Format of target name
dariober opened this issue · 1 comments
dariober commented
When aligning and mapping a query to a reference, it seems that spaln uses as Target name the string after | in the query name. For example:
>KAF4646005.1|foo
MGCTGSKAAAVKKPDSPEDKREANDKPQLSTGHAEALPGVVAAGGAQDSSDAKSAASLTT
...
After alignment, the Target key has value foo (i.e. Target=foo):
spaln -O:0 -Q7 -d ToxoDB-56_TgondiiRH88_Genome KAF4646005.faa
##gff-version 3
##sequence-region CM023082 1686529 1695744
CM023082 ALN gene 1687335 1690489 2025 - . ID=gene00001;Name=CM023082_1688
CM023082 ALN mRNA 1687335 1690489 2025 - . ID=mRNA00001;Parent=gene00001;Name=CM023082_1688
CM023082 ALN cds 1689930 1690489 1078 - 0 ID=cds00001;Parent=mRNA00001;Name=CM023082_1688;Target=foo 1 187 +
CM023082 ALN cds 1689053 1689225 365 - 1 ID=cds00002;Parent=mRNA00001;Name=CM023082_1688;Target=foo 188 244 +
CM023082 ALN cds 1688502 1688604 242 - 2 ID=cds00003;Parent=mRNA00001;Name=CM023082_1688;Target=foo 245 279 +
CM023082 ALN cds 1687839 1687987 298 - 1 ID=cds00004;Parent=mRNA00001;Name=CM023082_1688;Target=foo 280 328 +
CM023082 ALN cds 1687335 1687450 160 - 2 ID=cds00005;Parent=mRNA00001;Name=CM023082_1688;Target=foo 329 366 +
I would have expected Target to be the full name KAF4646005.1|foo. Is this behaviour documented? Can it be changed? I would prefer to have as target the sequence name up to the first blank space.
ogotoh commented
Dear Dario,
Accoding to your request, I have created the new option, -pF, to show full entry name rather than the last term separated by vergical bars.
Osamu,