[Biojava-l] Blast XML output with multiple sequences

[Ashika Umanga Umagiliya]

Hi charles and all,

Here is one of my actual input.txt :

 >seq 1
dssfyic
 >seq 2
dssfyic

And here is the result output for this. output.xml its actually two 
appended XML files ????

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" 
"NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastp</BlastOutput_program>
  <BlastOutput_version>blastp 2.2.18 [Mar-02-2008]</BlastOutput_version>
  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. 
Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, 
and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new 
generation of protein database search~programs&quot;,  Nucleic Acids 
Res. 25:3389-3402.</BlastOutput_reference>
  
<BlastOutput_db>/work/mysizuka-web/mysizouka2/src/main/webapp/WEB-INF/blast/db/tcrDB 
/work/mysizuka-web/mysizouka2/src/main/webapp/WEB-INF/blast/db/mabDB</BlastOutput_db>
  <BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
  <BlastOutput_query-def>seq 1</BlastOutput_query-def>
  <BlastOutput_query-len>7</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>10</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>F</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>6238</Statistics_db-num>
          <Statistics_db-len>565098</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>4.6796e+07</Statistics_eff-space>
          <Statistics_kappa>0.041</Statistics_kappa>
          <Statistics_lambda>0.267</Statistics_lambda>
          <Statistics_entropy>0.14</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
  </BlastOutput_iterations>
</BlastOutput>
<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" 
"NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastp</BlastOutput_program>
  <BlastOutput_version>blastp 2.2.18 [Mar-02-2008]</BlastOutput_version>
  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. 
Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, 
and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new 
generation of protein database search~programs&quot;,  Nucleic Acids 
Res. 25:3389-3402.</BlastOutput_reference>
  
<BlastOutput_db>/work/mysizuka-web/mysizouka2/src/main/webapp/WEB-INF/blast/db/tcrDB 
/work/mysizuka-web/mysizouka2/src/main/webapp/WEB-INF/blast/db/mabDB</BlastOutput_db>
  <BlastOutput_query-ID>lcl|QUERY</BlastOutput_query-ID>
  <BlastOutput_query-def>seq 2</BlastOutput_query-def>
  <BlastOutput_query-len>7</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>10</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>F</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_stat>
        <Statistics>
          <Statistics_db-num>6238</Statistics_db-num>
          <Statistics_db-len>565098</Statistics_db-len>
          <Statistics_hsp-len>0</Statistics_hsp-len>
          <Statistics_eff-space>4.6796e+07</Statistics_eff-space>
          <Statistics_kappa>0.041</Statistics_kappa>
          <Statistics_lambda>0.267</Statistics_lambda>
          <Statistics_entropy>0.14</Statistics_entropy>
        </Statistics>
      </Iteration_stat>
      <Iteration_message>No hits found</Iteration_message>
    </Iteration>
  </BlastOutput_iterations>
</BlastOutput>






Charles Imbusch wrote:
> Hello Umanga,
>
> in my understanding blast always writes all results to one file
> according to the sequences specified in the input file.
>
> So you could split the input file with multiple sequences into
> files containing one sequence each.
>
> cheers,
>  Charles
>
>