From pjotr.public14 at thebird.nl Wed Nov 25 11:27:31 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 25 Nov 2009 17:27:31 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib Message-ID: <20091125162731.GA3589@thebird.nl> The EMBOSS branch of biolib contains a first mapping of EMBOSS functions to Ruby. I'll add Perl and Python soon. More importantly I have done a writeup of the mapping process. It can be found at: http://biolib.open-bio.org/wiki/Mapping_EMBOSS I think it aptly describes what it takes to map 410 functions (below). Please have a look and comment. Including the write up it took about a day. Pj. AjOSeqCvt_size_set AjOSeqCvt_size_get AjOSeqCvt_len_set AjOSeqCvt_len_get AjOSeqCvt_missing_set AjOSeqCvt_missing_get AjOSeqCvt_nrlabels_set AjOSeqCvt_nrlabels_get AjOSeqCvt_bases_set AjOSeqCvt_bases_get AjOSeqCvt_rlabels_set AjOSeqCvt_rlabels_get AjOSeqCvt_clabels_set AjOSeqCvt_clabels_get AjOSeqCvt_table_set AjOSeqCvt_table_get AjOSeqCvt_nclabels_set AjOSeqCvt_nclabels_get AjOSeqCvt_Padding_set AjOSeqCvt_Padding_get AjOSeqCvt_allocate AjOSeqCvt_allocate new_AjOSeqCvt ajSeqtestIsAccession ajSeqtestIsSeqversion ajSeqallDel ajSeqallGetCount ajSeqallGetFilename ajSeqallGetseqName ajSeqallGetseqBegin ajSeqallGetseqEnd ajSeqallGetseqLen ajSeqallGetName ajSeqallGetseqRange ajSeqallGetTotlength ajSeqallGetUsa ajSeqallNew ajSeqallClear ajSeqallClearStats ajSeqallNext ajSeqallSetRange ajSeqallSetRangeRev ajSeqAssignAccC ajSeqAssignAccS ajSeqAssignDescC ajSeqAssignDescS ajSeqAssignEntryC ajSeqAssignEntryS ajSeqAssignFileC ajSeqAssignFileS ajSeqAssignFullC ajSeqAssignFullS ajSeqAssignGiC ajSeqAssignGiS ajSeqAssignNameC ajSeqAssignNameS ajSeqAssignSeqC ajSeqAssignSeqLenC ajSeqAssignSeqS ajSeqAssignSvC ajSeqAssignSvS ajSeqAssignUfoC ajSeqAssignUfoS ajSeqAssignUsaC ajSeqAssignUsaS ajSeqGetBegin ajSeqGetSeqC ajSeqGetSeqS ajSeqGetSeqCopyC ajSeqGetSeqCopyS ajSeqCalcCheckgcg ajSeqClear ajSeqComplement ajSeqstrComplement ajSeqstrConvertNum ajSeqGetFeatCopy ajSeqCalcCount ajSeqstrCountGaps ajSeqcvtDel ajSeqcvtGetCodeK ajSeqcvtGetCodeS ajSeqcvtGetCodeAsymS ajSeqcvtGetLen ajSeqcvtNewC ajSeqcvtNewNumberC ajSeqcvtNewEndC ajSeqcvtNewStr ajSeqcvtNewStrAsym ajSeqcvtTrace ajSeqdateNew ajSeqdateNewDate ajSeqdateSetCreateS ajSeqdateSetModifyS ajSeqdateSetModseqS ajSeqdateClear ajSeqdateDel ajSeqdescNew ajSeqdescNewDesc ajSeqdescClear ajSeqdescDel ajSeqdesclistClone ajSeqsubdescNew ajSeqsubdescNewSubdesc ajSeqsubdescClear ajSeqsubdescDel ajSeqsubdesclistClone ajSeqgeneNew ajSeqgeneNewGene ajSeqgeneNewName ajSeqgeneDel ajSeqrefNew ajSeqrefNewRef ajSeqrefDel ajSeqxrefNew ajSeqxrefNewDbC ajSeqxrefNewDbS ajSeqxrefNewRef ajSeqxrefDel ajSeqdescAppendName ajSeqdescSetName ajSeqsubdescAppendName ajSeqsubdescSetName ajSeqgeneAppendName ajSeqgeneAppendSynonyms ajSeqgeneAppendOrf ajSeqgeneAppendOln ajSeqgeneSetName ajSeqgeneSetSynonyms ajSeqgeneSetOrf ajSeqgeneSetOln ajSeqgenelistClone ajSeqrefAppendAuthors ajSeqrefAppendComment ajSeqrefAppendGroupname ajSeqrefAppendLocation ajSeqrefAppendPosition ajSeqrefAppendTitle ajSeqrefAppendXref ajSeqrefFmtAuthorsEmbl ajSeqrefFmtAuthorsGb ajSeqrefFmtLocationEmbl ajSeqrefFmtLocationGb ajSeqrefFmtTitleGb ajSeqreflistClone ajSeqreflistGetXrefs ajSeqrefSetAuthors ajSeqrefSetComment ajSeqrefSetGroupname ajSeqrefSetLocation ajSeqrefSetLoctype ajSeqrefSetnumNumber ajSeqrefSetPosition ajSeqrefSetTitle ajSeqrefSetXref ajSeqrefStandard ajSeqxreflistClone ajSeqSetName ajSeqSetNameMulti ajSeqDel ajSeqDelarray ajSeqGetEnd ajSeqExit ajSeqGapFill ajSeqCountGaps ajSeqGapStandard ajSeqGetAccC ajSeqGetAccS ajSeqGetDbC ajSeqGetDbS ajSeqGetDescC ajSeqGetDescS ajSeqGetEntryC ajSeqGetEntryS ajSeqGetFeat ajSeqGetGiC ajSeqGetGiS ajSeqGetNameC ajSeqGetNameS ajSeqGetOffend ajSeqGetOffset ajSeqGetRange ajSeqGetRev ajSeqGetSvC ajSeqGetSvS ajSeqGetTaxC ajSeqGetTaxS ajSeqGetTaxid ajSeqGetUsaC ajSeqGetUsaS ajSeqIsNuc ajSeqIsProt ajSeqGetLen ajSeqGetLenTrimmed ajSeqGetLenUngapped ajSeqclsGetEmbl ajSeqclsSetEmbl ajSeqclsSetGb ajSeqdivGetEmbl ajSeqdivGetGb ajSeqdivSetEmbl ajSeqdivSetGb ajSeqmolGetEmbl ajSeqmolGetGb ajSeqmolSetEmbl ajSeqmolSetGb ajSeqSetUnique ajSeqCalcMolwt ajSeqstrCalcMolwt ajSeqNew ajSeqNewNameC ajSeqNewNameS ajSeqNewRes ajSeqNewSeq ajSeqNewRangeC ajSeqNewRangeS ajSeqConvertNum ajSeqIsReversedTrue ajSeqIsReversed ajSeqIsSpeciesBsubtilis ajSeqIsSpeciesHuman ajSeqIsSpeciesMouse ajSeqIsSpeciesYeast ajSeqIsTaxon ajSeqIsTrimmed ajSeqReverseDo ajSeqReverseForce ajSeqstrReverse ajSeqReverseOnly ajSeqsetGetBegin ajSeqsetDel ajSeqsetDelarray ajSeqsetGetEnd ajSeqsetFill ajSeqsetGetFormat ajSeqsetGetNameC ajSeqsetGetNameS ajSeqsetGetOffend ajSeqsetGetOffset ajSeqsetGetRange ajSeqsetGetseqSeq ajSeqsetGetseqSeqC ajSeqsetGetseqSeqS ajSeqsetGetSeqarray ajSeqsetGetTotlength ajSeqsetGetUsa ajSeqsetGetFilename ajSeqsetIsDna ajSeqsetIsNuc ajSeqsetIsProt ajSeqsetIsRna ajSeqsetGetLen ajSeqsetGetseqAccC ajSeqsetGetseqAccS ajSeqsetGetseqNameC ajSeqsetGetseqNameS ajSeqsetNew ajSeqSetOffsets ajSeqSetRange ajSeqSetRangeRev ajSeqsetReverse ajSeqsetSetRange ajSeqsetGetSize ajSeqsetFmtLower ajSeqsetFmtUpper ajSeqsetGetTotweight ajSeqsetSortLen ajSeqsetTrim ajSeqsetGetseqWeight ajSeqFmtLower ajSeqFmtUpper ajSeqTagRev ajSeqTrace ajSeqTraceTitle ajSeqTrim ajSeqGetBeginTrue ajSeqGetEndTrue ajSeqGetLenTrue ajSeqCalcTruepos ajSeqCalcTrueposMin ajSeqdivGetDdbj ajSeqdivSetDdbj ajSeqmolGetDdbj ajSeqmolSetDdbj ajSeqallBegin ajSeqallEnd ajSeqallGetRange ajSeqsetToLower ajSeqsetToUpper ajSeqNewC ajSeqNewStr ajSeqNewRange ajSeqNewRangeCI ajSeqNewL ajSeqNewS ajSeqAssAcc ajSeqAssAccC ajSeqAssDesc ajSeqAssDescC ajSeqAssEntry ajSeqAssEntryC ajSeqAssFile ajSeqAssFileC ajSeqAssFull ajSeqAssFullC ajSeqAssGi ajSeqAssGiC ajSeqAssName ajSeqAssNameC ajSeqAssSeq ajSeqAssSeqC ajSeqAssSeqCI ajSeqAssSvC ajSeqAssSv ajSeqAssUfo ajSeqAssUfoC ajSeqAssUsa ajSeqAssUsaC ajSeqSetRangeDir ajSeqReplace ajSeqReplaceC ajSeqMakeUsa ajSeqMakeUsaS ajSeqCompOnly ajSeqToLower ajSeqToUpper ajSeqRevOnly ajSeqReverse ajSeqGetAcc ajSeqBegin ajSeqTrueBegin ajSeqGetDesc ajSeqEnd ajSeqTrueEnd ajSeqGetEntry ajSeqCopyFeat ajSeqGetGi ajSeqLen ajSeqTrueLen ajSeqName ajSeqGetName ajSeqOffend ajSeqOffset ajSeqGetReverse ajSeqGetReversed ajSeqStr ajSeqChar ajSeqStrCopy ajSeqCharCopy ajSeqCharCopyL ajSeqGetSv ajSeqGetTax ajSeqGetUsa ajSeqRev ajSeqCheckGcg ajSeqCount ajSeqPos ajSeqPosI ajSeqPosII ajSeqTruePos ajSeqTruePosI ajSeqTruePosII ajSeqallReverse ajSeqallToLower ajSeqallToUpper ajSeqReverseStr ajSeqCompOnlyStr ajSeqMW ajSeqCrc ajSeqCvtDel ajSeqCvtK ajSeqCvtKS ajSeqCvtKSRow ajSeqCvtKSColumn ajSeqCvtLen ajSeqCvtNew ajSeqCvtNewText ajSeqCvtNewZero ajSeqCvtNewZeroS ajSeqCvtNewZeroSS ajSeqCvtTrace ajIsAccession ajIsSeqversion ajSeqallLen