[BioLib-dev] EMBOSS mapping in Biolib

[Chris Fields]

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" <pjotr.public14 at thebird.nl>
> To: "BioLib Project" <biolib-dev at lists.open-bio.org>
> 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