[Bioperl-l] mummer3 output format

[Albert Vilella]

Hi,

I am trying to understand how to transform Mummer3's output format
into something I can pipe into another program, like MAF or similar.
How can I parse the results so that I can then do a write_aln into MAF
o similar?

Details:

If I run nucmer v.3.23 with the options below, I get an out.delta like this:

~/MUMmer3.23/nucmer -maxgap $g -l $l $ref $qry

------------------
Leishmania_major.LM2.12.dna.toplevel.fa
LtarParrotTarIIGenomic_TriTrypDB-4.0.fasta
NUCMER
>LmjF.34 ULAVAL|LtaPseq521 1866748 641
959335 959806 169 640 91 91 0
20
17
-3
-2
-183
5
0
>LmjF.12 ULAVAL|LtaPseq501 675346 1438
322990 324081 1436 342 178 178 0
-45
-1
-1
-1

This doesn't look like any of the formats in t/AlignIO/mummer.t to me.

I can also run:

~/MUMmer3.23/show-aligns out.delta $region1 $region2

Which gives me something that looks like a blast or exonerate output, like so:

------
Leishmania_major.LM2.12.dna.toplevel.fa
LtarParrotTarIIGenomic_TriTrypDB-4.0.fasta

============================================================
-- Alignments between LmjF.34 and ULAVAL|LtaPseq521

-- BEGIN alignment [ +1 959335 - 959806 | +1 169 - 640 ]


959335     cacacgcctcgtagaggtctccttgctttcgcgcggtgc.c.tcacttg
169        cacacgcctcgtagagatc.ccctgccttcgcgcgg.gctcttcacttg
                           ^  ^  ^   ^         ^  ^ ^

959382     cgcatgcggtagtagaagagaatgctgtgggcccacccagcgtagttgc
216        cgcatgcggtagtagaagagaatgctgtgtgcccacccagcgtagttgc
                                        ^

959431     caaacagcttccggaaggcctcctgaatgacgttatgatgccgctcgta
265        caaacagtttccagaaggcatcctggataacattatgatgccgttcgta
                  ^    ^      ^     ^  ^  ^           ^

959480     caagggtgggacaggcgtttttcgtgaggcgcgcagcggggctgctgca
314        caggggcggcacaggtgttttccgtaaggcacgtgaagaggtcgttgca
             ^   ^  ^     ^     ^   ^    ^  ^^^^ ^  ^^ ^

959529     gagcttccaccttcctctatcgccttta.cggtcgctggcgacacgcct
363        gagcctccgtttcccttcaccgcccgcagcgat.gatgatgtcactcct
               ^   ^^^ ^   ^^ ^    ^^^ ^  ^ ^ ^  ^^ ^   ^

959577     ttcttaaccttgagaacctccgcctgcttcctccactccagcagcagat
411        ttcttcaccttgagagcctccgcctggttcttccactccaggagaagat
                ^         ^          ^   ^          ^  ^

959626     tatcccgtgagcgggcttcctcttcgggcaacggacaccctggacgaga
460        cagtgggtgcgcagacttcttcttcgcgcagtagagaccctgagcgaga
           ^ ^^^^   ^  ^ ^    ^      ^   ^^^  ^      ^^

959675     gcgcttacgacccaccgccgtcgcggcgcttggtgcggcaaggtactcc
509        acgctttcgacccgccgatgtcacggtgcttgcggtggcaagatactcc
           ^     ^      ^   ^^   ^   ^     ^^ ^      ^

959724     accgcaacttgcgccatgtgcgtgtccacggggacaatgtgggtgcggt
558        accgaaacctgcgccatgtgtgtgtccacggggacgatgtgggtgcggt
               ^   ^           ^              ^

959773     tgagcgcgaagagcgccacgcagtcagcaacttt
607        tgagagcaaagagcgccacgcaatccgccacttt
               ^  ^              ^  ^  ^


--   END alignment [ +1 959335 - 959806 | +1 169 - 640 ]

============================================================