ajSeqallGetNameSeq ajSeqComplementOnly ajSeqstrComplementOnly ajSeqCalcCrc ajSeqDefName ajSeqFill ajSeqGapCount ajSeqGapCountS ajSeqGapStandardS ajSeqMod ajSeqNum ajSeqNumS ajSeqsetBegin ajSeqsetEnd ajSeqsetGetName ajSeqsetGetSeq ajSeqsetGetSeqArray ajSeqsetLen ajSeqsetName ajSeqsetAcc ajSeqsetSeq ajSeqsetSize ajSeqsetTotweight ajSeqsetWeight ajSeqTraceT ajTrnNewI ajTrnSeqOrig From maj at fortinbras.us Wed Nov 25 11:44:15 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 25 Nov 2009 11:44:15 -0500 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: <20091125162731.GA3589@thebird.nl> References: <20091125162731.GA3589@thebird.nl> Message-ID: Pjotr ROCKS! MAJ ----- Original Message ----- From: "Pjotr Prins" To: "BioLib Project" Sent: Wednesday, November 25, 2009 11:27 AM Subject: [BioLib-dev] EMBOSS mapping in Biolib > The EMBOSS branch of biolib contains a first mapping of EMBOSS > functions to Ruby. I'll add Perl and Python soon. More importantly I > have done a writeup of the mapping process. It can be found at: > > http://biolib.open-bio.org/wiki/Mapping_EMBOSS > > I think it aptly describes what it takes to map 410 functions > (below). Please have a look and comment. > > Including the write up it took about a day. > > Pj. > > > AjOSeqCvt_size_set > AjOSeqCvt_size_get > AjOSeqCvt_len_set > AjOSeqCvt_len_get > AjOSeqCvt_missing_set > AjOSeqCvt_missing_get > AjOSeqCvt_nrlabels_set > AjOSeqCvt_nrlabels_get > AjOSeqCvt_bases_set > AjOSeqCvt_bases_get > AjOSeqCvt_rlabels_set > AjOSeqCvt_rlabels_get > AjOSeqCvt_clabels_set > AjOSeqCvt_clabels_get > AjOSeqCvt_table_set > AjOSeqCvt_table_get > AjOSeqCvt_nclabels_set > AjOSeqCvt_nclabels_get > AjOSeqCvt_Padding_set > AjOSeqCvt_Padding_get > AjOSeqCvt_allocate > AjOSeqCvt_allocate > new_AjOSeqCvt > ajSeqtestIsAccession > ajSeqtestIsSeqversion > ajSeqallDel > ajSeqallGetCount > ajSeqallGetFilename > ajSeqallGetseqName > ajSeqallGetseqBegin > ajSeqallGetseqEnd > ajSeqallGetseqLen > ajSeqallGetName > ajSeqallGetseqRange > ajSeqallGetTotlength > ajSeqallGetUsa > ajSeqallNew > ajSeqallClear > ajSeqallClearStats > ajSeqallNext > ajSeqallSetRange > ajSeqallSetRangeRev > ajSeqAssignAccC > ajSeqAssignAccS > ajSeqAssignDescC > ajSeqAssignDescS > ajSeqAssignEntryC > ajSeqAssignEntryS > ajSeqAssignFileC > ajSeqAssignFileS > ajSeqAssignFullC > ajSeqAssignFullS > ajSeqAssignGiC > ajSeqAssignGiS > ajSeqAssignNameC > ajSeqAssignNameS > ajSeqAssignSeqC > ajSeqAssignSeqLenC > ajSeqAssignSeqS > ajSeqAssignSvC > ajSeqAssignSvS > ajSeqAssignUfoC > ajSeqAssignUfoS > ajSeqAssignUsaC > ajSeqAssignUsaS > ajSeqGetBegin > ajSeqGetSeqC > ajSeqGetSeqS > ajSeqGetSeqCopyC > ajSeqGetSeqCopyS > ajSeqCalcCheckgcg > ajSeqClear > ajSeqComplement > ajSeqstrComplement > ajSeqstrConvertNum > ajSeqGetFeatCopy > ajSeqCalcCount > ajSeqstrCountGaps > ajSeqcvtDel > ajSeqcvtGetCodeK > ajSeqcvtGetCodeS > ajSeqcvtGetCodeAsymS > ajSeqcvtGetLen > ajSeqcvtNewC > ajSeqcvtNewNumberC > ajSeqcvtNewEndC > ajSeqcvtNewStr > ajSeqcvtNewStrAsym > ajSeqcvtTrace > ajSeqdateNew > ajSeqdateNewDate > ajSeqdateSetCreateS > ajSeqdateSetModifyS > ajSeqdateSetModseqS > ajSeqdateClear > ajSeqdateDel > ajSeqdescNew > ajSeqdescNewDesc > ajSeqdescClear > ajSeqdescDel > ajSeqdesclistClone > ajSeqsubdescNew > ajSeqsubdescNewSubdesc > ajSeqsubdescClear > ajSeqsubdescDel > ajSeqsubdesclistClone > ajSeqgeneNew > ajSeqgeneNewGene > ajSeqgeneNewName > ajSeqgeneDel > ajSeqrefNew > ajSeqrefNewRef > ajSeqrefDel > ajSeqxrefNew > ajSeqxrefNewDbC > ajSeqxrefNewDbS > ajSeqxrefNewRef > ajSeqxrefDel > ajSeqdescAppendName > ajSeqdescSetName > ajSeqsubdescAppendName > ajSeqsubdescSetName > ajSeqgeneAppendName > ajSeqgeneAppendSynonyms > ajSeqgeneAppendOrf > ajSeqgeneAppendOln > ajSeqgeneSetName > ajSeqgeneSetSynonyms > ajSeqgeneSetOrf > ajSeqgeneSetOln > ajSeqgenelistClone > ajSeqrefAppendAuthors > ajSeqrefAppendComment > ajSeqrefAppendGroupname > ajSeqrefAppendLocation > ajSeqrefAppendPosition > ajSeqrefAppendTitle > ajSeqrefAppendXref > ajSeqrefFmtAuthorsEmbl > ajSeqrefFmtAuthorsGb > ajSeqrefFmtLocationEmbl > ajSeqrefFmtLocationGb > ajSeqrefFmtTitleGb > ajSeqreflistClone > ajSeqreflistGetXrefs > ajSeqrefSetAuthors > ajSeqrefSetComment > ajSeqrefSetGroupname > ajSeqrefSetLocation > ajSeqrefSetLoctype > ajSeqrefSetnumNumber > ajSeqrefSetPosition > ajSeqrefSetTitle > ajSeqrefSetXref > ajSeqrefStandard > ajSeqxreflistClone > ajSeqSetName > ajSeqSetNameMulti > ajSeqDel > ajSeqDelarray > ajSeqGetEnd > ajSeqExit > ajSeqGapFill > ajSeqCountGaps > ajSeqGapStandard > ajSeqGetAccC > ajSeqGetAccS > ajSeqGetDbC > ajSeqGetDbS > ajSeqGetDescC > ajSeqGetDescS > ajSeqGetEntryC > ajSeqGetEntryS > ajSeqGetFeat > ajSeqGetGiC > ajSeqGetGiS > ajSeqGetNameC > ajSeqGetNameS > ajSeqGetOffend > ajSeqGetOffset > ajSeqGetRange > ajSeqGetRev > ajSeqGetSvC > ajSeqGetSvS > ajSeqGetTaxC > ajSeqGetTaxS > ajSeqGetTaxid > ajSeqGetUsaC > ajSeqGetUsaS > ajSeqIsNuc > ajSeqIsProt > ajSeqGetLen > ajSeqGetLenTrimmed > ajSeqGetLenUngapped > ajSeqclsGetEmbl > ajSeqclsSetEmbl > ajSeqclsSetGb > ajSeqdivGetEmbl > ajSeqdivGetGb > ajSeqdivSetEmbl > ajSeqdivSetGb > ajSeqmolGetEmbl > ajSeqmolGetGb > ajSeqmolSetEmbl > ajSeqmolSetGb > ajSeqSetUnique > ajSeqCalcMolwt > ajSeqstrCalcMolwt > ajSeqNew > ajSeqNewNameC > ajSeqNewNameS > ajSeqNewRes > ajSeqNewSeq > ajSeqNewRangeC > ajSeqNewRangeS > ajSeqConvertNum > ajSeqIsReversedTrue > ajSeqIsReversed > ajSeqIsSpeciesBsubtilis > ajSeqIsSpeciesHuman > ajSeqIsSpeciesMouse > ajSeqIsSpeciesYeast > ajSeqIsTaxon > ajSeqIsTrimmed > ajSeqReverseDo > ajSeqReverseForce > ajSeqstrReverse > ajSeqReverseOnly > ajSeqsetGetBegin > ajSeqsetDel > ajSeqsetDelarray > ajSeqsetGetEnd > ajSeqsetFill > ajSeqsetGetFormat > ajSeqsetGetNameC > ajSeqsetGetNameS > ajSeqsetGetOffend > ajSeqsetGetOffset > ajSeqsetGetRange > ajSeqsetGetseqSeq > ajSeqsetGetseqSeqC > ajSeqsetGetseqSeqS > ajSeqsetGetSeqarray > ajSeqsetGetTotlength > ajSeqsetGetUsa > ajSeqsetGetFilename > ajSeqsetIsDna > ajSeqsetIsNuc > ajSeqsetIsProt > ajSeqsetIsRna > ajSeqsetGetLen > ajSeqsetGetseqAccC > ajSeqsetGetseqAccS > ajSeqsetGetseqNameC > ajSeqsetGetseqNameS > ajSeqsetNew > ajSeqSetOffsets > ajSeqSetRange > ajSeqSetRangeRev > ajSeqsetReverse > ajSeqsetSetRange > ajSeqsetGetSize > ajSeqsetFmtLower > ajSeqsetFmtUpper > ajSeqsetGetTotweight > ajSeqsetSortLen > ajSeqsetTrim > ajSeqsetGetseqWeight > ajSeqFmtLower > ajSeqFmtUpper > ajSeqTagRev > ajSeqTrace > ajSeqTraceTitle > ajSeqTrim > ajSeqGetBeginTrue > ajSeqGetEndTrue > ajSeqGetLenTrue > ajSeqCalcTruepos > ajSeqCalcTrueposMin > ajSeqdivGetDdbj > ajSeqdivSetDdbj > ajSeqmolGetDdbj > ajSeqmolSetDdbj > ajSeqallBegin > ajSeqallEnd > ajSeqallGetRange > ajSeqsetToLower > ajSeqsetToUpper > ajSeqNewC > ajSeqNewStr > ajSeqNewRange > ajSeqNewRangeCI > ajSeqNewL > ajSeqNewS > ajSeqAssAcc > ajSeqAssAccC > ajSeqAssDesc > ajSeqAssDescC > ajSeqAssEntry > ajSeqAssEntryC > ajSeqAssFile > ajSeqAssFileC > ajSeqAssFull > ajSeqAssFullC > ajSeqAssGi > ajSeqAssGiC > ajSeqAssName > ajSeqAssNameC > ajSeqAssSeq > ajSeqAssSeqC > ajSeqAssSeqCI > ajSeqAssSvC > ajSeqAssSv > ajSeqAssUfo > ajSeqAssUfoC > ajSeqAssUsa > ajSeqAssUsaC > ajSeqSetRangeDir > ajSeqReplace > ajSeqReplaceC > ajSeqMakeUsa > ajSeqMakeUsaS > ajSeqCompOnly > ajSeqToLower > ajSeqToUpper > ajSeqRevOnly > ajSeqReverse > ajSeqGetAcc > ajSeqBegin > ajSeqTrueBegin > ajSeqGetDesc > ajSeqEnd > ajSeqTrueEnd > ajSeqGetEntry > ajSeqCopyFeat > ajSeqGetGi > ajSeqLen > ajSeqTrueLen > ajSeqName > ajSeqGetName > ajSeqOffend > ajSeqOffset > ajSeqGetReverse > ajSeqGetReversed > ajSeqStr > ajSeqChar > ajSeqStrCopy > ajSeqCharCopy > ajSeqCharCopyL > ajSeqGetSv > ajSeqGetTax > ajSeqGetUsa > ajSeqRev > ajSeqCheckGcg > ajSeqCount > ajSeqPos > ajSeqPosI > ajSeqPosII > ajSeqTruePos > ajSeqTruePosI > ajSeqTruePosII > ajSeqallReverse > ajSeqallToLower > ajSeqallToUpper > ajSeqReverseStr > ajSeqCompOnlyStr > ajSeqMW > ajSeqCrc > ajSeqCvtDel > ajSeqCvtK > ajSeqCvtKS > ajSeqCvtKSRow > ajSeqCvtKSColumn > ajSeqCvtLen > ajSeqCvtNew > ajSeqCvtNewText > ajSeqCvtNewZero > ajSeqCvtNewZeroS > ajSeqCvtNewZeroSS > ajSeqCvtTrace > ajIsAccession > ajIsSeqversion > ajSeqallLen > ajSeqallGetNameSeq > ajSeqComplementOnly > ajSeqstrComplementOnly > ajSeqCalcCrc > ajSeqDefName > ajSeqFill > ajSeqGapCount > ajSeqGapCountS > ajSeqGapStandardS > ajSeqMod > ajSeqNum > ajSeqNumS > ajSeqsetBegin > ajSeqsetEnd > ajSeqsetGetName > ajSeqsetGetSeq > ajSeqsetGetSeqArray > ajSeqsetLen > ajSeqsetName > ajSeqsetAcc > ajSeqsetSeq > ajSeqsetSize > ajSeqsetTotweight > ajSeqsetWeight > ajSeqTraceT > ajTrnNewI > ajTrnSeqOrig > _______________________________________________ > BioLib-dev mailing list > BioLib-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biolib-dev > > From pjotr.public14 at thebird.nl Wed Nov 25 13:24:20 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 25 Nov 2009 19:24:20 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: <20091125182420.GA6558@thebird.nl> On Wed, Nov 25, 2009 at 12:19:07PM -0600, Chris Fields wrote: > Pjotr, the subject about how to make these easily accessible and > publicly available (i.e. via CPAN for perl, gems for ruby, etc) has > come up in the past. Has this been addressed? Not really. We are heading for a 1.0 release by X-mas. This will be a source tar-ball. Right after will come a Debian package. I can probably do a gem. CPAN is a different ball game - looks like I can use help there. Pj. From cjfields at illinois.edu Wed Nov 25 13:19:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 25 Nov 2009 12:19:07 -0600 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: Agreed. Pjotr, the subject about how to make these easily accessible and publicly available (i.e. via CPAN for perl, gems for ruby, etc) has come up in the past. Has this been addressed? chris On Nov 25, 2009, at 10:44 AM, Mark A. Jensen wrote: > Pjotr ROCKS! > MAJ > ----- Original Message ----- From: "Pjotr Prins" > To: "BioLib Project" > Sent: Wednesday, November 25, 2009 11:27 AM > Subject: [BioLib-dev] EMBOSS mapping in Biolib > > >> The EMBOSS branch of biolib contains a first mapping of EMBOSS >> functions to Ruby. I'll add Perl and Python soon. More importantly I >> have done a writeup of the mapping process. It can be found at: >> http://biolib.open-bio.org/wiki/Mapping_EMBOSS >> I think it aptly describes what it takes to map 410 functions >> (below). Please have a look and comment. >> Including the write up it took about a day. Pj. >> AjOSeqCvt_size_set >> AjOSeqCvt_size_get >> AjOSeqCvt_len_set >> AjOSeqCvt_len_get >> AjOSeqCvt_missing_set >> AjOSeqCvt_missing_get >> AjOSeqCvt_nrlabels_set >> AjOSeqCvt_nrlabels_get >> AjOSeqCvt_bases_set >> AjOSeqCvt_bases_get >> AjOSeqCvt_rlabels_set >> AjOSeqCvt_rlabels_get >> AjOSeqCvt_clabels_set >> AjOSeqCvt_clabels_get >> AjOSeqCvt_table_set >> AjOSeqCvt_table_get >> AjOSeqCvt_nclabels_set >> AjOSeqCvt_nclabels_get >> AjOSeqCvt_Padding_set >> AjOSeqCvt_Padding_get >> AjOSeqCvt_allocate >> AjOSeqCvt_allocate >> new_AjOSeqCvt >> ajSeqtestIsAccession >> ajSeqtestIsSeqversion >> ajSeqallDel >> ajSeqallGetCount >> ajSeqallGetFilename >> ajSeqallGetseqName >> ajSeqallGetseqBegin >> ajSeqallGetseqEnd >> ajSeqallGetseqLen >> ajSeqallGetName >> ajSeqallGetseqRange >> ajSeqallGetTotlength >> ajSeqallGetUsa >> ajSeqallNew >> ajSeqallClear >> ajSeqallClearStats >> ajSeqallNext >> ajSeqallSetRange >> ajSeqallSetRangeRev >> ajSeqAssignAccC >> ajSeqAssignAccS >> ajSeqAssignDescC >> ajSeqAssignDescS >> ajSeqAssignEntryC >> ajSeqAssignEntryS >> ajSeqAssignFileC >> ajSeqAssignFileS >> ajSeqAssignFullC >> ajSeqAssignFullS >> ajSeqAssignGiC >> ajSeqAssignGiS >> ajSeqAssignNameC >> ajSeqAssignNameS >> ajSeqAssignSeqC >> ajSeqAssignSeqLenC >> ajSeqAssignSeqS >> ajSeqAssignSvC >> ajSeqAssignSvS >> ajSeqAssignUfoC >> ajSeqAssignUfoS >> ajSeqAssignUsaC >> ajSeqAssignUsaS >> ajSeqGetBegin >> ajSeqGetSeqC >> ajSeqGetSeqS >> ajSeqGetSeqCopyC >> ajSeqGetSeqCopyS >> ajSeqCalcCheckgcg >> ajSeqClear >> ajSeqComplement >> ajSeqstrComplement >> ajSeqstrConvertNum >> ajSeqGetFeatCopy >> ajSeqCalcCount >> ajSeqstrCountGaps >> ajSeqcvtDel >> ajSeqcvtGetCodeK >> ajSeqcvtGetCodeS >> ajSeqcvtGetCodeAsymS >> ajSeqcvtGetLen >> ajSeqcvtNewC >> ajSeqcvtNewNumberC >> ajSeqcvtNewEndC >> ajSeqcvtNewStr >> ajSeqcvtNewStrAsym >> ajSeqcvtTrace >> ajSeqdateNew >> ajSeqdateNewDate >> ajSeqdateSetCreateS >> ajSeqdateSetModifyS >> ajSeqdateSetModseqS >> ajSeqdateClear >> ajSeqdateDel >> ajSeqdescNew >> ajSeqdescNewDesc >> ajSeqdescClear >> ajSeqdescDel >> ajSeqdesclistClone >> ajSeqsubdescNew >> ajSeqsubdescNewSubdesc >> ajSeqsubdescClear >> ajSeqsubdescDel >> ajSeqsubdesclistClone >> ajSeqgeneNew >> ajSeqgeneNewGene >> ajSeqgeneNewName >> ajSeqgeneDel >> ajSeqrefNew >> ajSeqrefNewRef >> ajSeqrefDel >> ajSeqxrefNew >> ajSeqxrefNewDbC >> ajSeqxrefNewDbS >> ajSeqxrefNewRef >> ajSeqxrefDel >> ajSeqdescAppendName >> ajSeqdescSetName >> ajSeqsubdescAppendName >> ajSeqsubdescSetName >> ajSeqgeneAppendName >> ajSeqgeneAppendSynonyms >> ajSeqgeneAppendOrf >> ajSeqgeneAppendOln >> ajSeqgeneSetName >> ajSeqgeneSetSynonyms >> ajSeqgeneSetOrf >> ajSeqgeneSetOln >> ajSeqgenelistClone >> ajSeqrefAppendAuthors >> ajSeqrefAppendComment >> ajSeqrefAppendGroupname >> ajSeqrefAppendLocation >> ajSeqrefAppendPosition >> ajSeqrefAppendTitle >> ajSeqrefAppendXref >> ajSeqrefFmtAuthorsEmbl >> ajSeqrefFmtAuthorsGb >> ajSeqrefFmtLocationEmbl >> ajSeqrefFmtLocationGb >> ajSeqrefFmtTitleGb >> ajSeqreflistClone >> ajSeqreflistGetXrefs >> ajSeqrefSetAuthors >> ajSeqrefSetComment >> ajSeqrefSetGroupname >> ajSeqrefSetLocation >> ajSeqrefSetLoctype >> ajSeqrefSetnumNumber >> ajSeqrefSetPosition >> ajSeqrefSetTitle >> ajSeqrefSetXref >> ajSeqrefStandard >> ajSeqxreflistClone >> ajSeqSetName >> ajSeqSetNameMulti >> ajSeqDel >> ajSeqDelarray >> ajSeqGetEnd >> ajSeqExit >> ajSeqGapFill >> ajSeqCountGaps >> ajSeqGapStandard >> ajSeqGetAccC >> ajSeqGetAccS >> ajSeqGetDbC >> ajSeqGetDbS >> ajSeqGetDescC >> ajSeqGetDescS >> ajSeqGetEntryC >> ajSeqGetEntryS >> ajSeqGetFeat >> ajSeqGetGiC >> ajSeqGetGiS >> ajSeqGetNameC >> ajSeqGetNameS >> ajSeqGetOffend >> ajSeqGetOffset >> ajSeqGetRange >> ajSeqGetRev >> ajSeqGetSvC >> ajSeqGetSvS >> ajSeqGetTaxC >> ajSeqGetTaxS >> ajSeqGetTaxid >> ajSeqGetUsaC >> ajSeqGetUsaS >> ajSeqIsNuc >> ajSeqIsProt >> ajSeqGetLen >> ajSeqGetLenTrimmed >> ajSeqGetLenUngapped >> ajSeqclsGetEmbl >> ajSeqclsSetEmbl >> ajSeqclsSetGb >> ajSeqdivGetEmbl >> ajSeqdivGetGb >> ajSeqdivSetEmbl >> ajSeqdivSetGb >> ajSeqmolGetEmbl >> ajSeqmolGetGb >> ajSeqmolSetEmbl >> ajSeqmolSetGb >> ajSeqSetUnique >> ajSeqCalcMolwt >> ajSeqstrCalcMolwt >> ajSeqNew >> ajSeqNewNameC >> ajSeqNewNameS >> ajSeqNewRes >> ajSeqNewSeq >> ajSeqNewRangeC >> ajSeqNewRangeS >> ajSeqConvertNum >> ajSeqIsReversedTrue >> ajSeqIsReversed >> ajSeqIsSpeciesBsubtilis >> ajSeqIsSpeciesHuman >> ajSeqIsSpeciesMouse >> ajSeqIsSpeciesYeast >> ajSeqIsTaxon >> ajSeqIsTrimmed >> ajSeqReverseDo >> ajSeqReverseForce >> ajSeqstrReverse >> ajSeqReverseOnly >> ajSeqsetGetBegin >> ajSeqsetDel >> ajSeqsetDelarray >> ajSeqsetGetEnd >> ajSeqsetFill >> ajSeqsetGetFormat >> ajSeqsetGetNameC >> ajSeqsetGetNameS >> ajSeqsetGetOffend >> ajSeqsetGetOffset >> ajSeqsetGetRange >> ajSeqsetGetseqSeq >> ajSeqsetGetseqSeqC >> ajSeqsetGetseqSeqS >> ajSeqsetGetSeqarray >> ajSeqsetGetTotlength >> ajSeqsetGetUsa >> ajSeqsetGetFilename >> ajSeqsetIsDna >> ajSeqsetIsNuc >> ajSeqsetIsProt >> ajSeqsetIsRna >> ajSeqsetGetLen >> ajSeqsetGetseqAccC >> ajSeqsetGetseqAccS >> ajSeqsetGetseqNameC >> ajSeqsetGetseqNameS >> ajSeqsetNew >> ajSeqSetOffsets >> ajSeqSetRange >> ajSeqSetRangeRev >> ajSeqsetReverse >> ajSeqsetSetRange >> ajSeqsetGetSize >> ajSeqsetFmtLower >> ajSeqsetFmtUpper >> ajSeqsetGetTotweight >> ajSeqsetSortLen >> ajSeqsetTrim >> ajSeqsetGetseqWeight >> ajSeqFmtLower >> ajSeqFmtUpper >> ajSeqTagRev >> ajSeqTrace >> ajSeqTraceTitle >> ajSeqTrim >> ajSeqGetBeginTrue >> ajSeqGetEndTrue >> ajSeqGetLenTrue >> ajSeqCalcTruepos >> ajSeqCalcTrueposMin >> ajSeqdivGetDdbj >> ajSeqdivSetDdbj >> ajSeqmolGetDdbj >> ajSeqmolSetDdbj >> ajSeqallBegin >> ajSeqallEnd >> ajSeqallGetRange >> ajSeqsetToLower >> ajSeqsetToUpper >> ajSeqNewC >> ajSeqNewStr >> ajSeqNewRange >> ajSeqNewRangeCI >> ajSeqNewL >> ajSeqNewS >> ajSeqAssAcc >> ajSeqAssAccC >> ajSeqAssDesc >> ajSeqAssDescC >> ajSeqAssEntry >> ajSeqAssEntryC >> ajSeqAssFile >> ajSeqAssFileC >> ajSeqAssFull >> ajSeqAssFullC >> ajSeqAssGi >> ajSeqAssGiC >> ajSeqAssName >> ajSeqAssNameC >> ajSeqAssSeq >> ajSeqAssSeqC >> ajSeqAssSeqCI >> ajSeqAssSvC >> ajSeqAssSv >> ajSeqAssUfo >> ajSeqAssUfoC >> ajSeqAssUsa >> ajSeqAssUsaC >> ajSeqSetRangeDir >> ajSeqReplace >> ajSeqReplaceC >> ajSeqMakeUsa >> ajSeqMakeUsaS >> ajSeqCompOnly >> ajSeqToLower >> ajSeqToUpper >> ajSeqRevOnly >> ajSeqReverse >> ajSeqGetAcc >> ajSeqBegin >> ajSeqTrueBegin >> ajSeqGetDesc >> ajSeqEnd >> ajSeqTrueEnd >> ajSeqGetEntry >> ajSeqCopyFeat >> ajSeqGetGi >> ajSeqLen >> ajSeqTrueLen >> ajSeqName >> ajSeqGetName >> ajSeqOffend >> ajSeqOffset >> ajSeqGetReverse >> ajSeqGetReversed >> ajSeqStr >> ajSeqChar >> ajSeqStrCopy >> ajSeqCharCopy >> ajSeqCharCopyL >> ajSeqGetSv >> ajSeqGetTax >> ajSeqGetUsa >> ajSeqRev >> ajSeqCheckGcg >> ajSeqCount >> ajSeqPos >> ajSeqPosI >> ajSeqPosII >> ajSeqTruePos >> ajSeqTruePosI >> ajSeqTruePosII >> ajSeqallReverse >> ajSeqallToLower >> ajSeqallToUpper >> ajSeqReverseStr >> ajSeqCompOnlyStr >> ajSeqMW >> ajSeqCrc >> ajSeqCvtDel >> ajSeqCvtK >> ajSeqCvtKS >> ajSeqCvtKSRow >> ajSeqCvtKSColumn >> ajSeqCvtLen >> ajSeqCvtNew >> ajSeqCvtNewText >> ajSeqCvtNewZero >> ajSeqCvtNewZeroS >> ajSeqCvtNewZeroSS >> ajSeqCvtTrace >> ajIsAccession >> ajIsSeqversion >> ajSeqallLen >> ajSeqallGetNameSeq >> ajSeqComplementOnly >> ajSeqstrComplementOnly >> ajSeqCalcCrc >> ajSeqDefName >> ajSeqFill >> ajSeqGapCount >> ajSeqGapCountS >> ajSeqGapStandardS >> ajSeqMod >> ajSeqNum >> ajSeqNumS >> ajSeqsetBegin >> ajSeqsetEnd >> ajSeqsetGetName >> ajSeqsetGetSeq >> ajSeqsetGetSeqArray >> ajSeqsetLen >> ajSeqsetName >> ajSeqsetAcc >> ajSeqsetSeq >> ajSeqsetSize >> ajSeqsetTotweight >> ajSeqsetWeight >> ajSeqTraceT >> ajTrnNewI >> ajTrnSeqOrig >> _______________________________________________ >> BioLib-dev mailing list >> BioLib-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biolib-dev >> > _______________________________________________ > BioLib-dev mailing list > BioLib-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biolib-dev From pjotr.public14 at thebird.nl Thu Nov 26 07:42:22 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 26 Nov 2009 13:42:22 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: <20091126124222.GA18048@thebird.nl> Even better: the EMBOSS version of translating a C.elegans genome into six reading frames is about 30 times faster than the Bioruby one: Bioruby version: # 22929 records 137574 times translated! # real 9m30.952s # user 8m42.877s # sys 0m32.878s Biolib version: # 22929 records 137574 times translated! # real 0m20.306s # user 0m15.997s # sys 0m1.344s This is including IO - which is handled by Ruby. The code is nt = FastaReader.new(fn) trnTable = Biolib::Emboss.ajTrnNewI(1); nt.each { | rec | (0..iter).each do | repeat | ajpseq = Biolib::Emboss.ajSeqNewNameC(rec.seq,"Test sequence") [-3,-2,-1,1,2,3].each do | frame | ajpseqt = Biolib::Emboss.ajTrnSeqOrig(trnTable,ajpseq,frame) aa = Biolib::Emboss.ajSeqGetSeqCopyC(ajpseqt) print "> ",rec.id," ",frame.to_s,"\n" print aa,"\n" end end } $stderr.print nt.size," records ",nt.size*6*iter," times translated!" It just shows. For BIGDATA C rules. With Biolib there are no concessions :-) Pj. From pjotr.public14 at thebird.nl Sat Nov 28 05:12:20 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 28 Nov 2009 11:12:20 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: <20091128101220.GA16682@thebird.nl> I just executed the EMBOSS mapping for Perl (and Python). The writeup at: http://biolib.open-bio.org/wiki/Mapping_EMBOSS#Mapping_EMBOSS_Perl_and_Python It took three hours, and was a bit harder than normal after a succesful Ruby mapping. Pj. From pjotr.public14 at thebird.nl Wed Nov 