⚠️ Warning: This is a draft ⚠️
This means it might contain formatting issues, incorrect code, conceptual problems, or other severe issues.
If you want to help to improve and eventually enable this page, please fork RosettaGit's repository and open a merge request on GitHub.
{{task}}
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 > (greater than) character at the beginning of the line.
;Task: Write a program that reads a FASTA file such as:
>Rosetta_Example_1
THERECANBENOSPACE
>Rosetta_Example_2
THERECANBESEVERAL
LINESBUTTHEYALLMUST
BECONCATENATED
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
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.
Ada
The simple solution just reads the file (from standard input) line by line and directly writes it to the standard output.
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;
{{out}}
./simple_fasta < test.txt
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
This is a boringly simple text transformation.
The following more complex solution reads the entire file into a map and then prints the data stored in the map. The output is exactly the same. as for the simple text transformation. ''"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."'' When processing FASTA files, one may use the input step by step to uptdate an internal data structure and, at the end, to output the answer to a given question. For the task at hand the required output is about the same as the input, thus we store the entire input. For another task, we would not store the entire file. If the task where, e.g., to count the number of characters for each string, we would store (name, number) pairs in our data structure.
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;
Aime
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);
{{Out}}
>Rosetta_Example_1: THERECANBENOSPACE
>Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
ALGOL W
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.
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
AutoHotkey
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
{{out}}
>Rosetta_Example_1: THERECANBENOSPACE
>Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
AWK
# 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
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
C
#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);
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
C++
#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;
}
{{out}}
Rosetta_Example_1 : THERECANBENOSPACE
Rosetta_Example_2 : THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
C#
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();
}
}
Clojure
(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)))))
Common Lisp
(defun fasta (pathname)
(with-open-file (s pathname)
(loop for line = (read-line s nil)
while line
do (if (char= #\> (char line 0))
(format t "~&~A: " (subseq line 1))
(princ line))
finally (fresh-line))))
D
import std.stdio, std.string;
void main() {
immutable fileName = "fasta_format_data.fasta";
bool first = true;
foreach (const line; fileName.File.byLine) {
if (line[0] == '>') {
if (first) {
first = false;
} else {
writeln;
}
write(line[1 .. $].strip, ": ");
} else {
line.strip.write;
}
}
writeln;
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
FreeBASIC
This program sticks to the task as described in the heading and doesn't allow for any of the (apparently) obsolete practices described in the Wikipedia article :
' 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
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Gambas
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
Output:
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Go
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)
}
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Haskell
We pass the file path as an argument to the parseFasta function, which only does the file loading and result printing.
'''The first way'''
We parse FASTA by hand (generally not a recommended approach). We use the fact that groupBy walks the list from the head and groups the items by a predicate; here we first concatenate all the fasta strings and then pair those with each respective name.
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
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
'''The second way'''
We parse FASTA using parser combinators. Normally you'd use something like Trifecta or Parsec, but here we use ReadP, because it is simple and also included in ghc by default. With other parsing libraries the code would be almost the same.
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'
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
J
Needs chunking to handle huge files.
require 'strings' NB. not needed for J versions greater than 6.
parseFasta=: ((': ' ,~ LF&taketo) , (LF -.~ LF&takeafter));._1
'''Example Usage'''
Fafile=: noun define
>Rosetta_Example_1
THERECANBENOSPACE
>Rosetta_Example_2
THERECANBESEVERAL
LINESBUTTHEYALLMUST
BECONCATENATED
)
parseFasta Fafile
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Java
{{trans|D}} {{works with|Java|7}}
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();
}
}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Rosetta_Example_3: THISISFASTA
jq
{{works with|jq|1.5rc1}} The following implementation uses "foreach" and "inputs" so that very large input files can be processed with minimal space requirements: in each cycle, only as many lines are read as are required to compose an output line.
Notice that an additional ">" must be provided to "foreach" to ensure the final block of lines of the input file are properly assembled.
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
{{out}}
$ jq -n -R -r -f FASTA_format.jq < FASTA_format.fasta
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Julia
{{works with|Julia|0.6}}
for line in eachline("data/fasta.txt")
if startswith(line, '>')
print(STDOUT, "\n$(line[2:end]): ")
else
print(STDOUT, "$line")
end
end
Kotlin
{{trans|FreeBASIC}}
// 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()
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Lua
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
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
OCaml
I keep it simple by sticking to the description of the FASTA format described in the task.
The program reads and processes the input one line at a time, and directly prints out the chunk of data available. The long strings are not concatenated in memory but just examined and processed as necessary: either printed out as is in the case of part of a sequence, or formatted in the case of the name (what I call the label), and managing the new lines where needed. {{works with|OCaml|4.03+}}
(* 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
{{out}} Rosetta_Example_1: THERECANBENOSPACE Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
M2000 Interpreter
Spaghetti code, using Goto, but works using partially reading of an input stream, with no known size of each reading (supposed data transmitted). We make an object as a FASTA_MACHINE, and run it. Object produce events, so we have some functions for services. These functions called as subs, but we have to use New if we want to shadow any same named variable. (subs always include the New (a Read New) so we didn't use there). If there no modules variables with same names as for arguments for these functions then we can exclude New. All these functions have same scope as the module where they belong.
