[BioLib-dev] EMBOSS mapping in Biolib

[Mark A. Jensen]

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
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