Data commit

Task/FASTA-format/00-META.yaml

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+---
+from: http://rosettacode.org/wiki/FASTA_format

Task/FASTA-format/00-TASK.txt

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+In [[wp:bioinformatics|bioinformatics]], long character strings are often encoded in a format called [[wp:FASTA format|FASTA]].  
+
+A FASTA file can contain several strings, each identified by a name marked by a <big><big><code>&gt;</code></big></big> (greater than) character at the beginning of the line.
+
+
+;Task:
+Write a program that reads a FASTA file such as:
+<pre>
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+</pre>
+{{out}}
+<pre>
+Rosetta_Example_1: THERECANBENOSPACE
+Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
+</pre>
+Note that a high-quality implementation will not hold the entire file in memory at once; real FASTA files can be multiple gigabytes in size.
+<br><br>
+

Task/FASTA-format/11l/fasta-format.11l

@@ -0,0 +1,25 @@
+V FASTA =
+|‘>Rosetta_Example_1
+  THERECANBENOSPACE
+  >Rosetta_Example_2
+  THERECANBESEVERAL
+  LINESBUTTHEYALLMUST
+  BECONCATENATED’
+
+F fasta_parse(infile_str)
+   V key = ‘’
+   V val = ‘’
+   [(String, String)] r
+   L(line) infile_str.split("\n")
+      I line.starts_with(‘>’)
+         I key != ‘’
+            r [+]= (key, val)
+         key = line[1..].split_py()[0]
+         val = ‘’
+      E I key != ‘’
+         val ‘’= line
+   I key != ‘’
+      r [+]= (key, val)
+   R r
+
+print(fasta_parse(FASTA).map((key, val) -> ‘#.: #.’.format(key, val)).join("\n"))

Task/FASTA-format/ALGOL-W/fasta-format.alg

@@ -0,0 +1,26 @@
+begin
+    % reads FASTA format data from standard input and write the results to standard output %
+    % only handles the ">" line start                                                      %
+    string(256) line;
+    % allow the program to continue after reaching end-of-file %
+    ENDFILE := EXCEPTION( false, 1, 0, false, "EOF" );
+    % handle the input %
+    readcard( line );
+    while not XCPNOTED(ENDFILE) do begin
+        % strings are fixed length in Algol W - we need to find the line lengh with trailing spaces removed %
+        integer len;
+        len := 255;
+        while len > 0 and line( len // 1 ) = " " do len := len - 1;
+        if len > 0 then begin % non-empty line %
+            integer pos;
+            pos := 0;
+            if line( 0 // 1 ) = ">" then begin % header line %
+                write();
+                pos := 1;
+            end if_header_line ;
+            for cPos := pos until len do writeon( line( cPos // 1 ) );
+            if line( 0 // 1 ) = ">" then writeon( ": " )
+        end if_non_empty_line ;
+        readcard( line );
+    end while_not_eof
+end.

Task/FASTA-format/AWK/fasta-format.awk

@@ -0,0 +1,51 @@
+# syntax: GAWK -f FASTA_FORMAT.AWK filename
+# stop processing each file when an error is encountered
+{   if (FNR == 1) {
+      header_found = 0
+      if ($0 !~ /^[;>]/) {
+        error("record is not valid")
+        nextfile
+      }
+    }
+    if ($0 ~ /^;/) { next } # comment begins with a ";"
+    if ($0 ~ /^>/) { # header
+      if (header_found > 0) {
+        printf("\n") # EOL for previous sequence
+      }
+      printf("%s: ",substr($0,2))
+      header_found = 1
+      next
+    }
+    if ($0 ~ /[ \t]/) { next } # ignore records with whitespace
+    if ($0 ~ /\*$/) { # sequence may end with an "*"
+      if (header_found > 0) {
+        printf("%s\n",substr($0,1,length($0)-1))
+        header_found = 0
+        next
+      }
+      else {
+        error("end of sequence found but header is missing")
+        nextfile
+      }
+    }
+    if (header_found > 0) {
+      printf("%s",$0)
+    }
+    else {
+      error("header not found")
+      nextfile
+    }
+}
+ENDFILE {
+    if (header_found > 0) {
+      printf("\n")
+    }
+}
+END {
+    exit (errors == 0) ? 0 : 1
+}
+function error(message) {
+    printf("error: FILENAME=%s, FNR=%d, %s, %s\n",FILENAME,FNR,message,$0) >"con"
+    errors++
+    return
+}

Task/FASTA-format/Action-/fasta-format.action

@@ -0,0 +1,30 @@
+PROC ReadFastaFile(CHAR ARRAY fname)
+  CHAR ARRAY line(256)
+  CHAR ARRAY tmp(256)
+  BYTE newLine,dev=[1]
+
+  newLine=0
+  Close(dev)
+  Open(dev,fname,4)
+  WHILE Eof(dev)=0
+  DO
+    InputSD(dev,line)
+    IF line(0)>0 AND line(1)='> THEN
+      IF newLine THEN
+        PutE()
+      FI
+      newLine=1
+      SCopyS(tmp,line,2,line(0))
+      Print(tmp) Print(": ")
+    ELSE
+      Print(line)
+    FI
+  OD
+  Close(dev)
+RETURN
+
+PROC Main()
+  CHAR ARRAY fname="H6:FASTA.TXT"
+
+  ReadFastaFile(fname)
+RETURN

Task/FASTA-format/Ada/fasta-format-1.ada

@@ -0,0 +1,28 @@
+with Ada.Text_IO; use Ada.Text_IO;
+
+procedure Simple_FASTA is
+
+   Current: Character;
+
+begin
+   Get(Current);
+   if Current /= '>' then
+      raise Constraint_Error with "'>' expected";
+   end if;
+   while not End_Of_File loop -- read name and string
+      Put(Get_Line & ": "); -- read name and write directly to output
+      Read_String:
+      loop
+	 exit Read_String when End_Of_File; -- end of input
+	 Get(Current);
+	 if Current = '>' then -- next name
+	    New_Line;
+	    exit Read_String;
+	 else
+	    Put(Current & Get_Line);
+	    -- read part of string and write directly to output
+	 end if;
+      end loop Read_String;
+   end loop;
+
+end Simple_FASTA;

Task/FASTA-format/Ada/fasta-format-2.ada

@@ -0,0 +1,46 @@
+with Ada.Text_IO, Ada.Containers.Indefinite_Ordered_Maps; use Ada.Text_IO;
+
+procedure FASTA is
+   package Maps is new  Ada.Containers.Indefinite_Ordered_Maps
+     (Element_Type => String, Key_Type => String);
+   Map: Maps.Map; -- Map holds the full file (as pairs of name and value)
+
+   function Get_Value(Previous: String := "") return String is
+      Current: Character;
+   begin
+      if End_Of_File then
+	 return Previous; -- file ends
+      else
+	 Get(Current); -- read first character
+	 if Current = '>' then -- ah, a new name begins
+	    return Previous; -- the string read so far is the value
+	 else -- the entire line is part of the value
+	    return Get_Value(Previous & Current & Get_Line);
+	 end if;
+      end if;
+   end Get_Value;
+
+   procedure Print_Pair(Position: Maps.Cursor) is
+   begin
+      Put_Line(Maps.Key(Position) & ": " & Maps.Element(Position));
+      -- Maps.Key(X) is the name and Maps.Element(X) is the value at X
+   end Print_Pair;
+
+   Skip_This: String := Get_Value;
+   -- consumes the entire file, until the first line starting with '>'.
+   -- the string Skip_This should be empty, but we don't verify this
+
+begin
+   while not End_Of_File loop -- read the file into Map
+      declare
+	 Name: String := Get_Line;
+	   -- reads all characters in the line, except for the first ">"
+	 Value: String := Get_Value;
+      begin
+	 Map.Insert(Key => Name, New_Item => Value);
+	 -- adds the pair (Name, Value) to Map
+      end;
+   end loop;
+
+   Map.Iterate(Process => Print_Pair'Access); -- print Map
+end FASTA;

