search

poeli / GOTTCHA

More details and updates can be found in our homepage and LANL-Bioinformatics Github site (https://github.com/LANL-Bioinformatics/GOTTCHA). Please visit our homepage at
http://lanl-bioinformatics.github.io/GOTTCHA
GNU General Public License v3.0
8 stars 10 forks source link

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

Open scholzmb opened 8 years ago

scholzmb commented 8 years ago

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