25 16:27:31 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 25 Nov 2009 17:27:31 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib Message-ID: <20091125162731.GA3589@thebird.nl> The EMBOSS branch of biolib contains a first mapping of EMBOSS functions to Ruby. I'll add Perl and Python soon. More importantly I have done a writeup of the mapping process. It can be found at: http://biolib.open-bio.org/wiki/Mapping_EMBOSS I think it aptly describes what it takes to map 410 functions (below). Please have a look and comment. Including the write up it took about a day. Pj. AjOSeqCvt_size_set AjOSeqCvt_size_get AjOSeqCvt_len_set AjOSeqCvt_len_get AjOSeqCvt_missing_set AjOSeqCvt_missing_get AjOSeqCvt_nrlabels_set AjOSeqCvt_nrlabels_get AjOSeqCvt_bases_set AjOSeqCvt_bases_get AjOSeqCvt_rlabels_set AjOSeqCvt_rlabels_get AjOSeqCvt_clabels_set AjOSeqCvt_clabels_get AjOSeqCvt_table_set AjOSeqCvt_table_get AjOSeqCvt_nclabels_set AjOSeqCvt_nclabels_get AjOSeqCvt_Padding_set AjOSeqCvt_Padding_get AjOSeqCvt_allocate AjOSeqCvt_allocate new_AjOSeqCvt ajSeqtestIsAccession ajSeqtestIsSeqversion ajSeqallDel ajSeqallGetCount ajSeqallGetFilename ajSeqallGetseqName ajSeqallGetseqBegin ajSeqallGetseqEnd ajSeqallGetseqLen ajSeqallGetName ajSeqallGetseqRange ajSeqallGetTotlength ajSeqallGetUsa ajSeqallNew ajSeqallClear ajSeqallClearStats ajSeqallNext ajSeqallSetRange ajSeqallSetRangeRev ajSeqAssignAccC ajSeqAssignAccS ajSeqAssignDescC ajSeqAssignDescS ajSeqAssignEntryC ajSeqAssignEntryS ajSeqAssignFileC ajSeqAssignFileS ajSeqAssignFullC ajSeqAssignFullS ajSeqAssignGiC ajSeqAssignGiS ajSeqAssignNameC ajSeqAssignNameS ajSeqAssignSeqC ajSeqAssignSeqLenC ajSeqAssignSeqS ajSeqAssignSvC ajSeqAssignSvS ajSeqAssignUfoC ajSeqAssignUfoS ajSeqAssignUsaC ajSeqAssignUsaS ajSeqGetBegin ajSeqGetSeqC ajSeqGetSeqS ajSeqGetSeqCopyC ajSeqGetSeqCopyS ajSeqCalcCheckgcg ajSeqClear ajSeqComplement ajSeqstrComplement ajSeqstrConvertNum ajSeqGetFeatCopy ajSeqCalcCount ajSeqstrCountGaps ajSeqcvtDel ajSeqcvtGetCodeK ajSeqcvtGetCodeS ajSeqcvtGetCodeAsymS ajSeqcvtGetLen ajSeqcvtNewC ajSeqcvtNewNumberC ajSeqcvtNewEndC ajSeqcvtNewStr ajSeqcvtNewStrAsym ajSeqcvtTrace ajSeqdateNew ajSeqdateNewDate ajSeqdateSetCreateS ajSeqdateSetModifyS ajSeqdateSetModseqS ajSeqdateClear ajSeqdateDel ajSeqdescNew ajSeqdescNewDesc ajSeqdescClear ajSeqdescDel ajSeqdesclistClone ajSeqsubdescNew ajSeqsubdescNewSubdesc ajSeqsubdescClear ajSeqsubdescDel ajSeqsubdesclistClone ajSeqgeneNew ajSeqgeneNewGene ajSeqgeneNewName ajSeqgeneDel ajSeqrefNew ajSeqrefNewRef ajSeqrefDel ajSeqxrefNew ajSeqxrefNewDbC ajSeqxrefNewDbS ajSeqxrefNewRef ajSeqxrefDel ajSeqdescAppendName ajSeqdescSetName ajSeqsubdescAppendName ajSeqsubdescSetName ajSeqgeneAppendName ajSeqgeneAppendSynonyms ajSeqgeneAppendOrf ajSeqgeneAppendOln ajSeqgeneSetName ajSeqgeneSetSynonyms ajSeqgeneSetOrf ajSeqgeneSetOln ajSeqgenelistClone ajSeqrefAppendAuthors ajSeqrefAppendComment ajSeqrefAppendGroupname ajSeqrefAppendLocation ajSeqrefAppendPosition ajSeqrefAppendTitle ajSeqrefAppendXref ajSeqrefFmtAuthorsEmbl ajSeqrefFmtAuthorsGb ajSeqrefFmtLocationEmbl ajSeqrefFmtLocationGb ajSeqrefFmtTitleGb ajSeqreflistClone ajSeqreflistGetXrefs ajSeqrefSetAuthors ajSeqrefSetComment ajSeqrefSetGroupname ajSeqrefSetLocation ajSeqrefSetLoctype ajSeqrefSetnumNumber ajSeqrefSetPosition ajSeqrefSetTitle ajSeqrefSetXref ajSeqrefStandard ajSeqxreflistClone ajSeqSetName ajSeqSetNameMulti ajSeqDel ajSeqDelarray ajSeqGetEnd ajSeqExit ajSeqGapFill ajSeqCountGaps ajSeqGapStandard ajSeqGetAccC ajSeqGetAccS ajSeqGetDbC ajSeqGetDbS ajSeqGetDescC ajSeqGetDescS ajSeqGetEntryC ajSeqGetEntryS ajSeqGetFeat ajSeqGetGiC ajSeqGetGiS ajSeqGetNameC ajSeqGetNameS ajSeqGetOffend ajSeqGetOffset ajSeqGetRange ajSeqGetRev ajSeqGetSvC ajSeqGetSvS ajSeqGetTaxC ajSeqGetTaxS ajSeqGetTaxid ajSeqGetUsaC ajSeqGetUsaS ajSeqIsNuc ajSeqIsProt ajSeqGetLen ajSeqGetLenTrimmed ajSeqGetLenUngapped ajSeqclsGetEmbl ajSeqclsSetEmbl ajSeqclsSetGb ajSeqdivGetEmbl ajSeqdivGetGb ajSeqdivSetEmbl ajSeqdivSetGb ajSeqmolGetEmbl ajSeqmolGetGb ajSeqmolSetEmbl ajSeqmolSetGb ajSeqSetUnique ajSeqCalcMolwt ajSeqstrCalcMolwt ajSeqNew ajSeqNewNameC ajSeqNewNameS ajSeqNewRes ajSeqNewSeq ajSeqNewRangeC ajSeqNewRangeS ajSeqConvertNum ajSeqIsReversedTrue ajSeqIsReversed ajSeqIsSpeciesBsubtilis ajSeqIsSpeciesHuman ajSeqIsSpeciesMouse ajSeqIsSpeciesYeast ajSeqIsTaxon ajSeqIsTrimmed ajSeqReverseDo ajSeqReverseForce ajSeqstrReverse ajSeqReverseOnly ajSeqsetGetBegin ajSeqsetDel ajSeqsetDelarray ajSeqsetGetEnd ajSeqsetFill ajSeqsetGetFormat ajSeqsetGetNameC ajSeqsetGetNameS ajSeqsetGetOffend ajSeqsetGetOffset ajSeqsetGetRange ajSeqsetGetseqSeq ajSeqsetGetseqSeqC ajSeqsetGetseqSeqS ajSeqsetGetSeqarray ajSeqsetGetTotlength ajSeqsetGetUsa ajSeqsetGetFilename ajSeqsetIsDna ajSeqsetIsNuc ajSeqsetIsProt ajSeqsetIsRna ajSeqsetGetLen ajSeqsetGetseqAccC ajSeqsetGetseqAccS ajSeqsetGetseqNameC ajSeqsetGetseqNameS ajSeqsetNew ajSeqSetOffsets ajSeqSetRange ajSeqSetRangeRev ajSeqsetReverse ajSeqsetSetRange ajSeqsetGetSize ajSeqsetFmtLower ajSeqsetFmtUpper ajSeqsetGetTotweight ajSeqsetSortLen ajSeqsetTrim ajSeqsetGetseqWeight ajSeqFmtLower ajSeqFmtUpper ajSeqTagRev ajSeqTrace ajSeqTraceTitle ajSeqTrim ajSeqGetBeginTrue ajSeqGetEndTrue ajSeqGetLenTrue ajSeqCalcTruepos ajSeqCalcTrueposMin ajSeqdivGetDdbj ajSeqdivSetDdbj ajSeqmolGetDdbj ajSeqmolSetDdbj ajSeqallBegin ajSeqallEnd ajSeqallGetRange ajSeqsetToLower ajSeqsetToUpper ajSeqNewC ajSeqNewStr ajSeqNewRange ajSeqNewRangeCI ajSeqNewL ajSeqNewS ajSeqAssAcc ajSeqAssAccC ajSeqAssDesc ajSeqAssDescC ajSeqAssEntry ajSeqAssEntryC ajSeqAssFile ajSeqAssFileC ajSeqAssFull ajSeqAssFullC ajSeqAssGi ajSeqAssGiC ajSeqAssName ajSeqAssNameC ajSeqAssSeq ajSeqAssSeqC ajSeqAssSeqCI ajSeqAssSvC ajSeqAssSv ajSeqAssUfo ajSeqAssUfoC ajSeqAssUsa ajSeqAssUsaC ajSeqSetRangeDir ajSeqReplace ajSeqReplaceC ajSeqMakeUsa ajSeqMakeUsaS ajSeqCompOnly ajSeqToLower ajSeqToUpper ajSeqRevOnly ajSeqReverse ajSeqGetAcc ajSeqBegin ajSeqTrueBegin ajSeqGetDesc ajSeqEnd ajSeqTrueEnd ajSeqGetEntry ajSeqCopyFeat ajSeqGetGi ajSeqLen ajSeqTrueLen ajSeqName ajSeqGetName ajSeqOffend ajSeqOffset ajSeqGetReverse ajSeqGetReversed ajSeqStr ajSeqChar ajSeqStrCopy ajSeqCharCopy ajSeqCharCopyL ajSeqGetSv ajSeqGetTax ajSeqGetUsa ajSeqRev ajSeqCheckGcg ajSeqCount ajSeqPos ajSeqPosI ajSeqPosII ajSeqTruePos ajSeqTruePosI ajSeqTruePosII ajSeqallReverse ajSeqallToLower ajSeqallToUpper ajSeqReverseStr ajSeqCompOnlyStr ajSeqMW ajSeqCrc ajSeqCvtDel ajSeqCvtK ajSeqCvtKS ajSeqCvtKSRow ajSeqCvtKSColumn ajSeqCvtLen ajSeqCvtNew ajSeqCvtNewText ajSeqCvtNewZero ajSeqCvtNewZeroS ajSeqCvtNewZeroSS ajSeqCvtTrace ajIsAccession ajIsSeqversion ajSeqallLen ajSeqallGetNameSeq ajSeqComplementOnly ajSeqstrComplementOnly ajSeqCalcCrc ajSeqDefName ajSeqFill ajSeqGapCount ajSeqGapCountS ajSeqGapStandardS ajSeqMod ajSeqNum ajSeqNumS ajSeqsetBegin ajSeqsetEnd ajSeqsetGetName ajSeqsetGetSeq ajSeqsetGetSeqArray ajSeqsetLen ajSeqsetName ajSeqsetAcc ajSeqsetSeq ajSeqsetSize ajSeqsetTotweight ajSeqsetWeight ajSeqTraceT ajTrnNewI ajTrnSeqOrig From maj at fortinbras.us Wed Nov 25 16:44:15 2009 From: maj at fortinbras.us (Mark A. Jensen) Date: Wed, 25 Nov 2009 11:44:15 -0500 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: <20091125162731.GA3589@thebird.nl> References: <20091125162731.GA3589@thebird.nl> Message-ID: Pjotr ROCKS! MAJ ----- Original Message ----- From: "Pjotr Prins" To: "BioLib Project" Sent: Wednesday, November 25, 2009 11:27 AM Subject: [BioLib-dev] EMBOSS mapping in Biolib > The EMBOSS branch of biolib contains a first mapping of EMBOSS > functions to Ruby. I'll add Perl and Python soon. More importantly I > have done a writeup of the mapping process. It can be found at: > > http://biolib.open-bio.org/wiki/Mapping_EMBOSS > > I think it aptly describes what it takes to map 410 functions > (below). Please have a look and comment. > > Including the write up it took about a day. > > Pj. > > > AjOSeqCvt_size_set > AjOSeqCvt_size_get > AjOSeqCvt_len_set > AjOSeqCvt_len_get > AjOSeqCvt_missing_set > AjOSeqCvt_missing_get > AjOSeqCvt_nrlabels_set > AjOSeqCvt_nrlabels_get > AjOSeqCvt_bases_set > AjOSeqCvt_bases_get > AjOSeqCvt_rlabels_set > AjOSeqCvt_rlabels_get > AjOSeqCvt_clabels_set > AjOSeqCvt_clabels_get > AjOSeqCvt_table_set > AjOSeqCvt_table_get > AjOSeqCvt_nclabels_set > AjOSeqCvt_nclabels_get > AjOSeqCvt_Padding_set > AjOSeqCvt_Padding_get > AjOSeqCvt_allocate > AjOSeqCvt_allocate > new_AjOSeqCvt > ajSeqtestIsAccession > ajSeqtestIsSeqversion > ajSeqallDel > ajSeqallGetCount > ajSeqallGetFilename > ajSeqallGetseqName > ajSeqallGetseqBegin > ajSeqallGetseqEnd > ajSeqallGetseqLen > ajSeqallGetName > ajSeqallGetseqRange > ajSeqallGetTotlength > ajSeqallGetUsa > ajSeqallNew > ajSeqallClear > ajSeqallClearStats > ajSeqallNext > ajSeqallSetRange > ajSeqallSetRangeRev > ajSeqAssignAccC > ajSeqAssignAccS > ajSeqAssignDescC > ajSeqAssignDescS > ajSeqAssignEntryC > ajSeqAssignEntryS > ajSeqAssignFileC > ajSeqAssignFileS > ajSeqAssignFullC > ajSeqAssignFullS > ajSeqAssignGiC > ajSeqAssignGiS > ajSeqAssignNameC > ajSeqAssignNameS > ajSeqAssignSeqC > ajSeqAssignSeqLenC > ajSeqAssignSeqS > ajSeqAssignSvC > ajSeqAssignSvS > ajSeqAssignUfoC > ajSeqAssignUfoS > ajSeqAssignUsaC > ajSeqAssignUsaS > ajSeqGetBegin > ajSeqGetSeqC > ajSeqGetSeqS > ajSeqGetSeqCopyC > ajSeqGetSeqCopyS > ajSeqCalcCheckgcg > ajSeqClear > ajSeqComplement > ajSeqstrComplement > ajSeqstrConvertNum > ajSeqGetFeatCopy > ajSeqCalcCount > ajSeqstrCountGaps > ajSeqcvtDel > ajSeqcvtGetCodeK > ajSeqcvtGetCodeS > ajSeqcvtGetCodeAsymS > ajSeqcvtGetLen > ajSeqcvtNewC > ajSeqcvtNewNumberC > ajSeqcvtNewEndC > ajSeqcvtNewStr > ajSeqcvtNewStrAsym > ajSeqcvtTrace > ajSeqdateNew > ajSeqdateNewDate > ajSeqdateSetCreateS > ajSeqdateSetModifyS > ajSeqdateSetModseqS > ajSeqdateClear > ajSeqdateDel > ajSeqdescNew > ajSeqdescNewDesc > ajSeqdescClear > ajSeqdescDel > ajSeqdesclistClone > ajSeqsubdescNew > ajSeqsubdescNewSubdesc > ajSeqsubdescClear > ajSeqsubdescDel > ajSeqsubdesclistClone > ajSeqgeneNew > ajSeqgeneNewGene > ajSeqgeneNewName > ajSeqgeneDel > ajSeqrefNew > ajSeqrefNewRef > ajSeqrefDel > ajSeqxrefNew > ajSeqxrefNewDbC > ajSeqxrefNewDbS > ajSeqxrefNewRef > ajSeqxrefDel > ajSeqdescAppendName > ajSeqdescSetName > ajSeqsubdescAppendName > ajSeqsubdescSetName > ajSeqgeneAppendName > ajSeqgeneAppendSynonyms > ajSeqgeneAppendOrf > ajSeqgeneAppendOln > ajSeqgeneSetName > ajSeqgeneSetSynonyms > ajSeqgeneSetOrf > ajSeqgeneSetOln > ajSeqgenelistClone > ajSeqrefAppendAuthors > ajSeqrefAppendComment > ajSeqrefAppendGroupname > ajSeqrefAppendLocation > ajSeqrefAppendPosition > ajSeqrefAppendTitle > ajSeqrefAppendXref > ajSeqrefFmtAuthorsEmbl > ajSeqrefFmtAuthorsGb > ajSeqrefFmtLocationEmbl > ajSeqrefFmtLocationGb > ajSeqrefFmtTitleGb > ajSeqreflistClone > ajSeqreflistGetXrefs > ajSeqrefSetAuthors > ajSeqrefSetComment > ajSeqrefSetGroupname > ajSeqrefSetLocation > ajSeqrefSetLoctype > ajSeqrefSetnumNumber > ajSeqrefSetPosition > ajSeqrefSetTitle > ajSeqrefSetXref > ajSeqrefStandard > ajSeqxreflistClone > ajSeqSetName > ajSeqSetNameMulti > ajSeqDel > ajSeqDelarray > ajSeqGetEnd > ajSeqExit > ajSeqGapFill > ajSeqCountGaps > ajSeqGapStandard > ajSeqGetAccC > ajSeqGetAccS > ajSeqGetDbC > ajSeqGetDbS > ajSeqGetDescC > ajSeqGetDescS > ajSeqGetEntryC > ajSeqGetEntryS > ajSeqGetFeat > ajSeqGetGiC > ajSeqGetGiS > ajSeqGetNameC > ajSeqGetNameS > ajSeqGetOffend > ajSeqGetOffset > ajSeqGetRange > ajSeqGetRev > ajSeqGetSvC > ajSeqGetSvS > ajSeqGetTaxC > ajSeqGetTaxS > ajSeqGetTaxid > ajSeqGetUsaC > ajSeqGetUsaS > ajSeqIsNuc > ajSeqIsProt > ajSeqGetLen > ajSeqGetLenTrimmed > ajSeqGetLenUngapped > ajSeqclsGetEmbl > ajSeqclsSetEmbl > ajSeqclsSetGb > ajSeqdivGetEmbl > ajSeqdivGetGb > ajSeqdivSetEmbl > ajSeqdivSetGb > ajSeqmolGetEmbl > ajSeqmolGetGb > ajSeqmolSetEmbl > ajSeqmolSetGb > ajSeqSetUnique > ajSeqCalcMolwt > ajSeqstrCalcMolwt > ajSeqNew > ajSeqNewNameC > ajSeqNewNameS > ajSeqNewRes > ajSeqNewSeq > ajSeqNewRangeC > ajSeqNewRangeS > ajSeqConvertNum > ajSeqIsReversedTrue > ajSeqIsReversed > ajSeqIsSpeciesBsubtilis > ajSeqIsSpeciesHuman > ajSeqIsSpeciesMouse > ajSeqIsSpeciesYeast > ajSeqIsTaxon > ajSeqIsTrimmed > ajSeqReverseDo > ajSeqReverseForce > ajSeqstrReverse > ajSeqReverseOnly > ajSeqsetGetBegin > ajSeqsetDel > ajSeqsetDelarray > ajSeqsetGetEnd > ajSeqsetFill > ajSeqsetGetFormat > ajSeqsetGetNameC > ajSeqsetGetNameS > ajSeqsetGetOffend > ajSeqsetGetOffset > ajSeqsetGetRange > ajSeqsetGetseqSeq > ajSeqsetGetseqSeqC > ajSeqsetGetseqSeqS > ajSeqsetGetSeqarray > ajSeqsetGetTotlength > ajSeqsetGetUsa > ajSeqsetGetFilename > ajSeqsetIsDna > ajSeqsetIsNuc > ajSeqsetIsProt > ajSeqsetIsRna > ajSeqsetGetLen > ajSeqsetGetseqAccC > ajSeqsetGetseqAccS > ajSeqsetGetseqNameC > ajSeqsetGetseqNameS > ajSeqsetNew > ajSeqSetOffsets > ajSeqSetRange > ajSeqSetRangeRev > ajSeqsetReverse > ajSeqsetSetRange > ajSeqsetGetSize > ajSeqsetFmtLower > ajSeqsetFmtUpper > ajSeqsetGetTotweight > ajSeqsetSortLen > ajSeqsetTrim > ajSeqsetGetseqWeight > ajSeqFmtLower > ajSeqFmtUpper > ajSeqTagRev > ajSeqTrace > ajSeqTraceTitle > ajSeqTrim > ajSeqGetBeginTrue > ajSeqGetEndTrue > ajSeqGetLenTrue > ajSeqCalcTruepos > ajSeqCalcTrueposMin > ajSeqdivGetDdbj > ajSeqdivSetDdbj > ajSeqmolGetDdbj > ajSeqmolSetDdbj > ajSeqallBegin > ajSeqallEnd > ajSeqallGetRange > ajSeqsetToLower > ajSeqsetToUpper > ajSeqNewC > ajSeqNewStr > ajSeqNewRange > ajSeqNewRangeCI > ajSeqNewL > ajSeqNewS > ajSeqAssAcc > ajSeqAssAccC > ajSeqAssDesc > ajSeqAssDescC > ajSeqAssEntry > ajSeqAssEntryC > ajSeqAssFile > ajSeqAssFileC > ajSeqAssFull > ajSeqAssFullC > ajSeqAssGi > ajSeqAssGiC > ajSeqAssName > ajSeqAssNameC > ajSeqAssSeq > ajSeqAssSeqC > ajSeqAssSeqCI > ajSeqAssSvC > ajSeqAssSv > ajSeqAssUfo > ajSeqAssUfoC > ajSeqAssUsa > ajSeqAssUsaC > ajSeqSetRangeDir > ajSeqReplace > ajSeqReplaceC > ajSeqMakeUsa > ajSeqMakeUsaS > ajSeqCompOnly > ajSeqToLower > ajSeqToUpper > ajSeqRevOnly > ajSeqReverse > ajSeqGetAcc > ajSeqBegin > ajSeqTrueBegin > ajSeqGetDesc > ajSeqEnd > ajSeqTrueEnd > ajSeqGetEntry > ajSeqCopyFeat > ajSeqGetGi > ajSeqLen > ajSeqTrueLen > ajSeqName > ajSeqGetName > ajSeqOffend > ajSeqOffset > ajSeqGetReverse > ajSeqGetReversed > ajSeqStr > ajSeqChar > ajSeqStrCopy > ajSeqCharCopy > ajSeqCharCopyL > ajSeqGetSv > ajSeqGetTax > ajSeqGetUsa > ajSeqRev > ajSeqCheckGcg > ajSeqCount > ajSeqPos > ajSeqPosI > ajSeqPosII > ajSeqTruePos > ajSeqTruePosI > ajSeqTruePosII > ajSeqallReverse > ajSeqallToLower > ajSeqallToUpper > ajSeqReverseStr > ajSeqCompOnlyStr > ajSeqMW > ajSeqCrc > ajSeqCvtDel > ajSeqCvtK > ajSeqCvtKS > ajSeqCvtKSRow > ajSeqCvtKSColumn > ajSeqCvtLen > ajSeqCvtNew > ajSeqCvtNewText > ajSeqCvtNewZero > ajSeqCvtNewZeroS > ajSeqCvtNewZeroSS > ajSeqCvtTrace > ajIsAccession > ajIsSeqversion > ajSeqallLen > ajSeqallGetNameSeq > ajSeqComplementOnly > ajSeqstrComplementOnly > ajSeqCalcCrc > ajSeqDefName > ajSeqFill > ajSeqGapCount > ajSeqGapCountS > ajSeqGapStandardS > ajSeqMod > ajSeqNum > ajSeqNumS > ajSeqsetBegin > ajSeqsetEnd > ajSeqsetGetName > ajSeqsetGetSeq > ajSeqsetGetSeqArray > ajSeqsetLen > ajSeqsetName > ajSeqsetAcc > ajSeqsetSeq > ajSeqsetSize > ajSeqsetTotweight > ajSeqsetWeight > ajSeqTraceT > ajTrnNewI > ajTrnSeqOrig > _______________________________________________ > BioLib-dev mailing list > BioLib-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biolib-dev > > From pjotr.public14 at thebird.nl Wed Nov 25 18:24:20 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 25 Nov 2009 19:24:20 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: <20091125182420.GA6558@thebird.nl> On Wed, Nov 25, 2009 at 12:19:07PM -0600, Chris Fields wrote: > Pjotr, the subject about how to make these easily accessible and > publicly available (i.e. via CPAN for perl, gems for ruby, etc) has > come up in the past. Has this been addressed? Not really. We are heading for a 1.0 release by X-mas. This will be a source tar-ball. Right after will come a Debian package. I can probably do a gem. CPAN is a different ball game - looks like I can use help there. Pj. From cjfields at illinois.edu Wed Nov 25 18:19:07 2009 From: cjfields at illinois.edu (Chris Fields) Date: Wed, 25 Nov 2009 12:19:07 -0600 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: Agreed. Pjotr, the subject about how to make these easily accessible and publicly available (i.e. via CPAN for perl, gems for ruby, etc) has come up in the past. Has this been addressed? chris On Nov 25, 2009, at 10:44 AM, Mark A. Jensen wrote: > Pjotr ROCKS! > MAJ > ----- Original Message ----- From: "Pjotr Prins" > To: "BioLib Project" > Sent: Wednesday, November 25, 2009 11:27 AM > Subject: [BioLib-dev] EMBOSS mapping in Biolib > > >> The EMBOSS branch of biolib contains a first mapping of EMBOSS >> functions to Ruby. I'll add Perl and Python soon. More importantly I >> have done a writeup of the mapping process. It can be found at: >> http://biolib.open-bio.org/wiki/Mapping_EMBOSS >> I think it aptly describes what it takes to map 410 functions >> (below). Please have a look and comment. >> Including the write up it took about a day. Pj. >> AjOSeqCvt_size_set >> AjOSeqCvt_size_get >> AjOSeqCvt_len_set >> AjOSeqCvt_len_get >> AjOSeqCvt_missing_set >> AjOSeqCvt_missing_get >> AjOSeqCvt_nrlabels_set >> AjOSeqCvt_nrlabels_get >> AjOSeqCvt_bases_set >> AjOSeqCvt_bases_get >> AjOSeqCvt_rlabels_set >> AjOSeqCvt_rlabels_get >> AjOSeqCvt_clabels_set >> AjOSeqCvt_clabels_get >> AjOSeqCvt_table_set >> AjOSeqCvt_table_get >> AjOSeqCvt_nclabels_set >> AjOSeqCvt_nclabels_get >> AjOSeqCvt_Padding_set >> AjOSeqCvt_Padding_get >> AjOSeqCvt_allocate >> AjOSeqCvt_allocate >> new_AjOSeqCvt >> ajSeqtestIsAccession >> ajSeqtestIsSeqversion >> ajSeqallDel >> ajSeqallGetCount >> ajSeqallGetFilename >> ajSeqallGetseqName >> ajSeqallGetseqBegin >> ajSeqallGetseqEnd >> ajSeqallGetseqLen >> ajSeqallGetName >> ajSeqallGetseqRange >> ajSeqallGetTotlength >> ajSeqallGetUsa >> ajSeqallNew >> ajSeqallClear >> ajSeqallClearStats >> ajSeqallNext >> ajSeqallSetRange >> ajSeqallSetRangeRev >> ajSeqAssignAccC >> ajSeqAssignAccS >> ajSeqAssignDescC >> ajSeqAssignDescS >> ajSeqAssignEntryC >> ajSeqAssignEntryS >> ajSeqAssignFileC >> ajSeqAssignFileS >> ajSeqAssignFullC >> ajSeqAssignFullS >> ajSeqAssignGiC >> ajSeqAssignGiS >> ajSeqAssignNameC >> ajSeqAssignNameS >> ajSeqAssignSeqC >> ajSeqAssignSeqLenC >> ajSeqAssignSeqS >> ajSeqAssignSvC >> ajSeqAssignSvS >> ajSeqAssignUfoC >> ajSeqAssignUfoS >> ajSeqAssignUsaC >> ajSeqAssignUsaS >> ajSeqGetBegin >> ajSeqGetSeqC >> ajSeqGetSeqS >> ajSeqGetSeqCopyC >> ajSeqGetSeqCopyS >> ajSeqCalcCheckgcg >> ajSeqClear >> ajSeqComplement >> ajSeqstrComplement >> ajSeqstrConvertNum >> ajSeqGetFeatCopy >> ajSeqCalcCount >> ajSeqstrCountGaps >> ajSeqcvtDel >> ajSeqcvtGetCodeK >> ajSeqcvtGetCodeS >> ajSeqcvtGetCodeAsymS >> ajSeqcvtGetLen >> ajSeqcvtNewC >> ajSeqcvtNewNumberC >> ajSeqcvtNewEndC >> ajSeqcvtNewStr >> ajSeqcvtNewStrAsym >> ajSeqcvtTrace >> ajSeqdateNew >> ajSeqdateNewDate >> ajSeqdateSetCreateS >> ajSeqdateSetModifyS >> ajSeqdateSetModseqS >> ajSeqdateClear >> ajSeqdateDel >> ajSeqdescNew >> ajSeqdescNewDesc >> ajSeqdescClear >> ajSeqdescDel >> ajSeqdesclistClone >> ajSeqsubdescNew >> ajSeqsubdescNewSubdesc >> ajSeqsubdescClear >> ajSeqsubdescDel >> ajSeqsubdesclistClone >> ajSeqgeneNew >> ajSeqgeneNewGene >> ajSeqgeneNewName >> ajSeqgeneDel >> ajSeqrefNew >> ajSeqrefNewRef >> ajSeqrefDel >> ajSeqxrefNew >> ajSeqxrefNewDbC >> ajSeqxrefNewDbS >> ajSeqxrefNewRef >> ajSeqxrefDel >> ajSeqdescAppendName >> ajSeqdescSetName >> ajSeqsubdescAppendName >> ajSeqsubdescSetName >> ajSeqgeneAppendName >> ajSeqgeneAppendSynonyms >> ajSeqgeneAppendOrf >> ajSeqgeneAppendOln >> ajSeqgeneSetName >> ajSeqgeneSetSynonyms >> ajSeqgeneSetOrf >> ajSeqgeneSetOln >> ajSeqgenelistClone >> ajSeqrefAppendAuthors >> ajSeqrefAppendComment >> ajSeqrefAppendGroupname >> ajSeqrefAppendLocation >> ajSeqrefAppendPosition >> ajSeqrefAppendTitle >> ajSeqrefAppendXref >> ajSeqrefFmtAuthorsEmbl >> ajSeqrefFmtAuthorsGb >> ajSeqrefFmtLocationEmbl >> ajSeqrefFmtLocationGb >> ajSeqrefFmtTitleGb >> ajSeqreflistClone >> ajSeqreflistGetXrefs >> ajSeqrefSetAuthors >> ajSeqrefSetComment >> ajSeqrefSetGroupname >> ajSeqrefSetLocation >> ajSeqrefSetLoctype >> ajSeqrefSetnumNumber >> ajSeqrefSetPosition >> ajSeqrefSetTitle >> ajSeqrefSetXref >> ajSeqrefStandard >> ajSeqxreflistClone >> ajSeqSetName >> ajSeqSetNameMulti >> ajSeqDel >> ajSeqDelarray >> ajSeqGetEnd >> ajSeqExit >> ajSeqGapFill >> ajSeqCountGaps >> ajSeqGapStandard >> ajSeqGetAccC >> ajSeqGetAccS >> ajSeqGetDbC >> ajSeqGetDbS >> ajSeqGetDescC >> ajSeqGetDescS >> ajSeqGetEntryC >> ajSeqGetEntryS >> ajSeqGetFeat >> ajSeqGetGiC >> ajSeqGetGiS >> ajSeqGetNameC >> ajSeqGetNameS >> ajSeqGetOffend >> ajSeqGetOffset >> ajSeqGetRange >> ajSeqGetRev >> ajSeqGetSvC >> ajSeqGetSvS >> ajSeqGetTaxC >> ajSeqGetTaxS >> ajSeqGetTaxid >> ajSeqGetUsaC >> ajSeqGetUsaS >> ajSeqIsNuc >> ajSeqIsProt >> ajSeqGetLen >> ajSeqGetLenTrimmed >> ajSeqGetLenUngapped >> ajSeqclsGetEmbl >> ajSeqclsSetEmbl >> ajSeqclsSetGb >> ajSeqdivGetEmbl >> ajSeqdivGetGb >> ajSeqdivSetEmbl >> ajSeqdivSetGb >> ajSeqmolGetEmbl >> ajSeqmolGetGb >> ajSeqmolSetEmbl >> ajSeqmolSetGb >> ajSeqSetUnique >> ajSeqCalcMolwt >> ajSeqstrCalcMolwt >> ajSeqNew >> ajSeqNewNameC >> ajSeqNewNameS >> ajSeqNewRes >> ajSeqNewSeq >> ajSeqNewRangeC >> ajSeqNewRangeS >> ajSeqConvertNum >> ajSeqIsReversedTrue >> ajSeqIsReversed >> ajSeqIsSpeciesBsubtilis >> ajSeqIsSpeciesHuman >> ajSeqIsSpeciesMouse >> ajSeqIsSpeciesYeast >> ajSeqIsTaxon >> ajSeqIsTrimmed >> ajSeqReverseDo >> ajSeqReverseForce >> ajSeqstrReverse >> ajSeqReverseOnly >> ajSeqsetGetBegin >> ajSeqsetDel >> ajSeqsetDelarray >> ajSeqsetGetEnd >> ajSeqsetFill >> ajSeqsetGetFormat >> ajSeqsetGetNameC >> ajSeqsetGetNameS >> ajSeqsetGetOffend >> ajSeqsetGetOffset >> ajSeqsetGetRange >> ajSeqsetGetseqSeq >> ajSeqsetGetseqSeqC >> ajSeqsetGetseqSeqS >> ajSeqsetGetSeqarray >> ajSeqsetGetTotlength >> ajSeqsetGetUsa >> ajSeqsetGetFilename >> ajSeqsetIsDna >> ajSeqsetIsNuc >> ajSeqsetIsProt >> ajSeqsetIsRna >> ajSeqsetGetLen >> ajSeqsetGetseqAccC >> ajSeqsetGetseqAccS >> ajSeqsetGetseqNameC >> ajSeqsetGetseqNameS >> ajSeqsetNew >> ajSeqSetOffsets >> ajSeqSetRange >> ajSeqSetRangeRev >> ajSeqsetReverse >> ajSeqsetSetRange >> ajSeqsetGetSize >> ajSeqsetFmtLower >> ajSeqsetFmtUpper >> ajSeqsetGetTotweight >> ajSeqsetSortLen >> ajSeqsetTrim >> ajSeqsetGetseqWeight >> ajSeqFmtLower >> ajSeqFmtUpper >> ajSeqTagRev >> ajSeqTrace >> ajSeqTraceTitle >> ajSeqTrim >> ajSeqGetBeginTrue >> ajSeqGetEndTrue >> ajSeqGetLenTrue >> ajSeqCalcTruepos >> ajSeqCalcTrueposMin >> ajSeqdivGetDdbj >> ajSeqdivSetDdbj >> ajSeqmolGetDdbj >> ajSeqmolSetDdbj >> ajSeqallBegin >> ajSeqallEnd >> ajSeqallGetRange >> ajSeqsetToLower >> ajSeqsetToUpper >> ajSeqNewC >> ajSeqNewStr >> ajSeqNewRange >> ajSeqNewRangeCI >> ajSeqNewL >> ajSeqNewS >> ajSeqAssAcc >> ajSeqAssAccC >> ajSeqAssDesc >> ajSeqAssDescC >> ajSeqAssEntry >> ajSeqAssEntryC >> ajSeqAssFile >> ajSeqAssFileC >> ajSeqAssFull >> ajSeqAssFullC >> ajSeqAssGi >> ajSeqAssGiC >> ajSeqAssName >> ajSeqAssNameC >> ajSeqAssSeq >> ajSeqAssSeqC >> ajSeqAssSeqCI >> ajSeqAssSvC >> ajSeqAssSv >> ajSeqAssUfo >> ajSeqAssUfoC >> ajSeqAssUsa >> ajSeqAssUsaC >> ajSeqSetRangeDir >> ajSeqReplace >> ajSeqReplaceC >> ajSeqMakeUsa >> ajSeqMakeUsaS >> ajSeqCompOnly >> ajSeqToLower >> ajSeqToUpper >> ajSeqRevOnly >> ajSeqReverse >> ajSeqGetAcc >> ajSeqBegin >> ajSeqTrueBegin >> ajSeqGetDesc >> ajSeqEnd >> ajSeqTrueEnd >> ajSeqGetEntry >> ajSeqCopyFeat >> ajSeqGetGi >> ajSeqLen >> ajSeqTrueLen >> ajSeqName >> ajSeqGetName >> ajSeqOffend >> ajSeqOffset >> ajSeqGetReverse >> ajSeqGetReversed >> ajSeqStr >> ajSeqChar >> ajSeqStrCopy >> ajSeqCharCopy >> ajSeqCharCopyL >> ajSeqGetSv >> ajSeqGetTax >> ajSeqGetUsa >> ajSeqRev >> ajSeqCheckGcg >> ajSeqCount >> ajSeqPos >> ajSeqPosI >> ajSeqPosII >> ajSeqTruePos >> ajSeqTruePosI >> ajSeqTruePosII >> ajSeqallReverse >> ajSeqallToLower >> ajSeqallToUpper >> ajSeqReverseStr >> ajSeqCompOnlyStr >> ajSeqMW >> ajSeqCrc >> ajSeqCvtDel >> ajSeqCvtK >> ajSeqCvtKS >> ajSeqCvtKSRow >> ajSeqCvtKSColumn >> ajSeqCvtLen >> ajSeqCvtNew >> ajSeqCvtNewText >> ajSeqCvtNewZero >> ajSeqCvtNewZeroS >> ajSeqCvtNewZeroSS >> ajSeqCvtTrace >> ajIsAccession >> ajIsSeqversion >> ajSeqallLen >> ajSeqallGetNameSeq >> ajSeqComplementOnly >> ajSeqstrComplementOnly >> ajSeqCalcCrc >> ajSeqDefName >> ajSeqFill >> ajSeqGapCount >> ajSeqGapCountS >> ajSeqGapStandardS >> ajSeqMod >> ajSeqNum >> ajSeqNumS >> ajSeqsetBegin >> ajSeqsetEnd >> ajSeqsetGetName >> ajSeqsetGetSeq >> ajSeqsetGetSeqArray >> ajSeqsetLen >> ajSeqsetName >> ajSeqsetAcc >> ajSeqsetSeq >> ajSeqsetSize >> ajSeqsetTotweight >> ajSeqsetWeight >> ajSeqTraceT >> ajTrnNewI >> ajTrnSeqOrig >> _______________________________________________ >> BioLib-dev mailing list >> BioLib-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biolib-dev >> > _______________________________________________ > BioLib-dev mailing list > BioLib-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biolib-dev From pjotr.public14 at thebird.nl Thu Nov 26 12:42:22 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 26 Nov 2009 13:42:22 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: <20091126124222.GA18048@thebird.nl> Even better: the EMBOSS version of translating a C.elegans genome into six reading frames is about 30 times faster than the Bioruby one: Bioruby version: # 22929 records 137574 times translated! # real 9m30.952s # user 8m42.877s # sys 0m32.878s Biolib version: # 22929 records 137574 times translated! # real 0m20.306s # user 0m15.997s # sys 0m1.344s This is including IO - which is handled by Ruby. The code is nt = FastaReader.new(fn) trnTable = Biolib::Emboss.ajTrnNewI(1); nt.each { | rec | (0..iter).each do | repeat | ajpseq = Biolib::Emboss.ajSeqNewNameC(rec.seq,"Test sequence") [-3,-2,-1,1,2,3].each do | frame | ajpseqt = Biolib::Emboss.ajTrnSeqOrig(trnTable,ajpseq,frame) aa = Biolib::Emboss.ajSeqGetSeqCopyC(ajpseqt) print "> ",rec.id," ",frame.to_s,"\n" print aa,"\n" end end } $stderr.print nt.size," records ",nt.size*6*iter," times translated!" It just shows. For BIGDATA C rules. With Biolib there are no concessions :-) Pj. From pjotr.public14 at thebird.nl Sat Nov 28 10:12:20 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 28 Nov 2009 11:12:20 +0100 Subject: [BioLib-dev] EMBOSS mapping in Biolib In-Reply-To: References: <20091125162731.GA3589@thebird.nl> Message-ID: <20091128101220.GA16682@thebird.nl> I just executed the EMBOSS mapping for Perl (and Python). The writeup at: http://biolib.open-bio.org/wiki/Mapping_EMBOSS#Mapping_EMBOSS_Perl_and_Python It took three hours, and was a bit harder than normal after a succesful Ruby mapping. Pj.