[BioLib-dev] EMBOSS mapping in Biolib

[Pjotr Prins]

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