Task/FASTA-format/Aime/fasta-format.aime

@@ -0,0 +1,15 @@
+file f;
+text n, s;
+
+f.affix(argv(1));
+
+while (f.line(s) ^ -1) {
+    if (s[0] == '>') {
+        o_(n, s, ": ");
+        n = "\n";
+    } else {
+        o_(s);
+    }
+}
+
+o_(n);

Task/FASTA-format/Arturo/fasta-format.arturo

@@ -0,0 +1,24 @@
+parseFasta: function [data][
+    result: #[]
+    current: ø
+    loop split.lines data 'line [
+        if? `>` = first line [
+            current: slice line 1 (size line)-1
+            set result current ""
+        ]
+        else ->
+            set result current (get result current)++line
+    ]
+    return result
+]
+
+text: {
+    >Rosetta_Example_1
+    THERECANBENOSPACE
+    >Rosetta_Example_2
+    THERECANBESEVERAL
+    LINESBUTTHEYALLMUST
+    BECONCATENATED
+}
+
+inspect.muted parseFasta text

Task/FASTA-format/AutoHotkey/fasta-format.ahk

@@ -0,0 +1,14 @@
+Data =
+(
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+)
+
+Data := RegExReplace(RegExReplace(Data, ">\V+\K\v+", ": "), "\v+(?!>)")
+Gui, add, Edit, w700,  % Data
+Gui, show
+return

Task/FASTA-format/BASIC256/fasta-format.basic

@@ -0,0 +1,33 @@
+open 1, "input.fasta"
+
+first = True
+
+while not eof(1)
+    ln = readline(1)
+    if left(ln, 1) = ">"  then
+        if not first then print
+        print mid(ln, 2, length(ln)-2) & ": ";
+        if first then first = False
+    else
+        if first then
+            print "Error : File does not begin with '>'"
+            exit while
+        else
+            if checkNoSpaces(ln) then
+                print left(ln, length(ln)-2);
+            else
+                print "Error : Sequence contains space(s)"
+                exit while
+            end if
+        end if
+    end if
+end while
+close 1
+end
+
+function checkNoSpaces(s)
+    for i = 1 to length(s) - 1
+        if chr(mid(s,i,1)) = 32 or chr(mid(s,i,1)) = 9 then return False
+    next i
+    return True
+end function

Task/FASTA-format/C++/fasta-format.cpp

@@ -0,0 +1,41 @@
+#include <iostream>
+#include <fstream>
+
+int main( int argc, char **argv ){
+    if( argc <= 1 ){
+        std::cerr << "Usage: "<<argv[0]<<" [infile]" << std::endl;
+        return -1;
+    }
+
+    std::ifstream input(argv[1]);
+    if(!input.good()){
+        std::cerr << "Error opening '"<<argv[1]<<"'. Bailing out." << std::endl;
+        return -1;
+    }
+
+    std::string line, name, content;
+    while( std::getline( input, line ).good() ){
+        if( line.empty() || line[0] == '>' ){ // Identifier marker
+            if( !name.empty() ){ // Print out what we read from the last entry
+                std::cout << name << " : " << content << std::endl;
+                name.clear();
+            }
+            if( !line.empty() ){
+                name = line.substr(1);
+            }
+            content.clear();
+        } else if( !name.empty() ){
+            if( line.find(' ') != std::string::npos ){ // Invalid sequence--no spaces allowed
+                name.clear();
+                content.clear();
+            } else {
+                content += line;
+            }
+        }
+    }
+    if( !name.empty() ){ // Print out what we read from the last entry
+        std::cout << name << " : " << content << std::endl;
+    }
+
+    return 0;
+}

Task/FASTA-format/C-sharp/fasta-format.cs

@@ -0,0 +1,52 @@
+using System;
+using System.Collections.Generic;
+using System.IO;
+using System.Text;
+
+class Program
+{
+    public class FastaEntry
+    {
+        public string Name { get; set; }
+        public StringBuilder Sequence { get; set; }
+    }
+
+    static IEnumerable<FastaEntry> ParseFasta(StreamReader fastaFile)
+    {
+        FastaEntry f = null;
+        string line;
+        while ((line = fastaFile.ReadLine()) != null)
+        {
+            // ignore comment lines
+            if (line.StartsWith(";"))
+                continue;
+
+            if (line.StartsWith(">"))
+            {
+                if (f != null)
+                    yield return f;
+                f = new FastaEntry { Name = line.Substring(1), Sequence = new StringBuilder() };
+            }
+            else if (f != null)
+                f.Sequence.Append(line);
+        }
+        yield return f;
+    }
+
+    static void Main(string[] args)
+    {
+        try
+        {
+            using (var fastaFile = new StreamReader("fasta.txt"))
+            {
+                foreach (FastaEntry f in ParseFasta(fastaFile))
+                    Console.WriteLine("{0}: {1}", f.Name, f.Sequence);
+            }
+        }
+        catch (FileNotFoundException e)
+        {
+            Console.WriteLine(e);
+        }
+        Console.ReadLine();
+    }
+}

Task/FASTA-format/C/fasta-format.c

@@ -0,0 +1,38 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+void main()
+{
+	FILE * fp;
+	char * line = NULL;
+	size_t len = 0;
+	ssize_t read;
+
+	fp = fopen("fasta.txt", "r");
+	if (fp == NULL)
+		exit(EXIT_FAILURE);
+
+	int state = 0;
+	while ((read = getline(&line, &len, fp)) != -1) {
+		/* Delete trailing newline */
+		if (line[read - 1] == '\n')
+			line[read - 1] = 0;
+		/* Handle comment lines*/
+		if (line[0] == '>') {
+			if (state == 1)
+				printf("\n");
+			printf("%s: ", line+1);
+			state = 1;
+		} else {
+			/* Print everything else */
+			printf("%s", line);
+		}
+	}
+	printf("\n");
+
+	fclose(fp);
+	if (line)
+		free(line);
+	exit(EXIT_SUCCESS);
+}

Task/FASTA-format/Clojure/fasta-format.clj

@@ -0,0 +1,6 @@
+(defn fasta [pathname]
+  (with-open [r (clojure.java.io/reader pathname)]
+    (doseq [line (line-seq r)]
+      (if (= (first line) \>)
+          (print (format "%n%s: " (subs line 1)))
+        (print line)))))

Task/FASTA-format/Common-Lisp/fasta-format.lisp

@@ -0,0 +1,14 @@
+;; * The input file as a parameter
+(defparameter *input* #p"fasta.txt"
+              "The input file name.")
+
+;; * Reading the data
+(with-open-file (data *input*)
+  (loop
+     :for line = (read-line data nil nil)
+     :while line
+     ;; Check if we have a comment using a simple test instead of a RegEx
+     :if (char= #\> (char line 0))
+     :do (format t "~&~a: " (subseq line 1))
+     :else
+     :do (format t "~a" line)))

Task/FASTA-format/Crystal/fasta-format.crystal

@@ -0,0 +1,26 @@
+# create tmp fasta file in /tmp/
+tmpfile = "/tmp/tmp"+Random.rand.to_s+".fasta"
+File.write(tmpfile, ">Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED")
+
+# read tmp fasta file and store to hash
+ref = tmpfile
+id = seq = ""
+fasta = {} of String => String
+File.each_line(ref) do |line|
+  if line.starts_with?(">")
+    fasta[id] = seq.sub(/\s/, "") if id != ""
+    id = line.split(/\s/)[0].lstrip(">")
+    seq = ""
+  else
+    seq += line
+  end
+end
+fasta[id] = seq.sub(/\s/, "")
+
+# show fasta component
+fasta.each { |k,v| puts "#{k}: #{v}"}

