# Purpose: Several file conversion routines (used for multiple alignments)
# Author:  Chantal Korostensky (5.1.95)
# Modif:   AR (April 2007)
# Info:   The executable files must be either in /home/rutishauser/oed4/darwin.hpux/bin/
#         (turings) or /a/rutishauser/export/project/oed/oed4/darwin/bin (mendel)

# Purpose: Convert an array of sequences to fasta format
WriteFasta := proc( seqs:list(string); labs:list(string), 
                    filename='temp.fasta':string )
  ne := length(seqs);
  if assigned(labs) and ne <> length(labs) then 
    error ('Sequence and label array lengths differ') fi;
  if not assigned(labs) then labs:=seq(i,i=1..ne) fi;
  OpenWriting(filename);
  for i to ne do
    printf('>%s\n%s\n',labs[i],seqs[i]);
  od; 
  OpenWriting(previous);
  NULL;
end:
  
# Purpose: Reads a map sequence file, returns an array of sequences
ReadMap:=proc()
  global order, temp;

  if nargs>0 then Filename:=args[1] else Filename:='/tmp/seq' fi;
  code:=CallSystem('maptodar '.Filename.'.map '.Filename.'.map.dar');
  if code<>0 then printf('ReadMap: returncode %d',code);fi;
  ReadProgram(Filename.'.map.dar');
  temp:=OrderArray(temp,order); 
  DashtoDel(temp);
  temp;
end:

ReadMsaFasta := proc(fname: string);
  refs := copy([]);
  seqs := copy([]);
  OpenPipe ('cat ' .  fname);
  do
    t := ReadLine ();
    if t = EOF then break; fi;
    print(t);
    if t <> '' then
      if t[1] = '>' then refs := append (refs,t[3..-2]);
      else seqs := append (seqs,t);
      fi;
    fi;
 od;
 msa := MultiAlign(seqs, refs);
 return(msa);
end:

# Purpose: Read a fasta sequence file, returns an array of sequences
ReadFasta:=proc(fn:string) 
    ReadFastaWithNames(fn) 
end:

# Purpose: Read a pir (clustalw) sequence file, returns an array of sequences
ReadPir:=proc()
  global  temp;

  if nargs>0 then Filename:=args[1] else Filename:='/tmp/seq' fi;
  code:=CallSystem('pirtodar '.Filename.'.pir '.Filename.'.pir.dar');
  if code<>0 then printf('ReadPir: returncode %d',code);fi;
  ReadProgram(Filename.'.pir.dar');
  DashtoDel(temp);
  print(temp);
  temp;
end:

ReadMsa:=proc(n: posint)
global temp;

 if nargs>1 then Filename:=args[2] else Filename:='/tmp/seq' fi;
 code:=CallSystem('msatodar '.Filename.'.msa '.Filename.'.msa.dar');
 if code<>0 then printf('ReadMsa: returncode %d',code);fi;
 ReadProgram(Filename.'.msa.dar');
 if length(temp)<n then return(0);fi;
 tmp:=temp[1..n];
 for i to length(temp)/n-1 do
    for j to n do tmp[j]:=tmp[j].temp[j+i*n]; od;
 od;
 DashtoDel(tmp);
 tmp;
end:

# Purpose: Read a .pima sequence file, returns an array of sequences
ReadPima:=proc(n: posint)
global order, temp;

 if nargs>1 then Filename:=args[2] else Filename:='/tmp/seq' fi;
 code:=CallSystem('pimatodar '.Filename.'-ML.pima '.Filename.'.pima.dar');
 if code<>0 then printf('ReadPima: returncode %d',code);fi;
 ReadProgram(Filename.'.pima.dar');
 temp:=OrderArray(temp,order); 
 DashtoDel(temp);
 temp;
end:

DashtoDel := proc(Seq: array(string));
 for i to length(Seq) do for j to length(Seq[i]) do
   if Seq[i, j] = '-' or Seq[i, j] = ' ' then Seq[i, j] := '_' fi;
 od od;
end: