Convert blastn (from blast+) output to old blastall -m 6 (Flat query-anchored, no identities and blunt ends) format

Question

[russianconcussion]

Hi, I am trying to locally align Hi-Seq 101bp reads to a reference sequence (using blastn) to generate a position-specific frequency matrix. I would like to format my command-line blastn results in the old blastall -m 6 format (where local alignments and gaps are padded by hyphens) without having to use the old blastall package. The closest -oufmt option in blast+ blastn is number 4 (), but that doesn't pad the alignment with hyphens on the end to let me build a matrix. Does anyone have any suggestions about how to do this?

Here is the -m 6 format that I am trying to get: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node89.html

[hpmcwill]

I suggest asking the NCBI BLAST folks directly ([e-mail]) so they can take this request into account in the development of NCBI BLAST+. It may be that they know of some possible solutions or can add the desired functionality the the next release.