Task/FASTA-format/F-Sharp/fasta-format.fs

@@ -0,0 +1,4 @@
+//FASTA format. Nigel Galloway: March 23rd., 2023.
+let fN(g:string)=match g[0] with '>'->printfn "\n%s:" g[1..] |_->printf "%s" g
+let lines=seq{use n=System.IO.File.OpenText("testFASTA.txt") in while not n.EndOfStream do yield n.ReadLine()}
+printfn "%s:" ((Seq.head lines)[1..]); Seq.tail lines|>Seq.iter fN; printfn ""

Task/FASTA-format/Factor/fasta-format.factor

@@ -0,0 +1,10 @@
+USING: formatting io kernel sequences ;
+IN: rosetta-code.fasta
+
+: process-fasta-line ( str -- )
+    dup ">" head? [ rest "\n%s: " printf ] [ write ] if ;
+
+: main ( -- )
+    readln rest "%s: " printf [ process-fasta-line ] each-line ;
+
+MAIN: main

Task/FASTA-format/Forth/fasta-format.fth

@@ -0,0 +1,16 @@
+1024      constant  max-Line
+char >    constant  marker
+
+: read-lines        begin  pad max-line >r over r> swap
+                           read-line throw
+                    while  pad dup c@ marker =
+                           if cr 1+ swap type ."  : "
+                           else swap  type
+                           then
+                    repeat drop  ;
+
+: Test              s" ./FASTA.txt" r/o open-file throw
+                    read-lines
+                    close-file throw
+                    cr ;
+Test

Task/FASTA-format/FreeBASIC/fasta-format.basic

@@ -0,0 +1,38 @@
+' FB 1.05.0 Win64
+
+Function checkNoSpaces(s As String) As Boolean
+  For i As UInteger = 0 To Len(s) - 1
+    If s[i] = 32 OrElse s[i] = 9 Then Return False  '' check for spaces or tabs
+  Next
+  Return True
+End Function
+
+Open "input.fasta" For Input As # 1
+
+Dim As String ln, seq
+Dim first As Boolean = True
+
+While Not Eof(1)
+  Line Input #1, ln
+  If Left(ln, 1) = ">"  Then
+    If Not first Then Print
+    Print Mid(ln, 2); ": ";
+    If first Then first = False
+  ElseIf first Then
+    Print: Print "Error : File does not begin with '>'";
+    Exit While
+  Else
+    If checkNoSpaces(ln) Then
+      Print ln;
+    Else
+      Print : Print "Error : Sequence contains space(s)";
+      Exit While
+    End If
+  End If
+Wend
+
+Close #1
+
+Print : Print
+Print "Press any key to quit"
+Sleep

Task/FASTA-format/Gambas/fasta-format.gambas

@@ -0,0 +1,16 @@
+Public Sub Main()
+Dim sList As String = File.Load("../FASTA")
+Dim sTemp, sOutput As String
+
+For Each sTemp In Split(sList, gb.NewLine)
+  If sTemp Begins ">" Then
+    If sOutput Then Print sOutput
+    sOutput = Right(sTemp, -1) & ": "
+  Else
+    sOutput &= sTemp
+  Endif
+Next
+
+Print sOutput
+
+End

Task/FASTA-format/Go/fasta-format.go

@@ -0,0 +1,43 @@
+package main
+
+import (
+        "bufio"
+        "fmt"
+        "os"
+)
+
+func main() {
+        f, err := os.Open("rc.fasta")
+        if err != nil {
+                fmt.Println(err)
+                return
+        }
+        defer f.Close()
+        s := bufio.NewScanner(f)
+        headerFound := false
+        for s.Scan() {
+                line := s.Text()
+                switch {
+                case line == "":
+                        continue
+                case line[0] != '>':
+                        if !headerFound {
+                                fmt.Println("missing header")
+                                return
+                        }
+                        fmt.Print(line)
+                case headerFound:
+                        fmt.Println()
+                        fallthrough
+                default:
+                        fmt.Printf("%s: ", line[1:])
+                        headerFound = true
+                }
+        }
+        if headerFound {
+                fmt.Println()
+        }
+        if err := s.Err(); err != nil {
+                fmt.Println(err)
+        }
+}

Task/FASTA-format/Haskell/fasta-format-1.hs

@@ -0,0 +1,17 @@
+import Data.List ( groupBy )
+
+parseFasta :: FilePath -> IO ()
+parseFasta fileName = do
+  file <- readFile fileName
+  let pairedFasta = readFasta $ lines file
+  mapM_ (\(name, code) -> putStrLn $ name ++ ": " ++ code) pairedFasta
+
+readFasta :: [String] -> [(String, String)]
+readFasta = pair . map concat . groupBy (\x y -> notName x && notName y)
+ where
+  notName :: String -> Bool
+  notName = (/=) '>' . head
+
+  pair :: [String] -> [(String, String)]
+  pair []           = []
+  pair (x : y : xs) = (drop 1 x, y) : pair xs

Task/FASTA-format/Haskell/fasta-format-2.hs

@@ -0,0 +1,18 @@
+import Text.ParserCombinators.ReadP
+import Control.Applicative ( (<|>) )
+import Data.Char ( isAlpha, isAlphaNum )
+
+parseFasta :: FilePath -> IO ()
+parseFasta fileName = do
+  file <- readFile fileName
+  let pairs = fst . last . readP_to_S readFasta $ file
+  mapM_ (\(name, code) -> putStrLn $ name ++ ": " ++ code) pairs
+
+
+readFasta :: ReadP [(String, String)]
+readFasta = many pair <* eof
+ where
+  pair    = (,) <$> name <*> code
+  name    = char '>' *> many (satisfy isAlphaNum <|> char '_') <* newline
+  code    = concat <$> many (many (satisfy isAlpha) <* newline)
+  newline = char '\n'

Task/FASTA-format/J/fasta-format-1.j

@@ -0,0 +1,2 @@
+require 'strings'  NB. not needed for J versions greater than 6.
+parseFasta=: ((': ' ,~ LF&taketo) , (LF -.~ LF&takeafter));._1

Task/FASTA-format/J/fasta-format-2.j

@@ -0,0 +1,11 @@
+   Fafile=: noun define
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+)
+   parseFasta Fafile
+Rosetta_Example_1: THERECANBENOSPACE
+Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED

Task/FASTA-format/J/fasta-format-3.j

@@ -0,0 +1,28 @@
+bs=: 2
+chunkFasta=: {{
+  r=. EMPTY
+  bad=. a.-.a.{~;48 65 97(+i.)each 10 26 26
+  dir=. x,'/'
+  off=. 0
+  siz=. fsize y
+  block=. dest=. ''
+  while. off < siz do.
+    block=. block,fread y;off([, [ -~ siz<.+)bs
+    off=. off+bs
+    while. LF e. block do.
+      line=. LF taketo block
+      select. {.line
+        case. ';' do.
+        case. '>' do.
+          start=. }.line-.CR
+          r=.r,(head=. name,'.head');<name=. dir,start -. bad
+          start fwrite head
+          '' fwrite name
+        case. do.
+          (line-.bad) fappend name
+      end.
+      block=. LF takeafter block
+    end.
+  end.
+  r
+}}

Task/FASTA-format/J/fasta-format-4.j

@@ -0,0 +1 @@
+   fasta=: '~temp' chunkFasta '~/fasta.txt'

Task/FASTA-format/J/fasta-format-5.j

@@ -0,0 +1,3 @@
+   ;(,': ',,&LF)each/"1 fread each fasta
+Rosetta_Example_1: THERECANBENOSPACE
+Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED

Task/FASTA-format/Java/fasta-format-1.java

@@ -0,0 +1,5 @@
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;

Task/FASTA-format/Java/fasta-format-2.java

@@ -0,0 +1,44 @@
+public static void main(String[] args) throws IOException {
+    List<FASTA> fastas = readFile("fastas.txt");
+    for (FASTA fasta : fastas)
+        System.out.println(fasta);
+}
+
+static List<FASTA> readFile(String path) throws IOException {
+    try (BufferedReader reader = new BufferedReader(new FileReader(path))) {
+        List<FASTA> list = new ArrayList<>();
+        StringBuilder lines = null;
+        String newline = System.lineSeparator();
+        String line;
+        while ((line = reader.readLine()) != null) {
+            if (line.startsWith(">")) {
+                if (lines != null)
+                    list.add(parseFASTA(lines.toString()));
+                lines = new StringBuilder();
+                lines.append(line).append(newline);
+            } else {
+                lines.append(line);
+            }
+        }
+        list.add(parseFASTA(lines.toString()));
+        return list;
+    }
+}
+
+static FASTA parseFASTA(String string) {
+    String description;
+    char[] sequence;
+    int indexOf = string.indexOf(System.lineSeparator());
+    description = string.substring(1, indexOf);
+    /* using 'stripLeading' will remove any additional line-separators */
+    sequence = string.substring(indexOf + 1).stripLeading().toCharArray();
+    return new FASTA(description, sequence);
+}
+
+/* using a 'char' array seems more logical */
+record FASTA(String description, char[] sequence) {
+    @Override
+    public String toString() {
+        return "%s: %s".formatted(description, new String(sequence));
+    }
+}

Task/FASTA-format/Java/fasta-format-3.java

@@ -0,0 +1,26 @@
+import java.io.*;
+import java.util.Scanner;
+
+public class ReadFastaFile {
+
+    public static void main(String[] args) throws FileNotFoundException {
+
+        boolean first = true;
+
+        try (Scanner sc = new Scanner(new File("test.fasta"))) {
+            while (sc.hasNextLine()) {
+                String line = sc.nextLine().trim();
+                if (line.charAt(0) == '>') {
+                    if (first)
+                        first = false;
+                    else
+                        System.out.println();
+                    System.out.printf("%s: ", line.substring(1));
+                } else {
+                    System.out.print(line);
+                }
+            }
+        }
+        System.out.println();
+    }
+}

Task/FASTA-format/JavaScript/fasta-format.js

@@ -0,0 +1,28 @@
+const fs = require("fs");
+const readline = require("readline");
+
+const args = process.argv.slice(2);
+if (!args.length) {
+    console.error("must supply file name");
+    process.exit(1);
+}
+
+const fname = args[0];
+
+const readInterface = readline.createInterface({
+    input: fs.createReadStream(fname),
+    console: false,
+});
+
+let sep = "";
+readInterface.on("line", (line) => {
+    if (line.startsWith(">")) {
+        process.stdout.write(sep);
+        sep = "\n";
+        process.stdout.write(line.substring(1) + ": ");
+    } else {
+        process.stdout.write(line);
+    }
+});
+
+readInterface.on("close", () => process.stdout.write("\n"));

Task/FASTA-format/Jq/fasta-format-1.jq

@@ -0,0 +1,11 @@
+def fasta:
+  foreach (inputs, ">") as $line
+    # state: [accumulator, print ]
+    ( [null, null];
+      if $line[0:1] == ">" then [($line[1:] + ": "), .[0]]
+      else [ (.[0] + $line), false]
+      end;
+      if .[1] then .[1] else empty end )
+    ;
+
+fasta

Task/FASTA-format/Jq/fasta-format-2.jq

@@ -0,0 +1,3 @@
+$ jq -n -R -r -f FASTA_format.jq < FASTA_format.fasta
+Rosetta_Example_1: THERECANBENOSPACE
+Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED

Task/FASTA-format/Julia/fasta-format.julia

@@ -0,0 +1,7 @@
+for line in eachline("data/fasta.txt")
+    if startswith(line, '>')
+        print(STDOUT, "\n$(line[2:end]): ")
+    else
+        print(STDOUT, "$line")
+    end
+end

Task/FASTA-format/Kotlin/fasta-format.kotlin

@@ -0,0 +1,30 @@
+// version 1.1.2
+
+import java.util.Scanner
+import java.io.File
+
+fun checkNoSpaces(s: String) = ' ' !in s && '\t' !in s
+
+fun main(args: Array<String>) {
+    var first = true
+    val sc = Scanner(File("input.fasta"))
+    while (sc.hasNextLine()) {
+        val line = sc.nextLine()
+        if (line[0] == '>') {
+            if (!first) println()
+            print("${line.substring(1)}: ")
+            if (first) first = false
+        }
+        else if (first) {
+            println("Error : File does not begin with '>'")
+            break
+        }
+        else if (checkNoSpaces(line))
+            print(line)
+        else {
+            println("\nError : Sequence contains space(s)")
+            break
+        }
+    }
+    sc.close()
+}

Task/FASTA-format/Lua/fasta-format.lua

@@ -0,0 +1,24 @@
+local file = io.open("input.txt","r")
+local data = file:read("*a")
+file:close()
+
+local output = {}
+local key = nil
+
+-- iterate through lines
+for line in data:gmatch("(.-)\r?\n") do
+	if line:match("%s") then
+		error("line contained space")
+	elseif line:sub(1,1) == ">" then
+		key = line:sub(2)
+		-- if key already exists, append to the previous input
+		output[key] = output[key] or ""
+	elseif key ~= nil then
+		output[key] = output[key] .. line
+	end
+end
+
+-- print result
+for k,v in pairs(output) do
+	print(k..": "..v)
+end

Task/FASTA-format/M2000-Interpreter/fasta-format.m2000

@@ -0,0 +1,103 @@
+Module CheckIt {
+      Class FASTA_MACHINE {
+            Events "GetBuffer", "header", "DataLine", "Quit"
+      Public:
+            Module Run {
+                  Const lineFeed$=chr$(13)+chr$(10)
+                  Const WhiteSpace$=" "+chr$(9)+chrcode$(160)
+                  Def long state=1, idstate=1
+                  Def boolean Quit=False
+                  Def Buf$, waste$, Packet$
+            GetNextPacket:
+                        Call Event "Quit", &Quit
+                        If Quit then exit
+                        Call Event "GetBuffer", &Packet$
+                        Buf$+=Packet$
+                        If len(Buf$)=0 Then exit
+                        On State Goto GetStartIdentifier, GetIdentifier, GetStartData, GetData, GetStartIdentifier2
+                        exit
+            GetStartIdentifier:
+                        waste$=rightpart$(Buf$, ">")
+            GetStartIdentifier2:
+                        If len(waste$)=0 Then waste$=rightpart$(Buf$, ";") : idstate=2
+                        If len(waste$)=0 Then idstate=1 : Goto GetNextPacket ' we have to read more
+                        buf$=waste$
+                        state=2
+            GetIdentifier:
+                        If Len(Buf$)=len(lineFeed$) then {
+                              if buf$<>lineFeed$ then Goto GetNextPacket
+                              waste$=""
+                        } Else {
+                              if instr(buf$, lineFeed$)=0 then Goto GetNextPacket
+                              waste$=rightpart$(Buf$, lineFeed$)
+                          }
+                        If idstate=2 Then {
+                            idstate=1
+                            \\ it's a comment, drop it
+                            state=1
+                            Goto GetNextPacket
+                        } Else Call Event "header", filter$(leftpart$(Buf$,lineFeed$), WhiteSpace$)
+                        Buf$=waste$
+                        State=3
+            GetStartData:
+                        while left$(buf$, 2)=lineFeed$ {buf$=Mid$(buf$,3)}
+                        waste$=Leftpart$(Buf$, lineFeed$)
+                        If len(waste$)=0 Then  Goto GetNextPacket ' we have to read more
+                        waste$=Filter$(waste$,WhiteSpace$)
+                        Call Event "DataLine", leftpart$(Buf$,lineFeed$)
+                        Buf$=Rightpart$(Buf$,lineFeed$)
+                        state=4
+            GetData:
+                        while left$(buf$, 2)=lineFeed$ {buf$=Mid$(buf$,3)}
+                        waste$=Leftpart$(Buf$, lineFeed$)
+                        If len(waste$)=0 Then  Goto GetNextPacket ' we have to read more
+                        If Left$(waste$,1)=";" Then wast$="": state=5 : Goto GetStartIdentifier2
+                        If Left$(waste$,1)=">" Then state=1 : Goto GetStartIdentifier
+                        waste$=Filter$(waste$,WhiteSpace$)
+                        Call Event "DataLine", waste$
+                        Buf$=Rightpart$(Buf$,lineFeed$)
+                        Goto GetNextPacket
+            }
+      }
+      Group WithEvents K=FASTA_MACHINE()
+      Document Final$, Inp$
+
+      \\ In documents, "="" used for append data. Final$="append this"
+      Const NewLine$=chr$(13)+chr$(10)
+      Const Center=2
+      \\ Event's Functions
+      Function K_GetBuffer (New &a$) {
+            Input "IN:", a$
+            inp$=a$+NewLine$
+            while right$(a$, 1)="\" {
+                  Input "IN:", b$
+                  inp$=b$+NewLine$
+                  if b$="" then b$="n"
+                  a$+=b$
+            }
+            a$= replace$("\N","\n", a$)
+            a$= replace$("\n",NewLine$, a$)
+      }
+      Function K_header (New a$) {
+            iF Doc.Len(Final$)=0 then {
+                  Final$=a$+": "
+            } Else Final$=Newline$+a$+": "
+      }
+      Function K_DataLine (New a$) {
+            Final$=a$
+      }
+      Function K_Quit (New &q) {
+            q=keypress(1)
+      }
+      Cls , 0
+      Report Center, "FASTA Format"
+      Report "Simulate input channel in packets (\n for new line). Use empty input to exit after new line, or press left mouse button and Enter to quit. Use ; to write comments. Use > to open a title"
+      Cls, row  ' scroll from current row
+      K.Run
+      Cls
+      Report Center, "Input File"
+      Report Inp$
+      Report Center, "Output File"
+      Report Final$
+}
+checkit

Task/FASTA-format/Mathematica/fasta-format.math

@@ -0,0 +1,7 @@
+ImportString[">Rosetta_Example_1
+ THERECANBENOSPACE
+ >Rosetta_Example_2
+ THERECANBESEVERAL
+ LINESBUTTHEYALLMUST
+ BECONCATENATED
+ ", "FASTA"]

Task/FASTA-format/Nim/fasta-format.nim

@@ -0,0 +1,20 @@
+import strutils
+
+let input = """>Rosetta_Example_1
+    THERECANBENOSPACE
+    >Rosetta_Example_2
+    THERECANBESEVERAL
+    LINESBUTTHEYALLMUST
+    BECONCATENATED""".unindent
+
+proc fasta*(input: string) =
+    var row = ""
+    for line in input.splitLines:
+        if line.startsWith(">"):
+            if row != "": echo row
+            row = line[1..^1] & ": "
+        else:
+            row &= line.strip
+    echo row
+
+fasta(input)

Task/FASTA-format/OCaml/fasta-format.ocaml

@@ -0,0 +1,40 @@
+(* This program reads from the standard input and writes to standard output.
+ * Examples of use:
+ *    $ ocaml fasta.ml < fasta_file.txt
+ *    $ ocaml fasta.ml < fasta_file.txt > my_result.txt
+ *
+ * The FASTA file is assumed to have a specific format, where the first line
+ * contains a label in the form of '>blablabla', i.e. with a '>' as the first
+ * character.
+ *)
+
+let labelstart = '>'
+
+let is_label s = s.[0] = labelstart
+let get_label s = String.sub s 1 (String.length s - 1)
+
+let read_in channel = input_line channel |> String.trim
+
+let print_fasta chan =
+  let rec doloop currlabel line =
+    if is_label line then begin
+        if currlabel <> "" then print_newline ();
+        let newlabel = get_label line in
+        print_string (newlabel ^ ": ");
+        doloop newlabel (read_in chan)
+    end
+    else begin
+        print_string line;
+        doloop currlabel (read_in chan)
+    end
+  in
+  try
+    match read_in chan with
+    | line when is_label line -> doloop "" line
+    | _ -> failwith "Badly formatted FASTA file?"
+  with
+    End_of_file -> print_newline ()
+
+
+let () =
+  print_fasta stdin

Task/FASTA-format/Objeck/fasta-format.objeck

@@ -0,0 +1,25 @@
+class Fasta {
+  function : Main(args : String[]) ~ Nil {
+    if(args->Size() = 1) {
+      is_line := false;
+      tokens := System.Utility.Parser->Tokenize(System.IO.File.FileReader->ReadFile(args[0]))<String>;
+      each(i : tokens) {
+          token := tokens->Get(i);
+          if(token->Get(0) = '>') {
+            is_line := true;
+            if(i <> 0) {
+              "\n"->Print();
+            };
+          }
+          else if(is_line) {
+            "{$token}: "->Print();
+            is_line := false;
+          }
+          else {
+            token->Print();
+          };
+        };
+      };
+    };
+  }
+}

Task/FASTA-format/Pascal/fasta-format.pas

@@ -0,0 +1,39 @@
+program FASTA_Format;
+// FPC 3.0.2
+var InF,
+    OutF: Text;
+    ch: char;
+    First: Boolean=True;
+    InDef: Boolean=False;
+
+begin
+  Assign(InF,'');
+  Reset(InF);
+  Assign(OutF,'');
+  Rewrite(OutF);
+  While Not Eof(InF) do
+  begin
+    Read(InF,ch);
+    Case Ch of
+      '>': begin
+            if Not(First) then
+              Write(OutF,#13#10)
+            else
+              First:=False;
+            InDef:=true;
+          end;
+      #13: Begin
+               if InDef then
+               begin
+                 InDef:=false;
+                 Write(OutF,': ');
+               end;
+               Ch:=#0;
+             end;
+      #10: ch:=#0;
+      else Write(OutF,Ch);
+    end;
+  end;
+  Close(OutF);
+  Close(InF);
+end.

Task/FASTA-format/Perl/fasta-format.pl

@@ -0,0 +1,19 @@
+my $fasta_example = <<'END_FASTA_EXAMPLE';
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+END_FASTA_EXAMPLE
+
+my $num_newlines = 0;
+while ( < $fasta_example > ) {
+	if (/\A\>(.*)/) {
+		print "\n" x $num_newlines, $1, ': ';
+	}
+	else {
+		$num_newlines = 1;
+		print;
+	}
+}

Task/FASTA-format/Phix/fasta-format.phix

@@ -0,0 +1,25 @@
+(notonline)-->
+ <span style="color: #004080;">bool</span> <span style="color: #000000;">first</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">true</span>
+ <span style="color: #004080;">integer</span> <span style="color: #000000;">fn</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">open</span><span style="color: #0000FF;">(</span><span style="color: #008000;">"fasta.txt"</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"r"</span><span style="color: #0000FF;">)</span>
+ <span style="color: #008080;">if</span> <span style="color: #000000;">fn</span><span style="color: #0000FF;">=-</span><span style="color: #000000;">1</span> <span style="color: #008080;">then</span> <span style="color: #0000FF;">?</span><span style="color: #000000;">9</span><span style="color: #0000FF;">/</span><span style="color: #000000;">0</span> <span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
+ <span style="color: #008080;">while</span> <span style="color: #004600;">true</span> <span style="color: #008080;">do</span>
+     <span style="color: #004080;">object</span> <span style="color: #000000;">line</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">trim</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">gets</span><span style="color: #0000FF;">(</span><span style="color: #000000;">fn</span><span style="color: #0000FF;">))</span>
+     <span style="color: #008080;">if</span> <span style="color: #004080;">atom</span><span style="color: #0000FF;">(</span><span style="color: #000000;">line</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span> <span style="color: #7060A8;">puts</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"\n"</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">exit</span> <span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
+     <span style="color: #008080;">if</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">line</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span>
+         <span style="color: #008080;">if</span> <span style="color: #000000;">line</span><span style="color: #0000FF;">[</span><span style="color: #000000;">1</span><span style="color: #0000FF;">]==</span><span style="color: #008000;">'&gt;'</span> <span style="color: #008080;">then</span>
+             <span style="color: #008080;">if</span> <span style="color: #008080;">not</span> <span style="color: #000000;">first</span> <span style="color: #008080;">then</span> <span style="color: #7060A8;">puts</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"\n"</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
+             <span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"%s: "</span><span style="color: #0000FF;">,{</span><span style="color: #000000;">line</span><span style="color: #0000FF;">[</span><span style="color: #000000;">2</span><span style="color: #0000FF;">..$]})</span>
+             <span style="color: #000000;">first</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">false</span>
+         <span style="color: #008080;">elsif</span> <span style="color: #000000;">first</span> <span style="color: #008080;">then</span>
+             <span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"Error : File does not begin with '&gt;'\n"</span><span style="color: #0000FF;">)</span>
+             <span style="color: #008080;">exit</span>
+         <span style="color: #008080;">elsif</span> <span style="color: #008080;">not</span> <span style="color: #7060A8;">find_any</span><span style="color: #0000FF;">(</span><span style="color: #008000;">" \t"</span><span style="color: #0000FF;">,</span><span style="color: #000000;">line</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">then</span>
+             <span style="color: #7060A8;">puts</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #000000;">line</span><span style="color: #0000FF;">)</span>
+         <span style="color: #008080;">else</span>
+             <span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"\nError : Sequence contains space(s)\n"</span><span style="color: #0000FF;">)</span>
+             <span style="color: #008080;">exit</span>
+         <span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
+     <span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
+ <span style="color: #008080;">end</span> <span style="color: #008080;">while</span>
+ <span style="color: #7060A8;">close</span><span style="color: #0000FF;">(</span><span style="color: #000000;">fn</span><span style="color: #0000FF;">)</span>
+<!--

Task/FASTA-format/PicoLisp/fasta-format.l

@@ -0,0 +1,8 @@
+(de fasta (F)
+   (in F
+      (while (from ">")
+         (prin (line T) ": ")
+         (until (or (= ">" (peek)) (eof))
+            (prin (line T)) )
+         (prinl) ) ) )
+(fasta "fasta.dat")

Task/FASTA-format/PowerShell/fasta-format-1.psh

@@ -0,0 +1,21 @@
+$file = @'
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+'@
+
+$lines = $file.Replace("`n","~").Split(">").ForEach({$_.TrimEnd("~").Split("`n",2,[StringSplitOptions]::RemoveEmptyEntries)})
+
+$output = New-Object -TypeName PSObject
+
+foreach ($line in $lines)
+{
+    $name, $value = $line.Split("~",2).ForEach({$_.Replace("~","")})
+
+    $output | Add-Member -MemberType NoteProperty -Name $name -Value $value
+}
+
+$output | Format-List

Task/FASTA-format/PowerShell/fasta-format-2.psh

@@ -0,0 +1,21 @@
+$file = @'
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+'@
+
+$lines = $file.Replace("`n","~").Split(">") | ForEach-Object {$_.TrimEnd("~").Split("`n",2,[StringSplitOptions]::RemoveEmptyEntries)}
+
+$output = New-Object -TypeName PSObject
+
+foreach ($line in $lines)
+{
+    $name, $value = $line.Split("~",2) | ForEach-Object {$_.Replace("~","")}
+
+    $output | Add-Member -MemberType NoteProperty -Name $name -Value $value
+}
+
+$output | Format-List

Task/FASTA-format/PureBasic/fasta-format.basic

@@ -0,0 +1,29 @@
+EnableExplicit
+Define Hdl_File.i,
+       Frm_File.i,
+       c.c,
+       header.b
+
+Hdl_File=ReadFile(#PB_Any,"c:\code_pb\rosettacode\data\FASTA_TEST.txt")
+If Not IsFile(Hdl_File) : End -1 : EndIf
+Frm_File=ReadStringFormat(Hdl_File)
+
+If OpenConsole("FASTA format")
+  While Not Eof(Hdl_File)
+    c=ReadCharacter(Hdl_File,Frm_File)
+    Select c
+      Case '>'
+        header=#True
+        PrintN("")
+      Case #LF, #CR
+        If header
+          Print(": ")
+          header=#False
+        EndIf
+      Default
+        Print(Chr(c))
+    EndSelect
+  Wend
+  CloseFile(Hdl_File)
+  Input()
+EndIf

Task/FASTA-format/Python/fasta-format.py

@@ -0,0 +1,25 @@
+import io
+
+FASTA='''\
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED'''
+
+infile = io.StringIO(FASTA)
+
+def fasta_parse(infile):
+    key = ''
+    for line in infile:
+        if line.startswith('>'):
+            if key:
+                yield key, val
+            key, val = line[1:].rstrip().split()[0], ''
+        elif key:
+            val += line.rstrip()
+    if key:
+        yield key, val
+
+print('\n'.join('%s: %s' % keyval for keyval in fasta_parse(infile)))

Task/FASTA-format/QBasic/fasta-format.basic

@@ -0,0 +1,30 @@
+FUNCTION checkNoSpaces (s$)
+    FOR i = 1 TO LEN(s$) - 1
+        IF MID$(s$, i, 1) = CHR$(32) OR MID$(s$, i, 1) = CHR$(9) THEN checkNoSpaces = 0
+    NEXT i
+    checkNoSpaces = 1
+END FUNCTION
+
+OPEN "input.fasta" FOR INPUT AS #1
+
+first = 1
+
+DO WHILE NOT EOF(1)
+    LINE INPUT #1, ln$
+    IF LEFT$(ln$, 1) = ">" THEN
+        IF NOT first THEN PRINT
+        PRINT MID$(ln$, 2); ": ";
+        IF first THEN first = 0
+    ELSEIF first THEN
+        PRINT : PRINT "Error : File does not begin with '>'"
+        EXIT DO
+    ELSE
+        IF checkNoSpaces(ln$) THEN
+            PRINT ln$;
+        ELSE
+            PRINT : PRINT "Error : Sequence contains space(s)"
+            EXIT DO
+        END IF
+    END IF
+LOOP
+CLOSE #1

Task/FASTA-format/R/fasta-format.r

@@ -0,0 +1,12 @@
+library("seqinr")
+
+data <- c(">Rosetta_Example_1","THERECANBENOSPACE",">Rosetta_Example_2","THERECANBESEVERAL","LINESBUTTHEYALLMUST","BECONCATENATED")
+fname <- "rosettacode.fasta"
+f <- file(fname,"w+")
+writeLines(data,f)
+close(f)
+
+fasta <- read.fasta(file = fname, as.string = TRUE, seqtype = "AA")
+for (aline in fasta) {
+  cat(attr(aline, 'Annot'), ":", aline, "\n")
+}

