GenBank filetype to Fasta filetype
Bioinfo~~~
GenBank filetype to Fasta filetype
.gb -> .fasta
public class G2F {
private String LOCUS = "LOCUS ", LOCUS_S = "begin", //"SOURCE(name)"+"." +"LOCUS"
ORGANISM = " ORGANISM ", ORGANISM_S = "begin",
ACCESSION = "ACCESSION ", ACCESSION_S = "begin",
VERSION = "VERSION ", VERSION_S = "begin",
DEFINITION = "DEFINITION ", DEFINITION_S = "begin",
ORIGIN = "ORIGIN ", ORIGIN_S = "begin",
END_DATA = "//";
String short_name = null, accession_name = null,
version_name = null, definition_name = null,
organism_name = null, warning_mess = null,
origin = null,
genbank_name = null,
sequence = "",
firstline = null, secondline =null;
public void resetState()
{
LOCUS_S = "begin";
ORGANISM_S = "begin";
ACCESSION_S = "begin";
VERSION_S = "begin";
DEFINITION_S = "begin";
ORIGIN_S = "begin";
}
public void resetName()
{
short_name = null;
accession_name = null;
version_name = null;
definition_name = null;
organism_name = null;
warning_mess = null;
genbank_name = null;
origin = null;
sequence = "";
firstline = null;
secondline =null;
}
public void scan1squence(String inputfile, String outputfile) throws IOException
{
BufferedReader in = new BufferedReader(new FileReader(inputfile));
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(outputfile)));
String sline = null;
/*String firstline = "";
String secondline = "";*/
while((sline = in.readLine()) != null){
if( ! sline.equals(END_DATA) && ! sline.equals("")){
String stemp = sline.substring(0, 12);
String resub = sline.substring(12);
//System.out.println(stemp);
if(stemp.equals(ORGANISM)){
organism_name = resub;
String s[] = resub.split(" ");
if(s[1].length() < 3){
s[1] = "XXX";
}
short_name = s[0].substring(0, 4)+ "_" + s[1].substring(0,4);
ORGANISM_S = "done";
}
if(stemp.equals(ACCESSION)){
accession_name = resub;
ACCESSION_S = "done";
}
if(stemp.equals(VERSION)){
String s[] = resub.split("GI:");
version_name = s[0].trim();
genbank_name = s[1].trim();
//System.out.println(version_name);
VERSION_S = "done";
}
if(stemp.equals(DEFINITION)){
definition_name = resub;
DEFINITION_S = "done";
}
if(stemp.equals(ORIGIN)){
ORIGIN_S = "done";
//sline = in.readLine();
}
if( ORIGIN_S.equals("done") ){
while( ! (sline = in.readLine()).equals(END_DATA) ){
String tempsequence = sline.substring(10);
sequence += tempsequence.replace(" ","").toUpperCase();
}
ORIGIN_S = "nextS";
//System.out.println(sequence);
}
if(ORGANISM_S.equals("done") && ACCESSION_S.equals("done")
&& VERSION_S.equals("done") && DEFINITION_S.equals("done")
&& ORIGIN_S.equals("nextS"))
{
firstline = ">"+short_name+"."+accession_name+
" ( "+version_name+" GI:"+genbank_name+" ) { "+definition_name+
" } [ "+organism_name+" ]";
/*if(firstline.equals(">Cich_endi.EL372564 ( EL372564.1 GI:125358052 ) { CCEL5375.b1_N24.ab1 CCE(LMS) endive Cichorium endivia cDNA clone } [ Cichorium endivia ]"))
System.out.println("----------true-----------");*/
secondline = sequence;
/*System.out.println(firstline);
System.out.println(secondline);
if(secondline.equals("TATTCCAGAATCTCACACCTTTTTACACTAGCAGAAAGCCAGAAACACAGACCAACAACAGACGAGGAGGCACGAATTCCAACACAGAAAGGTTTTGTCTTCTCTTTCAACATCAAAGAGGGCTCTAGAAGCCCCCTGAGACCAAATCTTCAAACCAACATGGAATACCAAGCAAACTATTCAATTTGGGATGGTTTATACTACCATCCACACCTATTCGGTGGCATTATGCTAACAGTTGCATTGCTTGGTCTTTCCACAAGCTATCTAAGTGGCATAGCTGGCTTCCCTACTTTACCCTACATGTTACCTTATTTAGGAAACTTCCAGAAACAAAAAACCAACAAGAAACGTATCCGTGTGTACATGGATGGATGTTTTGATCTCATGCATTATGGTCACGCAAATGCTTTAAGACAAGCTAAAGCTTTAGGAGACGAATTAGTGGTTGGAATTGTAAGTGATGAAGAAATCATCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAAGATTGGCACTTGTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCTTATGCTATTACTGAAGACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGATCCTTGTTTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAAAAGTTGGTCGTTACAA"))
System.out.println("----------true-----------");*/
out.println(firstline);
out.println(secondline);
resetName();
resetState();
continue;
}
}
else if(sline.equals(END_DATA)){
//resetName();
resetState();
}
}
out.close();
in.close();
}
}
public class G2F {
private String LOCUS = "LOCUS ", LOCUS_S = "begin", //"SOURCE(name)"+"." +"LOCUS"
ORGANISM = " ORGANISM ", ORGANISM_S = "begin",
ACCESSION = "ACCESSION ", ACCESSION_S = "begin",
VERSION = "VERSION ", VERSION_S = "begin",
DEFINITION = "DEFINITION ", DEFINITION_S = "begin",
ORIGIN = "ORIGIN ", ORIGIN_S = "begin",
END_DATA = "//";
String short_name = null, accession_name = null,
version_name = null, definition_name = null,
organism_name = null, warning_mess = null,
origin = null,
genbank_name = null,
sequence = "",
firstline = null, secondline =null;
public void resetState()
{
LOCUS_S = "begin";
ORGANISM_S = "begin";
ACCESSION_S = "begin";
VERSION_S = "begin";
DEFINITION_S = "begin";
ORIGIN_S = "begin";
}
public void resetName()
{
short_name = null;
accession_name = null;
version_name = null;
definition_name = null;
organism_name = null;
warning_mess = null;
genbank_name = null;
origin = null;
sequence = "";
firstline = null;
secondline =null;
}
public void scan1squence(String inputfile, String outputfile) throws IOException
{
BufferedReader in = new BufferedReader(new FileReader(inputfile));
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(outputfile)));
String sline = null;
/*String firstline = "";
String secondline = "";*/
while((sline = in.readLine()) != null){
if( ! sline.equals(END_DATA) && ! sline.equals("")){
String stemp = sline.substring(0, 12);
String resub = sline.substring(12);
//System.out.println(stemp);
if(stemp.equals(ORGANISM)){
organism_name = resub;
String s[] = resub.split(" ");
if(s[1].length() < 3){
s[1] = "XXX";
}
short_name = s[0].substring(0, 4)+ "_" + s[1].substring(0,4);
ORGANISM_S = "done";
}
if(stemp.equals(ACCESSION)){
accession_name = resub;
ACCESSION_S = "done";
}
if(stemp.equals(VERSION)){
String s[] = resub.split("GI:");
version_name = s[0].trim();
genbank_name = s[1].trim();
//System.out.println(version_name);
VERSION_S = "done";
}
if(stemp.equals(DEFINITION)){
definition_name = resub;
DEFINITION_S = "done";
}
if(stemp.equals(ORIGIN)){
ORIGIN_S = "done";
//sline = in.readLine();
}
if( ORIGIN_S.equals("done") ){
while( ! (sline = in.readLine()).equals(END_DATA) ){
String tempsequence = sline.substring(10);
sequence += tempsequence.replace(" ","").toUpperCase();
}
ORIGIN_S = "nextS";
//System.out.println(sequence);
}
if(ORGANISM_S.equals("done") && ACCESSION_S.equals("done")
&& VERSION_S.equals("done") && DEFINITION_S.equals("done")
&& ORIGIN_S.equals("nextS"))
{
firstline = ">"+short_name+"."+accession_name+
" ( "+version_name+" GI:"+genbank_name+" ) { "+definition_name+
" } [ "+organism_name+" ]";
/*if(firstline.equals(">Cich_endi.EL372564 ( EL372564.1 GI:125358052 ) { CCEL5375.b1_N24.ab1 CCE(LMS) endive Cichorium endivia cDNA clone } [ Cichorium endivia ]"))
System.out.println("----------true-----------");*/
secondline = sequence;
/*System.out.println(firstline);
System.out.println(secondline);
if(secondline.equals("TATTCCAGAATCTCACACCTTTTTACACTAGCAGAAAGCCAGAAACACAGACCAACAACAGACGAGGAGGCACGAATTCCAACACAGAAAGGTTTTGTCTTCTCTTTCAACATCAAAGAGGGCTCTAGAAGCCCCCTGAGACCAAATCTTCAAACCAACATGGAATACCAAGCAAACTATTCAATTTGGGATGGTTTATACTACCATCCACACCTATTCGGTGGCATTATGCTAACAGTTGCATTGCTTGGTCTTTCCACAAGCTATCTAAGTGGCATAGCTGGCTTCCCTACTTTACCCTACATGTTACCTTATTTAGGAAACTTCCAGAAACAAAAAACCAACAAGAAACGTATCCGTGTGTACATGGATGGATGTTTTGATCTCATGCATTATGGTCACGCAAATGCTTTAAGACAAGCTAAAGCTTTAGGAGACGAATTAGTGGTTGGAATTGTAAGTGATGAAGAAATCATCAAGAACAAAGGTCCTCCTGTTTTATCAATGGAGGAAAGATTGGCACTTGTTAGTGGATTGAAGTGGGTTGATGAAGTTATTGCTAATGCACCTTATGCTATTACTGAAGACTTCATGAACAGTCTATTTAAAGAACATAAGATTGATTATATCATTCATGGAGATGATCCTTGTTTGCTTCCTGATGGAAGTGATGCATATGCTTTAGCAAAAAAAAAGTTGGTCGTTACAA"))
System.out.println("----------true-----------");*/
out.println(firstline);
out.println(secondline);
resetName();
resetState();
continue;
}
}
else if(sline.equals(END_DATA)){
//resetName();
resetState();
}
}
out.close();
in.close();
}
}