Add species name to a multiple alignment format (MAF) file
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
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shinken123
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1 answer
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
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