Task/FASTA-format/REXX/fasta-format-1.rexx

@@ -0,0 +1,16 @@
+/*REXX program reads a (bio-informational)  FASTA  file  and  displays the contents.    */
+parse arg iFID .                                 /*iFID:  the input file to be read.    */
+if iFID==''  then iFID='FASTA.IN'                /*Not specified?  Then use the default.*/
+name=                                            /*the name of an output file (so far). */
+$=                                               /*the value of the output file's stuff.*/
+     do  while  lines(iFID)\==0                  /*process the  FASTA  file contents.   */
+     x=strip( linein(iFID), 'T')                 /*read a line (a record) from the file,*/
+                                                 /*───────── and strip trailing blanks. */
+     if left(x, 1)=='>'  then do
+                              if $\==''  then say name':'  $
+                              name=substr(x,  2)
+                              $=
+                              end
+                         else $=$ || x
+     end   /*j*/                                 /* [↓]  show output of last file used. */
+if $\==''  then say name':'  $                   /*stick a fork in it,  we're all done. */

Task/FASTA-format/REXX/fasta-format-2.rexx

@@ -0,0 +1,22 @@
+/*REXX program reads a  (bio-informational)  FASTA  file  and  displays the contents.   */
+parse arg iFID .                                 /*iFID:  the input file to be read.    */
+if iFID==''  then iFID='FASTA2.IN'               /*Not specified?  Then use the default.*/
+name=                                            /*the name of an output file (so far). */
+$=                                               /*the value of the output file's stuff.*/
+     do  while  lines(iFID)\==0                  /*process the  FASTA  file contents.   */
+     x=strip( linein(iFID), 'T')                 /*read a line (a record) from the file,*/
+                                                 /*───────── and strip trailing blanks. */
+     if x==''  then iterate                      /*If the line is all blank, ignore it. */
+     if left(x, 1)==';'  then do
+                              if name=='' then name=substr(x,2)
+                              say x
+                              iterate
+                              end
+     if left(x, 1)=='>'  then do
+                              if $\==''  then say name':'  $
+                              name=substr(x, 2)
+                              $=
+                              end
+                         else $=space($ || translate(x, , '*'),  0)
+     end   /*j*/                                 /* [↓]  show output of last file used. */
+if $\==''  then say name':'  $                   /*stick a fork in it,  we're all done. */

Task/FASTA-format/Racket/fasta-format.rkt

@@ -0,0 +1,9 @@
+#lang racket
+(let loop ([m #t])
+  (when m
+    (when (regexp-try-match #rx"^>" (current-input-port))
+      (unless (eq? #t m) (newline))
+      (printf "~a: " (read-line)))
+    (loop (regexp-match #rx"\n" (current-input-port) 0 #f
+                        (current-output-port)))))
+(newline)

Task/FASTA-format/Raku/fasta-format.raku

@@ -0,0 +1,21 @@
+grammar FASTA {
+
+    rule TOP    { <entry>+ }
+    rule entry  { \> <title> <sequence> }
+    token title { <.alnum>+ }
+    token sequence { ( <.alnum>+ )+ % \n { make $0.join } }
+
+}
+
+FASTA.parse: q:to /§/;
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+§
+
+for $/<entry>[] {
+    say ~.<title>, " : ", .<sequence>.made;
+}

Task/FASTA-format/Ring/fasta-format.ring

@@ -0,0 +1,22 @@
+# Project : FAST format
+
+a = ">Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED"
+
+i = 1
+while i <= len(a)
+      if substr(a,i,17) = ">Rosetta_Example_"
+         see nl
+         see substr(a,i,18) + ": " + nl
+         i = i + 17
+      else
+         if ascii(substr(a,i,1)) > 20
+            see a[i]
+         ok
+      ok
+      i = i + 1
+end

Task/FASTA-format/Ruby/fasta-format.rb

@@ -0,0 +1,23 @@
+def fasta_format(strings)
+  out, text = [], ""
+  strings.split("\n").each do |line|
+    if line[0] == '>'
+      out << text unless text.empty?
+      text = line[1..-1] + ": "
+    else
+      text << line
+    end
+  end
+  out << text unless text.empty?
+end
+
+data = <<'EOS'
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED
+EOS
+
+puts fasta_format(data)

Task/FASTA-format/Run-BASIC/fasta-format.basic

@@ -0,0 +1,18 @@
+a$ = ">Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED"
+
+i = 1
+while i <= len(a$)
+  if mid$(a$,i,17) = ">Rosetta_Example_" then
+    print
+    print mid$(a$,i,18);": ";
+    i = i + 17
+   else
+    if asc(mid$(a$,i,1)) > 20 then print mid$(a$,i,1);
+  end if
+  i = i + 1
+wend

Task/FASTA-format/Rust/fasta-format.rust

@@ -0,0 +1,63 @@
+use std::env;
+use std::io::{BufReader, Lines};
+use std::io::prelude::*;
+use std::fs::File;
+
+fn main() {
+    let args: Vec<String> = env::args().collect();
+    let f = File::open(&args[1]).unwrap();
+    for line in FastaIter::new(f) {
+        println!("{}", line);
+    }
+}
+
+struct FastaIter<T> {
+    buffer_lines: Lines<BufReader<T>>,
+    current_name: Option<String>,
+    current_sequence: String
+}
+
+impl<T: Read> FastaIter<T> {
+    fn new(file: T) -> FastaIter<T> {
+        FastaIter { buffer_lines: BufReader::new(file).lines(),
+                    current_name: None,
+                    current_sequence: String::new() }
+    }
+}
+
+impl<T: Read> Iterator for FastaIter<T> {
+    type Item = String;
+
+    fn next(&mut self) -> Option<String> {
+        while let Some(l) = self.buffer_lines.next() {
+            let line = l.unwrap();
+            if line.starts_with(">") {
+                if self.current_name.is_some() {
+                    let mut res = String::new();
+                    res.push_str(self.current_name.as_ref().unwrap());
+                    res.push_str(": ");
+                    res.push_str(&self.current_sequence);
+                    self.current_name = Some(String::from(&line[1..]));
+                    self.current_sequence.clear();
+                    return Some(res);
+                } else {
+                    self.current_name = Some(String::from(&line[1..]));
+                    self.current_sequence.clear();
+                }
+                continue;
+            }
+            self.current_sequence.push_str(line.trim());
+        }
+        if self.current_name.is_some() {
+            let mut res = String::new();
+            res.push_str(self.current_name.as_ref().unwrap());
+            res.push_str(": ");
+            res.push_str(&self.current_sequence);
+            self.current_name = None;
+            self.current_sequence.clear();
+            self.current_sequence.shrink_to_fit();
+            return Some(res);
+        }
+        None
+    }
+}

Task/FASTA-format/Scala/fasta-format.scala

@@ -0,0 +1,19 @@
+import java.io.File
+import java.util.Scanner
+
+object ReadFastaFile extends App {
+  val sc = new Scanner(new File("test.fasta"))
+  var first = true
+
+  while (sc.hasNextLine) {
+    val line = sc.nextLine.trim
+    if (line.charAt(0) == '>') {
+      if (first) first = false
+      else println()
+      printf("%s: ", line.substring(1))
+    }
+    else print(line)
+  }
+
+  println("~~~+~~~")
+}

Task/FASTA-format/Scheme/fasta-format.ss

@@ -0,0 +1,16 @@
+(import (scheme base)
+        (scheme file)
+        (scheme write))
+
+(with-input-from-file ; reads text from named file, one line at a time
+  "fasta.txt"
+  (lambda ()
+    (do ((first-line? #t #f)
+         (line (read-line) (read-line)))
+      ((eof-object? line) (newline))
+      (cond ((char=? #\> (string-ref line 0)) ; found a name
+             (unless first-line? ; no newline on first name
+               (newline))
+             (display (string-copy line 1)) (display ": "))
+            (else ; display the string directly
+              (display line))))))

