Concatinating/Merge blocks and order of output MAF

[amin saffari]

Dear maffilterist,

Below is my MAF file and filter parameters:

=========
tmp.MAF
=========

a score=568591.000000
s hg19.chr21           9421404 32 +  48129895 TGAGAAAAATTTTAAAAATTGAAAA----Gt-ttttt
s equCab2.chr1        43179296 32 - 185838109 TAATAAAAGTTAAAAGGATAAAAAAAGCT-----TAT
q equCab2.chr1                                99999999999999999999999999999-----999
s canFam2.chr30       16402545 25 +  43206070 AGATAAAGCTTAGAAGAATTTTTTA------------
q canFam2.chr30                               9999999999999999999999999------------
s bosTau4.chr10       41342912 11 - 106383598 TGGTAAcagtt--------------------------
q bosTau4.chr10                               99999999999--------------------------
s oryCun2.chr17       59453562 28 -  85008467 GGATGAAAAAGTTTAACATAAAATG----TAT-----
q oryCun2.chr17                               9999999999999999999999999----999-----
e cavPor3.scaffold_23  7330649  0 -  32209358 C
s panTro2.chrUn        5538216 25 +  58616431 TTAGAAAAATTTTAAAAATTGAAG------------t
q panTro2.chrUn                               999999999999999999999999------------9
s ponAbe2.chrUn       66603144 32 -  72422247 TGAGAAAAATTTTAAAAATTGAAAA----GA-ttttt
q ponAbe2.chrUn                               9999999999999999999999999----99-99999
s rheMac2.chr7        25417460 33 + 169801366 TGAGAAAAATGTTTAAAATTGAAAA----GTGttttt
q rheMac2.chr7                                9999999999999999999999999----99999999

a score=131881.000000
s hg19.chr21     9421436 67 +  48129895 tttttttttgagacggagtctcgctgtgtcatccaggctggagtgcagtggcgccatctcggctcac
s rheMac2.chr7  25417493 67 + 169801366 tttttttttgagacagagtcttactctgtcgcccaggctggagtgcagtggtgccatctcgactcac
q rheMac2.chr7                          9999999999999999999999999999999999999999999999999999999999999999999
s ponAbe2.chrUn 66603176 67 -  72422247 tttttttttgagatggagtcttgctgtgtcatccaggctggagtgcagtggcaccatcttggctcac
q ponAbe2.chrUn                         9999999999999999999999999999999999999999999999999999999999999999999
s panTro2.chrUn  5538241 67 +  58616431 tttttttttgagacagagtctcgctgtgtcacccaggctggagtgcagtggcgccacctcggctcac
q panTro2.chrUn                         9999999999999999999999999999999999999999999999999999999999999999999


=========
MafFilter.bpp
=========
DATA=tmp.chr21.parsed                                                                                               
input.file=$(DATA).maf                                                                                              
input.file.compression=none                                                                                         
input.format=Maf                                                                                                    
output.log=$(DATA).maffilter.log                                                                                    
maf.filter=\                                                                                                        
    Merge(species=hg19, dist_max=1),\                                                                               
    Output( \                                                                                                       
       file=Merg.$(DATA).maf,\                                                                                      
       mask=no \                                                                                                    
     )


What I am setting as my filter is fusing all consecutive blocks and Maffilter does that perfectly. However the species order of
the output maf is not the same as input maf and if I am not mistaken its alphabetically sorted!

=========
Merg.MAF
=========
a score=287249
s bosTau4.chr10 41342912  11 - 106383598 TGGTAACAGTT---------------------------------------------------------------------------------------------
s canFam2.chr30 16402545  25 +  43206070 AGATAAAGCTTAGAAGAATTTTTTA-------------------------------------------------------------------------------
s equCab2.chr1  43179296  32 - 185838109 TAATAAAAGTTAAAAGGATAAAAAAAGCT-----TAT-------------------------------------------------------------------
s hg19.chr21     9421404  99 +  48129895 TGAGAAAAATTTTAAAAATTGAAAA----GT-TTTTTTTTTTTTTTGAGACGGAGTCTCGCTGTGTCATCCAGGCTGGAGTGCAGTGGCGCCATCTCGGCTCAC
s oryCun2.chr17 59453562  28 -  85008467 GGATGAAAAAGTTTAACATAAAATG----TAT------------------------------------------------------------------------
s panTro2.chrUn  5538216  92 +  58616431 TTAGAAAAATTTTAAAAATTGAAG------------TTTTTTTTTTGAGACAGAGTCTCGCTGTGTCACCCAGGCTGGAGTGCAGTGGCGCCACCTCGGCTCAC
s ponAbe2.chrUn 66603144  99 -  72422247 TGAGAAAAATTTTAAAAATTGAAAA----GA-TTTTTTTTTTTTTTGAGATGGAGTCTTGCTGTGTCATCCAGGCTGGAGTGCAGTGGCACCATCTTGGCTCAC
s rheMac2.chr7  25417460 100 + 169801366 TGAGAAAAATGTTTAAAATTGAAAA----GTGTTTTTTTTTTTTTTGAGACAGAGTCTTACTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCCATCTCGACTCAC




So I am wondering to ask if there is any switches, which I should turn them on, to receive what I want?!

Cheers,
Amin

[Julien Yann Dutheil]

Dear Amin,

Indeed, in order to compare efficiently blocks with potentially distinct species in distinct orders, maffilter sort the sequences by alphabetical order of names.
If you need species to be in a particular order, you should look at the maf_order program from mutliz and use it in combination with maffilter.

Hope this helps,

J.