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Support BLAST archive format (ASN.1)

Open peterjc opened this issue 11 years ago • 2 comments

The BLAST+ tools offer several ASN.1 based output formats, the most interesting of which is the BLAST archive format introduced in BLAST+ 2.2.24,

 -outfmt 
   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)

We could add this as a new output format, and a wrapper for the associated tool Blast_formatter which can convert it into the other formats.

This could replace BLAST XML as the "rich" output format from which tabular output etc can be extracted... although the XML output is more widely supported.

peterjc avatar Dec 24 '13 15:12 peterjc

Also, it appears that the -outfmt options:

  • Query-anchored (text/html)
  • Flat query-anchored (text/html)

are for the "no identities" settings. Could you please add the "showing identities" options, or at the very least, display which option it precisely is that we're selecting. There's no way to know without running it and scrolling through the output.

hepcat72 avatar Jan 14 '20 16:01 hepcat72

Query anchored suggestion logged as #121.

peterjc avatar Jan 14 '20 17:01 peterjc