPGQVGIKVTRQV*GDQ*KLGMWRQRRLLGF**ALTLSAYWSIFPPLGCWWSTLGPRGSLSPLGI
CPLLMLLWATLR*RLMARKCSVPLVMAWLTWTTSRAPLPH*VSCTVTSCTWILRTSG*VYGTLDVFFPLLFYG*VH
VIGRG*VTGYSLEWETDE*LHQCGSLRIVLVSFICCS*QLFSFV*FLLSFFFFSAIFTIILNALTLCITKGNISEI
H*VT*KKTLHSLPSTLLFGIYVCLFAYS*SPYFIFFYF*LIHNHYTYLWVKV*CFNMCTHIDQIRVILHL*F*KML
SSFNILFCLSYF*YFP*SLSFRAIMIQCIMPLCTILKNNSDNFWVKAIAISLHINISAYKL*LM*EVSYC**QLQS
SYHSAFILWLG*GWIILSPS*ALLLIMFIPLIFLPQLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHK
YH*ARFLAVQFLLKVPLFPKSNY*TGGYYEGP*ASGFCLIKNIYFHCNDVFKLFLNILLKRECGRSVHLKHKEMKS
*FKPWENTLYLKLHERR*GCKQLMHIGNSPDAYALFIPQKRIQVEA*FGG*SFAMLYFTLLIVLAVLMNVFSLPIC
LSCISQP*LHSVLLLRDTTFPLKCSFHVLRRDGFSSPGHSALVVSVVL*RST*RRKNRGHGLTVL*ALLPCLPHSQ
*PGICSASLPELS
translation = 
PPI*HH*LPH**SHFGL*VTFYLFVFLTALRGL*FFTSCFPKPNK*LMHRAH*FVFILFLDIIY*HA*AN*EKQQQ
MNAYICICMCVHIHIYIYIYFFFSYQKVLIQIRRRYA*N*GRVFIHSVL*VFCIFWRRRKRSIYISQS*IMVDKTL
PLLVHQLLICVIRKLGKRSSICLPSCDSKYYVNTLAKEDVFSSNLY*WYGAKRYILEGGLRV*SPTPKPVPEEPRT
GTAVIT*TSPCGATP*GWPIYSQEQGGQEPGLGIKVRAEPSIAYICF*HNCVH*QPQTDTMVHLTPEEKSAVTALW
GKVNVDEVGGEALGRLVSRLQDRFKETNRNWACGDREDSWVSDRH*LSLPIGLFSHP*AAGGLPLDPEVL*VLWGS
VHS*CCYGQP*GEGSWQESARCL**WPGSPGQPQGHLCHTE*AAL*QAARGS*ELQGESMGPLMFSFPFFSMVKFM
S*EGDK*QGTV*NGKQTNDCISVEVSGSF*FLLFAVHNNCFLLFNSCFLFFSSPQFLLLYLMP*HCV*QKEISLRY
IK*LKKKLYTVCLVHYYLEYMCAYLHIHNLPTLFSFIFN*YIIIIHIYGLKCNVLICVHILTKSG*FCICNFKKCF
LLLIYFFVYLISNTFPNLFLSGQ**YNVSCLFAPF*RITVIISGLRQ*QYLCI*IFLHINCN*CKRFHIANSSYNP
ATILLLFYGWDKAGLF*VQARPFC*SCSYLLSSSHSSWATCWSVCWPITLAKNSPHQCRLPIRKWWLVWLMPWPTS
ITKLAFLLSNFY*RFLCSLSPTTKLGDIMKGLEHLDSA**KTFIFIAMMYLNYF*IFY*KGNVGGQCI*NIKK*RA
SSNLGKIHYILNSMKEGEAANS*CTLATALMHMPYSSLRKGFK*RLDLEVKVLLCCILHYLLF*LSS*MSFHYPFA
YPASLSLDSTQFSCLEIPPFP*SVPSMFYGEMVSPRLATQP*LSLLSYRGLLEEGKTGVMV*LSCEPFFPASPTHS
DPESAVLVSRNY
translation = 
LLFDTTDYPIDSHTLGCK*LFIYLYF*LH*EVSSFLPLVSQNLISN*CTEHIDLYLFYF*T*FISMHEQIKKNNNK
*MHIYVYVCVYIYTYIYIYIFSFLTRRF*SK*GEDMLRTEVEFSSILSCKYFAYSGDAGRDPSTYPKAELW*TKLF
HF*CINFLFV**ENWENDLQYAYQAVIPNIT*IHLQRRMFLVAICTDGMGPRDIS*REG*GFEVQLLSQCQKSQGQ
VRLSSLRPHPVEPHPRVGQSTPRSREGRSQGWA*KSGQSHLLLTFASDTTVFTSNLKQTPWCI*LLRRSLPLLPCG
AR*TWMKLVVRPWAGWYQGYKTGLRRPIETGHVETEKTLGFLIGTDSLCLLVYFPTLRLLVVYPWTQRFFESFGDL
STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRVSLWDP*CFLSPSFLWLSSC
HRKGISNRVQFRMGNRRMIASVWKSQDRFSFFYLLFITIVFFCLILAFFFFLLRNFYYYT*CLNIVYNKRKYL*DT
LSNLKKNFTQSA*YITIWNICVLICIFIISLLYFLLFLIDT*SLYIFMG*SVMF*YVYTY*PNQGNFAFVILKNAF
FF*YTFLFILFLILSLISFFQGNNDTMYHASLHHSKE*Q**FLG*GNSNISAYKYFCI*IVTDVRGFILLIAATIQ
LPFCFYFMVGIRLDYSESKLGPFANHVHTSYLPPTAPGQRAGLCAGPSLWQRIHPTSAGCLSESGGWCG*CPGPQV
SLSSLSCCPISIKGSFVP*VQLLNWGIL*RALSIWILPNKKHLFSLQ*CI*IISEYFTKKGMWEVSAFKT*RNEEL
VQTLGKYTIS*TP*KKVRLQTANAHWQQP*CICLIHPSEKDSSRGLIWRLKFCYAVFYITYCFSCPHECLFTTHLL
ILHLSALTPLSSLA*RYHLSPEVFLPCFTARWFLLAWPLSLSCLCCLIEVYLKKEKQGSWFDCPVSPSSLPPPLTV
TRNLQC*SPGTI



On 10/15/07 2:50 PM, "Eric E. Snyder" <esnyder at vbi.vt.edu> wrote:

> Hello,
> 
> I am having trouble with translate() when supplying parameters such as
> -frame, -codontable_id, etc.  I am working straight out of the tutorial
> with a very simple program-- which has me stumped!
> 
> use Bio::SeqIO;
> foreach my $file ( @ARGV ){
>      my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
>                                      -format =>  "fasta" );
>      my $seq_obj = $seqio_obj->next_seq;
> 
>      print "loaded one sequence:\n\tdisplay_id\t" .
>   $seq_obj->display_id() . "\n" .
>   "\tdescription\t" . $seq_obj->description() . "\n";
> 
>      foreach my $frame ( 0 .. 2){
>          $prot_obj = $seq_obj->translate( '-frame' => $frame );
>          print "translation = " . $prot_obj->seq . "\n";
>      }
> }
> 
> Everything works as expected until calling translate.  The output I get
> is the translation of my FASTA sequence (in frame zero, repeated three
> times) in which every "stop" is replaced with "-frame" (!!).  However,
> with no parameters, translate works as advertised.
> 
> This is getting me down because by using the full complement of
> translate options, including specifying frame, genetic code, alternative
> start codons, etc., BioPerl will save me a huge amount of time... but
> only if I can figure out how to use it properly!
> 
> Any assistance would be greatly appreciated!!!
> 
> Sincerely,
> eesnyder
>