blast_formatter -rid <String> -out output_file


 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1) 
    
    
   Options 6, 7, and 10 can be additionally configured to produce
   a custom format specified by space delimited format specifiers.
   The supported format specifiers are:
   	    qseqid means Query Seq-id
   	       qgi means Query GI
   	      qacc means Query accesion
   	   qaccver means Query accesion.version
   	      qlen means Query sequence length
   	    sseqid means Subject Seq-id
   	 sallseqid means All subject Seq-id(s), separated by a ';'
   	       sgi means Subject GI
   	    sallgi means All subject GIs
   	      sacc means Subject accession
   	   saccver means Subject accession.version
   	   sallacc means All subject accessions
   	      slen means Subject sequence length
   	    qstart means Start of alignment in query
   	      qend means End of alignment in query
   	    sstart means Start of alignment in subject
   	      send means End of alignment in subject
   	      qseq means Aligned part of query sequence
   	      sseq means Aligned part of subject sequence
   	    evalue means Expect value
   	  bitscore means Bit score
   	     score means Raw score
   	    length means Alignment length
   	    pident means Percentage of identical matches
   	    nident means Number of identical matches
   	  mismatch means Number of mismatches
   	  positive means Number of positive-scoring matches
   	   gapopen means Number of gap openings
   	      gaps means Total number of gaps
   	      ppos means Percentage of positive-scoring matches
   	    frames means Query and subject frames separated by a '/'
   	    qframe means Query frame
   	    sframe means Subject frame
   	      btop means Blast traceback operations (BTOP)    

blast_formatter -rid SYYMVJR6014 -outfmt 0  -out PEADRRB.blast.pairwise
blast_formatter -rid SYYMVJR6014 -outfmt 5  -out PEADRRB.blast.xml
blast_formatter -rid SYYMVJR6014 -outfmt 6  -out PEADRRB.blast.tabular
blast_formatter -rid SYYMVJR6014 -outfmt 7  -out PEADRRB.blast.tabcom
blast_formatter -rid SYYMVJR6014 -outfmt 10  -out PEADRRB.blast.csv

#html output - virtually useless, as there is no real formatting, and few links
blast_formatter -rid SYYMVJR6014 -outfmt 0  -html -out PEADRRB.blast.html
blast_formatter -rid SYYMVJR6014 -outfmt 5  -html -out PEADRRB.blast.xml.html 
blast_formatter -rid SYYMVJR6014 -outfmt 7  -html -out PEADRRB.blast.tabcom.html
blast_formatter -rid SYYMVJR6014 -outfmt 10  -html -out PEADRRB.blast.csv.html


# Table format
blast_formatter -rid SYYMVJR6014 -outfmt "6 sseqid sgi slen evalue"
blast_formatter -rid SYYMVJR6014 -outfmt "7 sseqid sgi slen evalue"
blast_formatter -rid SYYMVJR6014 -outfmt "10 sseqid sgi slen evalue" -out PEADRRB.blast.csv