Fasta support

Author: AndrewRadev

autoload/sj/fasta.vim

@@ -0,0 +1,56 @@
+function! sj#fasta#SplitSequence() abort
+  " Check we're on a header line:
+  if getline('.') !~ '^>'
+    return 0
+  endif
+  let header_lineno = line('.')
+
+  " Check that the next line is a sequence
+  if getline(header_lineno + 1) =~ '^>'
+    return 0
+  endif
+  let sequence_lineno = header_lineno + 1
+  let sequence_line = getline(sequence_lineno)
+
+  " Check that the next next line is a header
+  if getline(header_lineno + 2) !~ '^>'
+    return 0
+  endif
+
+  let width = sj#settings#Read('fasta_textwidth')
+  if width <= 0
+    let width = &textwidth
+  endif
+  if width <= 0
+    let width = 80
+  endif
+
+  let split_sequence_line = substitute(sequence_line, '.\{'..width..'}', '\0\n', 'g')
+  call sj#ReplaceLines(sequence_lineno, sequence_lineno, split_sequence_line)
+  return 1
+endfunction
+
+function! sj#fasta#JoinSequence() abort
+  " Check we're on a header line:
+  if getline('.') !~ '^>'
+    return 0
+  endif
+  let header_lineno = line('.')
+  let start_lineno = header_lineno + 1
+
+  " Find next header line, if any:
+  let next_header_lineno = search('^>', 'W')
+  if next_header_lineno > 0
+    let end_lineno = next_header_lineno - 1
+  else
+    let end_lineno = line('$')
+  endif
+
+  if end_lineno - start_lineno <= 0
+    " No sequence lines to join
+    return 0
+  endif
+
+  call sj#Keeppatterns(start_lineno..','..(end_lineno - 1)..'s/\n//g')
+  return 1
+endfunction

doc/splitjoin.txt

@@ -14,11 +14,12 @@ CONTENTS                                          *splitjoin* *splitjoin-content
     Elixir.................................: |splitjoin-elixir|
     Elm....................................: |splitjoin-elm|
     Eruby..................................: |splitjoin-eruby|
+    FASTA..................................: |splitjoin-fasta|
     Go.....................................: |splitjoin-go|
     HAML...................................: |splitjoin-haml|
+    HTML...................................: |splitjoin-html|
     Handlebars.............................: |splitjoin-handlebars|
     Hare...................................: |splitjoin-hare|
-    HTML...................................: |splitjoin-html|
     Java...................................: |splitjoin-java|
     Javascript.............................: |splitjoin-javascript| |splitjoin-json|
     JSX/TSX................................: |splitjoin-jsx| |splitjoin-tsx|
@@ -513,6 +514,20 @@ Option hashes ~
     } %>
 <
 
+==============================================================================
+FASTA                                                          *splitjoin-fasta*
+
+Sequences ~
+>
+    > E.coli_K12 Cysteine--tRNA ligase
+    MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDK...
+
+    > E.coli_K12 Cysteine--tRNA ligase
+    MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYK
+    LKYVRNITDIDDKIIKRANENGESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAE
+    ...
+<
+
 ==============================================================================
 GO                                                                *splitjoin-go*
 
@@ -2133,6 +2148,18 @@ part. However, if it's broken at a `.`, it could cause parsing problems. Not
 leaving a space might be safer, set to 0 to do that.
 
 
+                                                     *splitjoin_fasta_textwidth*
+>
+    let g:splitjoin_fasta_textwidth = 100
+<
+Default value: 0
+
+Fasta files get split into lines based on textwidth. If this variable is set
+to anything greater than 0, that will be considered the desired textwidth.
+Otherwise, the built-in 'textwidth' will be used. If that's set to 0, the
+plugin will arbitrarily use 100 as the threshold.
+
+
 ==============================================================================
 INTERNALS                                                *splitjoin-internals*
 

ftplugin/fasta/splitjoin.vim

@@ -0,0 +1,7 @@
+let b:splitjoin_split_callbacks = [
+      \ 'sj#fasta#SplitSequence',
+      \ ]
+
+let b:splitjoin_join_callbacks = [
+      \ 'sj#fasta#JoinSequence',
+      \ ]

plugin/splitjoin.vim

@@ -38,6 +38,7 @@ let g:splitjoin_default_settings = {
       \ 'java_argument_split_first_newline':       0,
       \ 'java_argument_split_last_newline':        0,
       \ 'vim_split_whitespace_after_backslash':    1,
+      \ 'fasta_textwidth':                         0,
       \ }
 
 if !exists('g:splitjoin_join_mapping')

spec/plugin/fasta_spec.rb

@@ -0,0 +1,43 @@
+require 'spec_helper'
+
+describe "fasta" do
+  let(:filename) { 'test.fasta' }
+
+  specify "sequences" do
+    set_file_contents <<~EOF
+      >Something else
+      ELVIS-LIVES
+      > E.coli_K12 Cysteine--tRNA ligase
+      MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDK...
+      > Another one
+      LIVES-ELVIS*
+    EOF
+
+    vim.set :filetype, 'fasta'
+    vim.set :textwidth, 50
+
+    vim.search '> E\.coli'
+    split
+
+    assert_file_contents <<~EOF
+      >Something else
+      ELVIS-LIVES
+      > E.coli_K12 Cysteine--tRNA ligase
+      MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVV
+      ARYLRFLGYKLKYVRNITDIDDK...
+      > Another one
+      LIVES-ELVIS*
+    EOF
+
+    join
+
+    assert_file_contents <<~EOF
+      >Something else
+      ELVIS-LIVES
+      > E.coli_K12 Cysteine--tRNA ligase
+      MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDK...
+      > Another one
+      LIVES-ELVIS*
+    EOF
+  end
+end