Task/FASTA-format/Seed7/fasta-format.seed7

@@ -0,0 +1,27 @@
+$ include "seed7_05.s7i";
+
+const proc: main is func
+  local
+    var file: fastaFile is STD_NULL;
+    var string: line is "";
+    var boolean: first is TRUE;
+  begin
+    fastaFile := open("fasta_format.in", "r");
+    if fastaFile <> STD_NULL then
+      while hasNext(fastaFile) do
+        line := getln(fastaFile);
+        if startsWith(line, ">") then
+          if first then
+            first := FALSE;
+          else
+            writeln;
+          end if;
+          write(line[2 ..] <& ": ");
+        else
+          write(line);
+        end if;
+      end while;
+      close(fastaFile);
+    end if;
+    writeln;
+  end func;

Task/FASTA-format/Sidef/fasta-format.sidef

@@ -0,0 +1,25 @@
+func fasta_format(strings) {
+    var out = []
+    var text = ''
+    for line in (strings.lines) {
+        if (line.begins_with('>')) {
+            text.len && (out << text)
+            text = line.substr(1)+': '
+        }
+        else {
+            text += line
+        }
+    }
+    text.len && (out << text)
+    return out
+}
+
+fasta_format(DATA.slurp).each { .say }
+
+__DATA__
+>Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED

Task/FASTA-format/TMG/fasta-format.tmg

@@ -0,0 +1,14 @@
+prog:   ignore(spaces)
+loop:   parse(line)\loop parse(( = {*} ));
+line:   ( name | * = {} | seqns );
+name:   <>> ignore(none) smark string(nonl) scopy *
+        ( [f>0?] = {} | = {*} ) [f=0]
+        = { 1 2 <: > };
+seqns:  smark string(nonl) scopy * [f=0];
+
+none:   <<>>;
+nonl:   !<<
+>>;
+spaces:	<< 	>>;
+
+f:      1;

Task/FASTA-format/Tcl/fasta-format.tcl

@@ -0,0 +1,16 @@
+proc fastaReader {filename} {
+    set f [open $filename]
+    set sep ""
+    while {[gets $f line] >= 0} {
+	if {[string match >* $line]} {
+	    puts -nonewline "$sep[string range $line 1 end]: "
+	    set sep "\n"
+	} else {
+	    puts -nonewline $line
+	}
+    }
+    puts ""
+    close $f
+}
+
+fastaReader ./rosettacode.fas

Task/FASTA-format/True-BASIC/fasta-format.basic

@@ -0,0 +1,34 @@
+DEF EOF(f)
+    IF END #f THEN LET EOF = -1 ELSE LET EOF = 0
+END DEF
+
+FUNCTION checknospaces(s$)
+    FOR i = 1 TO LEN(s$)-1
+        IF (s$)[i:1] = CHR$(32) OR (s$)[i:1] = CHR$(9) THEN LET checkNoSpaces = 0
+    NEXT i
+    LET checknospaces = 1
+END FUNCTION
+
+OPEN #1: NAME "m:\input.fasta", org text, ACCESS INPUT, create old
+
+LET first = 1
+DO WHILE (NOT EOF(1)<>0)
+   LINE INPUT #1: ln$
+   IF (ln$)[1:1] = ">" THEN
+      IF (NOT first<>0) THEN PRINT
+      PRINT (ln$)[2:maxnum]; ": ";
+      IF first<>0 THEN LET first = 0
+   ELSEIF first<>0 THEN
+      PRINT "Error : File does not begin with '>'"
+      EXIT DO
+   ELSE
+      IF checknospaces(ln$)<>0 THEN
+         PRINT ln$;
+      ELSE
+         PRINT "Error : Sequence contains space(s)"
+         EXIT DO
+      END IF
+   END IF
+LOOP
+CLOSE #1
+END

Task/FASTA-format/V-(Vlang)/fasta-format.v

@@ -0,0 +1,22 @@
+const data = (
+">Rosetta_Example_1
+THERECANBENOSPACE
+>Rosetta_Example_2
+THERECANBESEVERAL
+LINESBUTTHEYALLMUST
+BECONCATENATED"
+)
+
+fn main() {
+	mut i := 0
+	for i <= data.len {
+		if data.substr_ni(i, i + 17) == ">Rosetta_Example_" {
+			print("\n" + data.substr_ni(i, i + 18) + ": ")
+			i = i + 17
+		}
+		else {
+			if data.substr_ni(i, i + 1) > "\x20" {print(data[i].ascii_str())}
+		}
+		i++
+	}
+}

Task/FASTA-format/Wren/fasta-format.wren

@@ -0,0 +1,40 @@
+import "io" for File
+
+var checkNoSpaces = Fn.new { |s| !s.contains(" ") && !s.contains("\t") }
+
+var first = true
+
+var process = Fn.new { |line|
+    if (line[0] == ">") {
+        if (!first) System.print()
+        System.write("%(line[1..-1]): ")
+        if (first) first = false
+    } else if (first) {
+        Fiber.abort("File does not begin with '>'.")
+    } else if (checkNoSpaces.call(line)) {
+        System.write(line)
+    } else {
+        Fiber.abort("Sequence contains space(s).")
+    }
+}
+
+var fileName = "input.fasta"
+File.open(fileName) { |file|
+    var offset = 0
+    var line = ""
+    while(true) {
+        var b = file.readBytes(1, offset)
+        offset = offset + 1
+        if (b == "\n") {
+            process.call(line)
+            line = "" // reset line variable
+        } else if (b == "\r") { // Windows
+            // wait for following "\n"
+        } else if (b == "") { // end of stream
+            System.print()
+            return
+        } else {
+            line = line + b
+        }
+    }
+}

Task/FASTA-format/XPL0/fasta-format.xpl0

@@ -0,0 +1,23 @@
+proc Echo;      \Echo line of characters from file to screen
+int Ch;
+def LF=$0A, EOF=$1A;
+[loop   [Ch:= ChIn(3);
+        case Ch of
+          EOF:  exit;
+          LF:   quit
+        other ChOut(0, Ch);
+        ];
+];
+
+int Ch;
+[FSet(FOpen("fasta.txt", 0), ^i);
+loop    [Ch:= ChIn(3);
+        if Ch = ^> then
+                [CrLf(0);
+                Echo;
+                Text(0, ": ");
+                ]
+        else    ChOut(0, Ch);
+        Echo;
+        ];
+]

Task/FASTA-format/Zkl/fasta-format-1.zkl

@@ -0,0 +1,8 @@
+fcn fasta(data){ // a lazy cruise through a FASTA file
+   fcn(w){      // one string at a time, -->False garbage at front of file
+      line:=w.next().strip();
+      if(line[0]==">") w.pump(line[1,*]+": ",'wrap(l){
+         if(l[0]==">") { w.push(l); Void.Stop } else l.strip()
+      })
+   }.fp(data.walker()) : Utils.Helpers.wap(_);
+}

Task/FASTA-format/Zkl/fasta-format-2.zkl

@@ -0,0 +1 @@
+foreach l in (fasta(File("fasta.txt"))) { println(l) }

Task/FASTA-format/Zkl/fasta-format-3.zkl

@@ -0,0 +1,5 @@
+data:=Data(0,String,
+   ">Rosetta_Example_1\nTHERECANBENOSPACE\n"
+   ">Rosetta_Example_2\nTHERECANBESEVERAL\nLINESBUTTHEYALLMUST\n"
+     "BECONCATENATED");
+foreach l in (fasta(data)) { println(l) }