We can use ";" for comments, ">" for title. We can input one char, or many, in each input packet. Linefeed by default is CRLF. Whitespaces are spaces, nbsp, and tabs.
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
Mathematica
Mathematica has built-in support for FASTA files and strings
ImportString[">Rosetta_Example_1
THERECANBENOSPACE
>Rosetta_Example_2
THERECANBESEVERAL
LINESBUTTHEYALLMUST
BECONCATENATED
", "FASTA"]
{{out}}
{"THERECANBENOSPACE", "THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED"}
Nim
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)
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Pascal
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.
FASTA_Format < test.fst
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Perl
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;
}
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Perl 6
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 $/<entry>[] {
say ~.<title>, " : ", .<sequence>.made;
}
{{out}}
Rosetta_Example_1 : THERECANBENOSPACE
Rosetta_Example_2 : THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Phix
bool first = true
integer fn = open("fasta.txt","r")
if fn=-1 then ?9/0 end if
while true do
object line = trim(gets(fn))
if atom(line) then puts(1,"\n") exit end if
if length(line) then
if line[1]=='>' then
if not first then puts(1,"\n") end if
printf(1,"%s: ",{line[2..$]})
first = false
elsif first then
printf(1,"Error : File does not begin with '>'\n")
exit
elsif not find_any(" \t",line) then
puts(1,line)
else
printf(1,"\nError : Sequence contains space(s)\n")
exit
end if
end if
end while
close(fn)
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
PicoLisp
(de fasta (F)
(in F
(while (from ">")
(prin (line T) ": ")
(until (or (= ">" (peek)) (eof))
(prin (line T)) )
(prinl) ) ) )
(fasta "fasta.dat")
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
PowerShell
When working with a real file, the content of the $file variable would be: Get-Content -Path .\FASTA_file.txt -ReadCount 1000. The -ReadCount parameter value for large files is unknown, yet sure to be a value between 1,000 and 10,000 depending upon the length of file and length of the records in the file. Experimentation is the only way to know the optimum value.
{{works with|PowerShell|4.0+}}
$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
{{Out}}
Rosetta_Example_1 : THERECANBENOSPACE
Rosetta_Example_2 : THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Version 3.0 Or Less
$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
{{Out}}
Rosetta_Example_1 : THERECANBENOSPACE
Rosetta_Example_2 : THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
PureBasic
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
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Python
I use a string to mimic an input file. If it was an input file, then the file is read line-by-line and I use a generator expression yielding key, value pairs as soon as they are read, keeping the minimum in memory.
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)))
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
R
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")
}
{{out}}
>Rosetta_Example_1 : THERECANBENOSPACE
>Rosetta_Example_2 : THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Racket
#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)
REXX
Neither REXX version reads the entire file into memory at one time; lines are processed as they are read (one line at a time).
version 1
This REXX version correctly processes the examples shown.
/*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. */
{{out|output|text= when using the default input filename:}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
version 2
This REXX version handles (see the ''talk'' page): ::* blank lines ::* sequences that end in an asterisk [''''''] :: sequences that contain blanks, tabs, and other whitespace ::* sequence names that are identified with a semicolon [''';''']
/*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. */
'''input:''' The '''FASTA2.IN''' file is shown below:
```txt
;LCBO - Prolactin precursor - Bovine
; a sample sequence in FASTA format
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
DIDGDGQVNYEEFVQMMTAK*
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
{{out|output|text= when using the default input filename:}}
;LCBO - Prolactin precursor - Bovine
; a sample sequence in FASTA format
LCBO - Prolactin precursor - Bovine: MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSSEMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHLVTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDEDARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC
MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken: ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]: LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY
Ring
# 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
Output:
>Rosetta_Example_1: THERECANBENOSPACE
>Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Ruby
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)
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Run BASIC
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
{{out}}
>Rosetta_Example_1: THERECANBENOSPACE
>Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Rust
This example is implemented using an [https://doc.rust-lang.org/book/iterators.html iterator] to reduce memory requirements and encourage code reuse.
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
}
}
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Scala
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("~~~+~~~")
}
Scheme
(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))))))
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Seed7
$ 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;
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Sidef
{{trans|Ruby}}
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
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
Tcl
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
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED
zkl
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(_);
}
*This assumes that white space at front or end of string is extraneous (excepting ">" lines). *Lazy, works for objects that support iterating over lines (ie most). *The fasta function returns an iterator that wraps a function taking an iterator. Uh, yeah. An initial iterator (Walker) is used to get lines, hold state and do push back when read the start of the next string. The function sucks up one string (using the iterator). The wrapping iterator (wap) traps the exception when the function waltzes off the end of the data and provides API for foreach (etc). FASTA file:
foreach l in (fasta(File("fasta.txt"))) { println(l) }
FASTA data blob:
data:=Data(0,String,
">Rosetta_Example_1\nTHERECANBENOSPACE\n"
">Rosetta_Example_2\nTHERECANBESEVERAL\nLINESBUTTHEYALLMUST\n"
"BECONCATENATED");
foreach l in (fasta(data)) { println(l) }
{{out}}
Rosetta_Example_1: THERECANBENOSPACE
Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED