add plot of natural diversity vs DMS (#16)

* add plot of natural diversity vs DMS

* write natural sequence diversity and escape to CSV

natural_diversity/README.md

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+# Analysis of natural spike diversity performed outside the main pipeline
+This subdirectory contains analysis of the natural diversity of spike at different sites, and is run manually by the Jupyter notebook in this subdirectory (so outside the main pipeline).
+It plots natural sequence diversity versus DMS.
+
+The file [data/NC_045512.2.gp](data/NC_045512.2.gp) defines the domain structure of spike.
+
+The file [data/ncov_open_global_all-time.json](data/ncov_open_global_all-time.json) is the Nextstrain JSON downloaded from [https://nextstrain.org/ncov/open/global/all-time](https://nextstrain.org/ncov/open/global/all-time) on Dec-28-2024 that contains all of the data on the submsampled Nextstrain global SARS-CoV-2 phylogeny using open sequences.
+
+The Jupyter notebook [spike_schematic.ipynb](spike_schematic.ipynb) is run manually to analyze this JSON and other data files to make schematics of the spike with the number of effective amino acids at each site, which are place in `.results/`.

natural_diversity/data/NC_045512.2.gp

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+LOCUS       YP_009724390            1273 aa            linear   VRL 18-JUL-2020
+DEFINITION  surface glycoprotein [Severe acute respiratory syndrome coronavirus
+            2].
+ACCESSION   YP_009724390
+VERSION     YP_009724390.1
+DBLINK      BioProject: PRJNA485481
+DBSOURCE    REFSEQ: accession NC_045512.2
+KEYWORDS    RefSeq.
+SOURCE      Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
+  ORGANISM  Severe acute respiratory syndrome coronavirus 2
+            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
+            Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae;
+            Betacoronavirus; Sarbecovirus.
+REFERENCE   1  (residues 1 to 1273)
+  AUTHORS   Wu,F., Zhao,S., Yu,B., Chen,Y.M., Wang,W., Song,Z.G., Hu,Y.,
+            Tao,Z.W., Tian,J.H., Pei,Y.Y., Yuan,M.L., Zhang,Y.L., Dai,F.H.,
+            Liu,Y., Wang,Q.M., Zheng,J.J., Xu,L., Holmes,E.C. and Zhang,Y.Z.
+  TITLE     A new coronavirus associated with human respiratory disease in
+            China
+  JOURNAL   Nature 579 (7798), 265-269 (2020)
+   PUBMED   32015508
+  REMARK    Erratum:[Nature. 2020 Apr;580(7803):E7. PMID: 32296181]
+REFERENCE   2  (residues 1 to 1273)
+  CONSRTM   NCBI Genome Project
+  TITLE     Direct Submission
+  JOURNAL   Submitted (17-JAN-2020) National Center for Biotechnology
+            Information, NIH, Bethesda, MD 20894, USA
+REFERENCE   3  (residues 1 to 1273)
+  AUTHORS   Wu,F., Zhao,S., Yu,B., Chen,Y.-M., Wang,W., Hu,Y., Song,Z.-G.,
+            Tao,Z.-W., Tian,J.-H., Pei,Y.-Y., Yuan,M.L., Zhang,Y.-L.,
+            Dai,F.-H., Liu,Y., Wang,Q.-M., Zheng,J.-J., Xu,L., Holmes,E.C. and
+            Zhang,Y.-Z.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (05-JAN-2020) Shanghai Public Health Clinical Center &
+            School of Public Health, Fudan University, Shanghai, China
+COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
+            NCBI review. The reference sequence is identical to QHD43416.
+            Annotation was added using homology to SARSr-CoV NC_004718.3. ###
+            Formerly called 'Wuhan seafood market pneumonia virus.' If you have
+            questions or suggestions, please email us at [email protected]
+            and include the accession number NC_045512.### Protein structures
+            can be found at
+            https://www.ncbi.nlm.nih.gov/structure/?term=sars-cov-2.### Find
+            all other Severe acute respiratory syndrome coronavirus 2
+            (SARS-CoV-2) sequences at
+            https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/
+
+            ##Assembly-Data-START##
+            Assembly Method       :: Megahit v. V1.1.3
+            Sequencing Technology :: Illumina
+            ##Assembly-Data-END##
+            COMPLETENESS: full length.
+            Method: conceptual translation.
+FEATURES             Location/Qualifiers
+     Spike           1..1273
+     S1              16..681
+     S2              682..1211
+     NTD             13..304
+     RBD             319..541
+     binding_loop_1  417..420
+     binding_loop_2  446..456
+     binding_loop_3  486..505
+ORIGIN      
+        1 mfvflvllpl vssqcvnltt rtqlppaytn sftrgvyypd kvfrssvlhs tqdlflpffs
+       61 nvtwfhaihv sgtngtkrfd npvlpfndgv yfasteksni irgwifgttl dsktqslliv
+      121 nnatnvvikv cefqfcndpf lgvyyhknnk swmesefrvy ssannctfey vsqpflmdle
+      181 gkqgnfknlr efvfknidgy fkiyskhtpi nlvrdlpqgf saleplvdlp iginitrfqt
+      241 llalhrsylt pgdsssgwta gaaayyvgyl qprtfllkyn engtitdavd caldplsetk
+      301 ctlksftvek giyqtsnfrv qptesivrfp nitnlcpfge vfnatrfasv yawnrkrisn
+      361 cvadysvlyn sasfstfkcy gvsptklndl cftnvyadsf virgdevrqi apgqtgkiad
+      421 ynyklpddft gcviawnsnn ldskvggnyn ylyrlfrksn lkpferdist eiyqagstpc
+      481 ngvegfncyf plqsygfqpt ngvgyqpyrv vvlsfellha patvcgpkks tnlvknkcvn
+      541 fnfngltgtg vltesnkkfl pfqqfgrdia dttdavrdpq tleilditpc sfggvsvitp
+      601 gtntsnqvav lyqdvnctev pvaihadqlt ptwrvystgs nvfqtragcl igaehvnnsy
+      661 ecdipigagi casyqtqtns prrarsvasq siiaytmslg aensvaysnn siaiptnfti
+      721 svtteilpvs mtktsvdctm yicgdstecs nlllqygsfc tqlnraltgi aveqdkntqe
+      781 vfaqvkqiyk tppikdfggf nfsqilpdps kpskrsfied llfnkvtlad agfikqygdc
+      841 lgdiaardli caqkfngltv lpplltdemi aqytsallag titsgwtfga gaalqipfam
+      901 qmayrfngig vtqnvlyenq klianqfnsa igkiqdslss tasalgklqd vvnqnaqaln
+      961 tlvkqlssnf gaissvlndi lsrldkveae vqidrlitgr lqslqtyvtq qliraaeira
+     1021 sanlaatkms ecvlgqskrv dfcgkgyhlm sfpqsaphgv vflhvtyvpa qeknfttapa
+     1081 ichdgkahfp regvfvsngt hwfvtqrnfy epqiittdnt fvsgncdvvi givnntvydp
+     1141 lqpeldsfke eldkyfknht spdvdlgdis ginasvvniq keidrlneva knlneslidl
+     1201 qelgkyeqyi kwpwyiwlgf iagliaivmv timlccmtsc csclkgccsc gscckfdedd
+     1261 sepvlkgvkl hyt
+//
+