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), ~"Gapped BLAST and PSI-BLAST: a new
generation of protein database search~programs", 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), ~"Gapped BLAST and PSI-BLAST: a new
generation of protein database search~programs", 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
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