Input Formatting
================

.. _smlf:

Simple Mutation List Format
----------------

| The smlf format is essential a tab-separated values with three columns. The columns represent:
#. Protein identifier
#. Amino acid change notation *Optional*
#. Tags *Optional*

| An example:

::

  NP_000007.1     R29L    label:Pathogenic
  NP_000007.1     Q45H    label:Pathogenic
  NP_000007.1     R53C    label:Pathogenic
  NP_000007.1     Y67H    label:Pathogenic
  NP_000007.1     Y73C    label:Pathogenic
  NP_000007.1     P74L    label:Pathogenic
  NP_000007.1     I78V    label:Pathogenic
  NP_000007.1     I78T    label:Pathogenic
  NP_000007.1     I78M    label:Pathogenic
  NP_000007.1     A81T    label:Pathogenic
  NP_000007.1     L84F    label:Pathogenic
  NP_000007.1     G85S    label:Pathogenic
  NP_000007.1     G85R    label:Pathogenic
  NP_000007.1     M87T    label:Pathogenic
  NP_000007.1     M87I    label:Benign
  NP_000007.1     D104N   label:Pathogenic
  NP_000007.1     D104G   label:Pathogenic
  NP_000007.1     L107F   label:Pathogenic
  NP_000007.1     A113T   label:Pathogenic
  NP_000007.1     A113D   label:Pathogenic
  NP_000007.1     Y114C   label:Pathogenic
  NP_000007.1     C116Y   label:Pathogenic
  NP_000007.1     G118A   label:Pathogenic
  NP_000007.1     P132H   label:Pathogenic
  NP_000007.1     A136V   label:Pathogenic
  NP_000007.1     R148K   label:Pathogenic
  NP_000007.1     R148I   label:Pathogenic
  NP_000007.1     M149I   label:Pathogenic
  NP_000007.1     M155T   label:Pathogenic
  NP_000007.1     Y158H   label:Pathogenic
  NP_000007.1     C159W   label:Benign
  NP_000007.1     A165T   label:Pathogenic
  NP_000007.1     D168G   label:Pathogenic
  NP_000007.1     I185T   label:Pathogenic
  NP_000007.1     I185M   label:Pathogenic

.. _fasta:

Fasta Format
------------

| StructMAn can process a slightly modified version of fasta-formatted files. The header of each sequence should contain an unique protein identifier without whitespace (preceeded by the typical fasta >-symbol):
| ``>Protein_ABC123``
| Between the header and the sequence line can be any number of mutation information lines that start with an <-symbol.
.. note::
  Those lines are not supported by the standard fasta format.
| ``<A23G [Tags-String]``
| The sequence line works identical to the standard fasta format by simply providing an amino acid sequence in one-letter code:
| ``MAGGHKLMRAARAFTP``
| A complete example:

::

  >NUDT15_urn:mavedb:00000055-0-1
  MTASAQPRGRRPGVGVGVVVTSCKHPRCVLLGKRKGSVGAGSFQLPGGHLEFGETWEECAQRETWEEAALHLKNVHFASVVNSFIEKENYHYVTILMKGEVDVTHDSEPKNVEPEKNESWEWVPWEELPPLDQLFWGLRCLKEQGYDPFKEDLNHLVGYKGNHL
  >RHO_urn:mavedb:00000099-a-1
  MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
  >TEM-1_beta-lactamase_urn:mavedb:00000070-a-3
  MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
  >CcdB_urn:mavedb:00000084-a
  MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEVADLSHRENDIKNAINLMFWGI
  >PTEN_urn:mavedb:00000054-a
  MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQITKV
  >p53_urn:mavedb:00000059-a
  MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

.. _structguy_inputs:

Inputs dedicated for further procession with StructGuy
----------------------------------------

| Generally all StructMAn readable formats can be used with StructGuy for prediction. For the featurization of a training dataset, effect values need to be assigned for each mutation and can be done with the following formats:

.. _smlf_sg:

Simple Mutation List Format for StructGuy Training
----------------
| The effect values are assigned using the tags column with the general form: `#effect_name:float`. The `effect_name` can be any normal text-string, but should be consistent throughout the file. `float` needs to be a floating point number.
| An example:

::

  A0A140D2T1  I291A  #effect:0.0302686862600679
  A0A140D2T1  I291Y  #effect:0.048604163054757
  A0A140D2T1  I291W  #effect:0.0936416537015749
  A0A140D2T1  I291V  #effect:0.626746537538822
  A0A140D2T1  I291T  #effect:1.76206628831371
  A0A140D2T1  I291S  #effect:0.017235384036755
  A0A140D2T1  I291R  #effect:0.008824236279643
  A0A140D2T1  I291Q  #effect:0.064509419785469
  A0A140D2T1  I291P  #effect:0.006903087964492
  A0A140D2T1  I291C  #effect:0.050460709116445
  A0A140D2T1  I291M  #effect:1.55445997909363
  A0A140D2T1  I291D  #effect:0.067708005015844
  A0A140D2T1  I291E  #effect:0.051098705641169
  A0A140D2T1  I291F  #effect:0.048359762811103
  A0A140D2T1  I291N  #effect:0.047549277753243
  A0A140D2T1  I291H  #effect:0.018586107041444
  A0A140D2T1  I291K  #effect:0.021642108328451
  A0A140D2T1  I291L  #effect:0.024099011187566
  A0A140D2T1  I291G  #effect:0.023833827356767

.. _fasta_sg:

Fasta Format for StructGuy Training
------------
| The effect values are assigned using the special `<` lines with the general form:  `<[AA1][POS][AA2] #effect_name:float`. `AA1` is the wildtype amino acid, `POS` is the position number of the amino acid, `AA1` is the mutant amino acid. The `effect_name` can be any normal text-string, but should be consistent throughout the file. `float` needs to be a floating point number.
| An example:

::

  >A0A140D2T1_ZIKV_Sourisseau_2019
  <I291A #effect:0.0302686862600679
  <I291Y #effect:0.048604163054757
  <I291W #effect:0.0936416537015749
  <I291V #effect:0.626746537538822
  <I291T #effect:1.76206628831371
  <I291S #effect:0.017235384036755
  <I291R #effect:0.008824236279643
  <I291Q #effect:0.064509419785469
  <I291P #effect:0.006903087964492
  <I291C #effect:0.050460709116445
  <I291M #effect:1.55445997909363
  <I291D #effect:0.067708005015844
  <I291E #effect:0.051098705641169
  <I291F #effect:0.048359762811103
  <I291N #effect:0.047549277753243
  <I291H #effect:0.018586107041444
  <I291K #effect:0.021642108328451
  <I291L #effect:0.024099011187566
  MKNPKKKSGGFRIVNMLKRGVARVNPLGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIKPSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKERKRRGADTSIGIIGLLLTTAMAAEITRRGSAYYMYLDRSD
  AGKAISFATTLGVNKCHVQIMDLGHMCDATMSYECPMLDEGVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVTLPSHSTRKLQTRSQTWLESREYTKHLIKVENWIFRNPGFALVAVAIAWLLGSSTSQKVIYLV
  MILLIAPAYSIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFTCSKKMTGKSI
  QPENLEYRIMLSVHGSQHSGMIVNDTGYETDENRAKVEVTPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALA
  GALEAEMDGAKGKLFSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKVPAETLHGTVTVEVQYAGTDGPCKIPVQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGDKKITHHWHRSGSTIGKA
  FEATVRGAKRMAVLGDTAWDFGSVGGVFNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLVWLGLNTKNGSISLTCLALGGVMIFLSTAVSADVGCSVDFSKKETRCGTGVFIYNDVEAWRDRYKYHPDSPRRLAAAV
  KQAWEEGICGISSVSRMENIMWKSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPVPVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKECPLEHRAWNSFLVEDHGFGVFHTSVWLKVREDYSLECDPAVIGT
  AVKGREAAHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWPKSHTLWTDGVEESDLIIPKSLAGPLSHHNTREGYRTQVKGPWHSEELEIRFEECPGTKVYVEETCGTRGPSLRSTTASGRVIEEWCCRECTMPPLSFRAK
  DGCWYGMEIRPRKEPESNLVRSMVTAGSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIMSTSMAVLVVMILGGFSMSDLAKLVILMGATFAEMNTGGDVAHLALVAAFKVRPALLVSFIFRANWTPRESMLLALASCLL
  QTAISALEGDLMVLINGFALAWLAIRAMAVPRTDNIALPILAALTPLARGTLLVAWRAGLATCGGIMLLSLKGKGSVKKNLPFVMALGLTAVRVVDPINVVGLLLLTRSGKRSWPPSEVLTAVGLICALAGGFAKADIEM
  AGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEEDGPPMREIILKVVLMAICGMNPIAIPFAAGAWYVYVKTGKRSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGV
  GVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERARNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKREEETPVEC
  FEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKKRLRTVILAPTRVVAAEMEEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDPSSIAARGYISTRVEMGEAAAIFMTAT
  PPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKNQEWDFVITTDISEMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRG
  RIGRNPNKPGDEYMYGGGCAETDEGHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRKTFVELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTKYGEKRVLKPRWMDAR
  VCSDHAALKSFKEFAAGKRGAALGVMEALGTLPGHMTERFQEAIDNLAVLMRAETGSRPYKAAAAQLPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLGASAWLMWLSEIEPARIACVLIVVFLLLVVLIP
  EPEKQRSPQDNQMAIIIMVAVGLLGLITANELGWLERTKNDIAHLMGRREEGATMGFSMDIDLRPASAWAIYAALTTLITPAVQHAVTTSYNNYSLMAMATQAGVLFGMGKGMPFYAWDLGVPLLMMGCYSQLTPLTLIV
  AIILLVAHYMYLIPGLQAAAARAAQKRTAAGIMKNPVVDGIVVTDIDTMTIDPQVEKKMGQVLLIAVAISSAVLLRTAWGWGEAGALITAATSTLWEGSPNKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRR
  GGGTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLRWLVERGYLQPYGKVVDLGCGRGGWSYYAATIRKVQEVRGYTKGGPGHEEPMLVQSYGWNIVRLKSGVDVFHMAAEPC
  DTLLCDIGESSSSPEVEETRTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMMETMERLQRRHGGGLVRVPLSRNSTHEMYWVSGAKSNIIKSVSTTSQLLLGRMDGPRRPVKYEEDVNLGSGTRAVASCAEAPNMKIIGR
  RIERIRNEHAETWFLDENHPYRTWAYHGSYEAPTQGSASSLVNGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPDPQEGTRQVMNIVSSWLWKELGKRKRPRVCTKEEFINKVRSNAALGAIFEEEKEW
  KTAVEAVNDPRFWALVDREREHHLRGECHSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYILEEMNRAPGGKMYADDTAGWDTRISKFDLENEALITNQMEE
  GHRTLALAVIKYTYQNKVVKVLRPAEGGKTVMDIISRQDQRGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRKPEKVTRWLQSNGWDRLKRMAVSGDDCVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPST
  GWSNWEEVPFCSHHFNKLYLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSAVPVDWVPTGRTTWSIHGKGEWMTTEDMLMVWNRVWIEENDHMEDKTPVTKWTDIPY
  LGKREDLWCGSLIGHRPRTTWAENIKDTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTPGVL