//$MENU window=main;popup=file;insertafter=delete experiment file;name=Import sequence file(s)
//$BUTTON window=main;hint=Import sequence file(s) in EMBL, GenBank or FASTA format;position=1

string filenamelist,filename,fileformat;
string experlist,expername,fieldlist,line,st,seqstring;
string key,report;
DIALOG dlg,dlg2;
integer x,ok,i,j,x0,y0,xmax,ymax,ct,seqstarted,seqended,basesstarted;
integer tagcount,keytag,currenttag;
string tags[],taginfo[],tagfield[],tagcontent[];
string str_tagnr[];
integer tagnr[];
FILE fp;
SEQUENCE cs;

if not(FilePromptName("Select the sequence file(s) you want to import",filenamelist,1)) then stop;

//Prompt for file type & experiment name
fileformat="EMBL";
for i=1 to DbGetExperCount do if DbGetExperClass(i)="SEQ" then 
   experlist=experlist+DbGetExperName(i)+"	";
expername=experlist;expername=splitstring(expername,"	");
DlgAddFrame(dlg,"File format",190,20,110,95);
DlgAddList(dlg,"EMBL	GenBank	FASTA",fileformat,210,40,70,70,"LIST");
DlgAddFrame(dlg,"Experiment",20,20,150,190);
DlgAddList(dlg,experlist,expername,40,40,110,170,"LIST");
x=DlgShow(dlg,"Import sequence file",330,260);
if x=0 then stop;
fieldlist="-- none --	Key	";
for i=1 to DbGetFieldCount do fieldlist=fieldlist+DbGetFieldName(i)+"	";


//*************************************************************
//***                    IMPORT EMBL                        ***
//*************************************************************
if fileformat="EMBL" then {
//prompt for EMBL tag -- database field links
   tagcount=10;
   tags[1]="AC";taginfo[1]="Accession";
   tags[2]="ID";taginfo[2]="Identity";
   tags[3]="DT";taginfo[3]="Date";
   tags[4]="DE";taginfo[4]="Description";
   tags[5]="KW";taginfo[5]="Keyword";
   tags[6]="OS";taginfo[6]="Organism sp.";
   tags[7]="OC";taginfo[7]="Organism class";
   tags[8]="OG";taginfo[8]="Organelle";
   tags[9]="SV";taginfo[9]="Sequence ver.";
   tags[10]="NI";taginfo[10]="Nucl. ident.";
   for i=1 to tagcount do {
      x0=40;y0=i*30+10;
      tagfield[i]="-- none --";
      DlgAddText(dlg2,tags[i],x0,y0,30,20);
      DlgAddText(dlg2,"("+taginfo[i]+")",x0+30,y0,85,20);
      DlgAddList(dlg2,fieldlist,tagfield[i],x0+130,y0-2,115,120,"DROP");
   }
   DlgAddFrame(dlg2,"EMBL tag",20,20,140,330);
   DlgAddFrame(dlg2,"Database field",160-1,20,140,330);
   ok=0;
   while not(ok) do {
      x=DlgShow(dlg2,"Import EMBL file",420,390);
      if x=0 then stop;
      ok=1;
      for i=1 to tagcount do if tagfield[i]<>"-- none --" then
         for j=1 to i-1 do if ok and (tagfield[i]=tagfield[j]) then {
            ok=0;
            message("ERROR~n~nField '"+tagfield[i]+"' is specified several times.~nEach database field should be specified no more than once");
         }
   }
   keytag=0;
   for i=1 to tagcount do if tagfield[i]="key" then keytag=i;

