Add species name to a multiple alignment format (MAF) file

Question

[shinken123]

Hi, I have MAF files like this:

##maf version=1
a       score=-1274
s       Chr10                                            34972197            2927       +       190919061         AACCTTGGGG
s       Chr11                                            36777315            2442       +       244384623         AACCTTGGGG

a       score=-60687
s       Chr1                                             81897274           61972       +       159217232          CGTTTTCCCGG
s       Chr1                                             33997294           32248       +       200980605          CGTTTTCCCGG

Is there a tool to add automatically species names to this format to have something like this?

##maf version=1
a       score=-1274
s       species1.Chr10                                            34972197            2927       +       190919061         AACCTTGGGG
s       species2.Chr11                                            36777315            2442       +       244384623         AACCTTGGGG

a       score=-60687
s       species1.Chr1                                             81897274           61972       +       159217232          CGTTTTCCCGG
s       species2.Chr1                                             33997294           32248       +       200980605          CGTTTTCCCGG

Many thanks

Answer 1

[cmdcolin]

it is likely better to do this before creating your MAF file, it may not be possible to unambiguously add species names after the fact. specifically: you can have MAF entries that have more than 2 lines for example, here is from a MAF file

a
s   elegans.X   17703901    60  +   17718942    CTATATCCGCAAAGTTGGGACGGACGGGCTCTGCGGAGCCCAAGTGACAACACTCCGGGG
s   elegans.I   3625790 60  -   15072434    CTATATCCGCAAAGTTGGGACGGACGGGCTCTGCGGAGCCCAAGTGACAACACTCCGGGG
s   elegans.IV  9548578 60  +   17493829    ATACATCCGCAAAGTTGGGACGGACGGGCTCTGCGGAGCCCAAGTGACAACACTCCGGGG
s   elegans.V   791349  60  +   20924180    ATACATCAGCAAAGTTGGGACGAATGGGCTCTGAGGGGCCCAAGTCACAACACTCCGGGG
s   elegans.V   19270529    60  +   20924180    TATAATCCGCAAAGTTGGGGCGGAGGACCTCTACGGAGGCGAAGTCACAACATTCCGGGG
s   elegans_vc2010.V    786777  60  +   20182852    ATACATCAGCAAAGTTGGGACGAATGGGCTCTGAGGGGCCCAAGTCACAACACTCCGGGG
s   elegans_vc2010.X    17522306    60  +   17537347    CTATATCCGCAAAGTTGGGACGGACGGGCTCTGCGGAGCCCAAGTGACAACACTCCGGGG

you would not know which of those rows would be elegans and which are elegans_vc2010 without that species annotation already being there if the chromosome names are similar in both elegans and elegans_vc2010