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Feature request: report ALL levels of taxonomy in .tsv #7

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scholzmb opened this issue Oct 22, 2015 · 0 comments
Open

Feature request: report ALL levels of taxonomy in .tsv #7

scholzmb opened this issue Oct 22, 2015 · 0 comments

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@scholzmb
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Example:
In report when using genus level db, output in tsv is so:
LEVEL TAXA REL_ABUNDANCE LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
phylum Proteobacteria 0.5140 9609 18928 376 0 376 1.96981996045374 0.51399583287166
phylum Actinobacteria 0.4860 27922 52006 1049 0 1049 1.86254566291813 0.48600416712834
class Gammaproteobacteria 0.5140 9609 18928 376 0 376 1.96981996045374 0.51399583287166
class Actinobacteria 0.4860 27922 52006 1049 0 1049 1.86254566291813 0.48600416712834
order Enterobacteriales 0.5140 9609 18928 376 0 376 1.96981996045374 0.51399583287166
order Propionibacteriales 0.4860 27922 52006 1049 0 1049 1.86254566291813 0.48600416712834
family Enterobacteriaceae 0.5140 9609 18928 376 0 376 1.96981996045374 0.51399583287166
family Propionibacteriaceae 0.4860 27922 52006 1049 0 1049 1.86254566291813 0.48600416712834
genus Escherichia 0.5140 9609 18928 376 0 376 1.96981996045374 0.51399583287166
genus Propionibacterium 0.4860 27922 52006 1049 0 1049 1.86254566291813 0.48600416712834

However, in .log file, results for Species/strain/etc are also calculated:
STRAIN LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
Escherichia coli BL21(DE3) uid161949 3054 6764 135 0 135 2.21480026195154 0.235267203791031
Escherichia coli BW2952 2997 5926 117 0 117 1.97731064397731 0.210039864192938
Escherichia coli str. K-12 substr. DH10B 855 1315 26 0 26 1.53801169590643 0.163375324317045
Escherichia coli str. K-12 substr. MDS42 2703 4923 98 0 98 1.82130965593785 0.193468656000853

Propionibacterium acnes ATCC 11828 27922 52006 1049 0 1049 1.86254566291813 0.197848951698132

SPECIES LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
Escherichia coli 9609 18928 376 0 376 1.96981996045374 0.51399583287166

Propionibacterium acnes 27922 52006 1049 0 1049 1.86254566291813 0.48600416712834

Request that this output also placed in .tsv output

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