//read all the files      
   ct=1;
   while filenamelist<>"" do {
      filename=splitstring(filenamelist,"	");
      if not(FileOpenRead(fp,filename)) then {
         message("ERROR~n~nUnable to read the file '"+filename+"'");
         stop;
      }
      ok=1;seqstarted=0;seqended=0;basesstarted=0;
      for i=1 to tagcount do tagcontent[i]="";
      setbusy("Importing sequence "+str(ct,0,0));
      while ok and not(FileIsEnd(fp)) do {
         line=FileRead(fp,9999);
         if not(basesstarted) and (length(line)>5) and (substring(line,3,5)="   ") then {
            st=substring(line,1,2);
            for i=1 to tagcount do
               if st=tags[i] then {
                  seqstarted=1;
                  if tagcontent[i]<>"" then tagcontent[i]=tagcontent[i]+" ";
                  tagcontent[i]=tagcontent[i]+substring(line,6,9999);
               }
         }
         if substring(line,1,2)="//" then { seqended=1;basesstarted=0; }
         if basesstarted then seqstring=seqstring+line;
         if FileIsEnd(fp) then { ok=0; seqended=1; }
         if substring(line,1,2)="SQ" then { seqstarted=1; basesstarted=1; }
         
         if seqended then {
            if seqstarted then {
               for i=1 to tagcount do tagcontent[i]=substring(tagcontent[i],1,79);
               if substring(tagcontent[1],length(tagcontent[1]),length(tagcontent[1]))=";" then
                  tagcontent[1]=substring(tagcontent[1],1,length(tagcontent[1])-1);
               key="";
               if keytag>0 then key=tagcontent[keytag];
               if key="" then key=DbAddEntry("");
               if not(DbIsKeyPresent(key)) then DbAddEntry(key);
               ok=SeqLoad(cs,key,expername);
               if not(ok) then ok=SeqCreate(cs,expername,"",key);
               if ok then {
                  SeqSet(cs,seqstring);
                  SeqSave(cs);
               }
               else report=report+"Unable to create sequence for key '"+key+"'~n";
               for i=1 to tagcount do
                  if (tagfield[i]<>"-- none --") and (tagfield[i]<>"key") then
                     DbSetField(key,tagfield[i],tagcontent[i]);
            }
            seqstarted=0;seqended=0;basesstarted=0;
            seqstring="";
            for i=1 to tagcount do tagcontent[i]="";
            ct=ct+1;
            setbusy("Importing sequence "+str(ct,0,0));
         }
      }
      FileClose(fp);
   }
   DbSaveFields;
   setbusy("");
}






//*************************************************************
//***                    IMPORT GenBank                     ***
//*************************************************************
if fileformat="GenBank" then {
//prompt for EMBL tag -- database field links
   tagcount=8;
   tags[1]="ACCESSION";
   tags[2]="LOCUS";
   tags[3]="DEFINITION";
   tags[4]="KEYWORDS";
   tags[5]="SOURCE";
   tags[6]="ORGANISM";
   tags[7]="VERSION";
   tags[8]="NID";
   for i=1 to tagcount do {
      x0=40;y0=i*30+10;
      tagfield[i]="-- none --";
      DlgAddText(dlg2,tags[i],x0,y0,60,20);
      DlgAddList(dlg2,fieldlist,tagfield[i],x0+90,y0-2,115,120,"DROP");
   }
   DlgAddFrame(dlg2,"GenBank tag",20,20,100,300);
   DlgAddFrame(dlg2,"Database field",120-1,20,140,300);
   ok=0;
   while not(ok) do {
      x=DlgShow(dlg2,"Import GenBank file",420,330);
      if x=0 then stop;
      ok=1;
      for i=1 to tagcount do if tagfield[i]<>"-- none --" then
         for j=1 to i-1 do if ok and (tagfield[i]=tagfield[j]) then {
            ok=0;
            message("ERROR~n~nField '"+tagfield[i]+"' is specified several times.~nEach database field should be specified no more than once");
         }
   }
   keytag=0;
   for i=1 to tagcount do if tagfield[i]="key" then keytag=i;

//read all the files      
   ct=1;
   while filenamelist<>"" do {
      filename=splitstring(filenamelist,"	");
      if not(FileOpenRead(fp,filename)) then {
         message("ERROR~n~nUnable to read the file '"+filename+"'");
         stop;
      }
      ok=1;seqstarted=0;seqended=0;basesstarted=0;
      for i=1 to tagcount do tagcontent[i]="";
      setbusy("Importing sequence "+str(ct,0,0));
      currenttag=0;
      while ok and not(FileIsEnd(fp)) do {
         line=FileRead(fp,9999);
         if not(basesstarted) and (length(line)>13) then {
            st=substring(line,1,12);
            if st<>"            " then currenttag=0;
            for i=1 to tagcount do
               if find(st,tags[i]+"  ",1)>0 then { currenttag=i;seqstarted=1; }
            if currenttag>0 then {
               if tagcontent[currenttag]<>"" then tagcontent[currenttag]=tagcontent[currenttag]+" ";
               tagcontent[currenttag]=tagcontent[currenttag]+substring(line,13,9999);
            }
         }
         if substring(line,1,2)="//" then { seqended=1;basesstarted=0; }
         if basesstarted then seqstring=seqstring+line;
         if FileIsEnd(fp) then { ok=0; seqended=1; }
         if substring(line,1,6)="ORIGIN" then { seqstarted=1; basesstarted=1; }
         
         if seqended then {
            if seqstarted then {
               for i=1 to tagcount do tagcontent[i]=substring(tagcontent[i],1,79);
               if substring(tagcontent[1],length(tagcontent[1]),length(tagcontent[1]))=";" then
                  tagcontent[1]=substring(tagcontent[1],1,length(tagcontent[1])-1);
               key="";
               if keytag>0 then key=tagcontent[keytag];
               if key="" then key=DbAddEntry("");
               if not(DbIsKeyPresent(key)) then DbAddEntry(key);
               ok=SeqLoad(cs,key,expername);
               if not(ok) then ok=SeqCreate(cs,expername,"",key);
               if ok then {
                  SeqSet(cs,seqstring);
                  SeqSave(cs);
               }
               else report=report+"Unable to create sequence for key '"+key+"'~n";
               for i=1 to tagcount do
                  if (tagfield[i]<>"-- none --") and (tagfield[i]<>"key") then
                     DbSetField(key,tagfield[i],tagcontent[i]);
            }
            seqstarted=0;seqended=0;basesstarted=0;
            seqstring="";currenttag="";
            for i=1 to tagcount do tagcontent[i]="";
            ct=ct+1;
            setbusy("Importing sequence "+str(ct,0,0));
         }
      }
      FileClose(fp);
   }
   DbSaveFields;
   setbusy("");
}





//***********************************************************
//***                    Import FASTA                     ***
//***********************************************************
if fileformat="FASTA" then {
   x0=20;y0=20;xmax=20;ymax=20;
   for i=0 to DbGetFieldCount do {
      y0=y0+30;
      if y0>250 then { x0=x0+160; y0=50; }
      if x0>xmax then xmax=x0;
      if y0>ymax then ymax=y0;
      st="Key";if i>0 then st=DbGetFieldName(i);
      for j=1 to 100 do st=st+" .";
      DlgAddText(dlg2,st,x0,y0,100,15);
      DlgAddEdit(dlg2,str_tagnr[i],x0+105,y0,30,20);
   }
   DlgAddText(dlg2,"Please enter for every database field the corresponding FASTA field number (if any)",20,10,230,30);
   x=DlgShow(dlg2,"Import FASTA file",xmax+270,ymax+60);
   if x=0 then stop;
   for i=0 to DbGetFieldCount do tagnr[i]=val(str_tagnr[i]);
   ct=1;
   while filenamelist<>"" do {
      filename=splitstring(filenamelist,"	");
         if not(FileOpenRead(fp,filename)) then {
            message("ERROR~n~nUnable to read the file '"+filename+"'");
            stop;
         }
      ok=1;seqstarted=0;
      while ok and not(FileIsEnd(fp)) do {
         line=FileRead(fp,9999);
         if (seqstarted) and ((substring(line,1,1)=">") or (FileIsEnd(fp))) then {
            for i=1 to tagcount do tagcontent[i]=substring(tagcontent[i],1,79);
            key="";j=tagnr[0];
            if (j>0) and (j<=tagcount) then key=tagcontent[j];
            if key="" then key=DbAddEntry("");
            if not(DbIsKeyPresent(key)) then DbAddEntry(key);
            ok=SeqLoad(cs,key,expername);
            if not(ok) then ok=SeqCreate(cs,expername,"",key);
            if ok then {
               SeqSet(cs,seqstring);
               SeqSave(cs);
            }
            else report=report+"Unable to create sequence for key '"+key+"'~n";
            for i=1 to DbGetFieldCount do {
               j=tagnr[i];
               if (j>0) and (j<=tagcount) then {
                  DbSetField(key,DbGetFieldName(i),tagcontent[j]);
               }
            }
         }
         if substring(line,1,1)=">" then {
            ct=ct+1;
            setbusy("Importing sequence "+str(ct,0,0));
            tagcount=0;
            splitstring(line,">");
            while line<>"" do {
               tagcount=tagcount+1;
               tagcontent[tagcount]=splitstring(line,"|");
            }
            seqstring="";
            seqstarted=1;
         }
         else seqstring=seqstring+line;
      }
      FileClose(fp);
   }
   DbSaveFields;
   setbusy("");
}
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IGABAANFEACLAAKAIGABAAMAMAMAMAMAMAMAMAMA
MBMBMBMJMJMJMEMEMELPLPLPLNLNLNMCMCMCMIMI
MIMPMPMPNHNHNHNMNMNMOAOAOAOAOAOANONONONG
NGNGMKMKMKMAMAMAMAMAMAMAMAMAMAMAMAMAMAMA
MAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMEMEMELBLB
LBJPJPJPINININJAJAJAJGJGJGKAKAKAKKKKKKLG
LGLGMEMEMENDNDNDNPNPNPOLOLOLPFPFPFPLPLPL
PGPGPGPCPCPCOMOMOMNNNNNNMHMHMHMAMAMAMAMA
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HLHLIAIAIAIFIFIFIKIKIKJBJBJBJKJKJKKFKFKF
LDLDLDMDMDMDNENENEODODODPAPAPAPKPKPKPHPH
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OIOIOIOEOEOENJNJNJLCLCLCJFJFJFLHLHLHMAMA
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MAMALMLMLMKPKPKPKLKLKLLCLCLCKOKOKOKFKFKF
KFKFKFKIKIKIKNKNKNLCLCLCLFLFLFKIKIKIJFJF
JFIEIEIEGLGLGLFCFCFCFHFHFHKOKOKOMAMAMAMA
MAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMA
MAMAMAMAMAMALKLKLKKNKNKNKHKHKHKBKBKBJKJK
JKJCJCJCIKIKIKICICICHJHJHJHBHBHBGJGJGJGB
GBGBFKFKFKFEFEFEFEFEFEKHKHKHMAMAMAMAMAMA
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FPFPFPFHFHFHFDFDFDJPJPJPIOIOIOJBJBJBMAMA
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JPJPJPJGJGJGINININIDIDIDHIHIHIGOGOGOGEGE
GEFMFMFMFEFEFEJGJGJGLCLCLCIBIBIBIAIAIALF
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GCGCFIFIFIINININMAMAMAJIJIJIJHJHJHJEJEJE
JLJLJLLCLCLCIAIAIALOLOLOMAMAMALPLPLPMAMA
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LPLPKPKPKPJMJMJMJBJBJBIEIEIEHGHGHGGJGJGJ
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LLLLMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMAMA
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