Skip to content

Added MGnify test data sets #47

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jungbluth wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Added MGnify test data sets #47

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
137 changes: 137 additions & 0 deletions test/example_data/MGnify_MGYS00002008_tara_marine_w_metadata.tsv
View file
Open in desktop

Large diffs are not rendered by default.

2 changes: 2 additions & 0 deletions test/example_data/MGnify_MGYS00002071_human_associated.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
_sample_id collection date collection date_unit geographic location (country and/or sea,region) geographic location (country and/or sea,region)_unit geographic location (latitude) geographic location (latitude)_unit geographic location (longitude) geographic location (longitude)_unit instrument model instrument model_unit mgnify_accession mgnify_analysis_completed mgnify_biome mgnify_biosample mgnify_collection_date mgnify_environment_biome mgnify_environment_feature mgnify_environment_material mgnify_geo_loc_name mgnify_host_tax_id mgnify_last_update mgnify_latitude mgnify_longitude mgnify_sample_alias mgnify_sample_desc mgnify_sample_name mgnify_species mgnify_study_ids
SRS1124878 2012-01-01/2012-12-31 USA:Ohio 40.10721 -82.18359 Illumina HiSeq 2000 SRS1124878 2017-11-27 root:Environmental:Aquatic:Freshwater:Drinking water SAMN04201344 2012-01-01 USA:Ohio 2017-11-27T13:48:43 40.1072 -82.1836 hopital shower hoses biofilms we characterized the biofilm microbial communities of shower hoses in a hospital using shotgun whole-metagenome DNA sequencing hopital shower hoses biofilms ['MGYS00002071']
41 changes: 41 additions & 0 deletions test/example_data/MGnify_MGYS00002681_compost.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
_sample_id collection date collection date_unit elevation elevation_unit environment (biome) environment (biome)_unit environment (feature) environment (feature)_unit environment (material) environment (material)_unit environmental package environmental package_unit geographic location (country and/or sea,region) geographic location (country and/or sea,region)_unit geographic location (latitude) geographic location (latitude)_unit geographic location (longitude) geographic location (longitude)_unit instrument model instrument model_unit investigation type investigation type_unit mgnify_accession mgnify_analysis_completed mgnify_biome mgnify_biosample mgnify_collection_date mgnify_environment_biome mgnify_environment_feature mgnify_environment_material mgnify_geo_loc_name mgnify_host_tax_id mgnify_last_update mgnify_latitude mgnify_longitude mgnify_sample_alias mgnify_sample_desc mgnify_sample_name mgnify_species mgnify_study_ids sequencing method sequencing method_unit
ERS2625736 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625736 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805826 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_CATTANEO_4 Compost tea CT_CATTANEO_4 ['MGYS00002681'] Amplicon
ERS2625758 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625758 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805848 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n9 d Litter Litter n9 d ['MGYS00002681'] Amplicon
ERS2625757 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625757 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805847 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n9 c Litter Litter n9 c ['MGYS00002681'] Amplicon
ERS2625759 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625759 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805849 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n3 c Litter Litter n3 c ['MGYS00002681'] Amplicon
ERS2625741 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625741 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805831 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_SPADOLA_1 Compost tea CT_SPADOLA_1 ['MGYS00002681'] Amplicon
ERS2625739 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625739 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805829 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_HANENZY_3 Compost tea CT_HANENZY_3 ['MGYS00002681'] Amplicon
ERS2625732 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625732 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805822 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 9-4 Teku kana tek 9-4 ['MGYS00002681'] Amplicon
ERS2625747 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625747 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805837 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_GALLUCCI_3 Compost tea CT_GALLUCCI_3 ['MGYS00002681'] Amplicon
ERS2625737 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625737 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805827 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_HANENZY_1 Compost tea CT_HANENZY_1 ['MGYS00002681'] Amplicon
ERS2625733 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625733 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805823 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_CATTANEO_1 Compost tea CT_CATTANEO_1 ['MGYS00002681'] Amplicon
ERS2625746 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625746 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805836 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_GALLUCCI_2 Compost tea CT_GALLUCCI_2 ['MGYS00002681'] Amplicon
ERS2625738 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625738 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805828 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_HANENZY_2 Compost tea CT_HANENZY_2 ['MGYS00002681'] Amplicon
ERS2625734 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625734 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805824 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_CATTANEO_2 Compost tea CT_CATTANEO_2 ['MGYS00002681'] Amplicon
ERS2625742 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625742 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805832 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_SPADOLA_2 Compost tea CT_SPADOLA_2 ['MGYS00002681'] Amplicon
ERS2625723 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625723 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805813 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 3-3 Teku kana tek 3-3 ['MGYS00002681'] Amplicon
ERS2625735 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625735 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805825 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_CATTANEO_3 Compost tea CT_CATTANEO_3 ['MGYS00002681'] Amplicon
ERS2625725 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625725 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805815 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 4-1 Teku kana tek 4-1 ['MGYS00002681'] Amplicon
ERS2625731 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625731 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805821 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 9-3 Teku kana tek 9-3 ['MGYS00002681'] Amplicon
ERS2625753 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625753 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805843 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n4 c Litter Litter n4 c ['MGYS00002681'] Amplicon
ERS2625744 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625744 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805834 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_SPADOLA_4 Compost tea CT_SPADOLA_4 ['MGYS00002681'] Amplicon
ERS2625750 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625750 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805840 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n3 b Litter Litter n3 b ['MGYS00002681'] Amplicon
ERS2625721 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625721 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805811 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 3-1 Teku kana tek 3-1 ['MGYS00002681'] Amplicon
ERS2625729 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625729 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805819 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 9-1 Teku kana tek 9-1 ['MGYS00002681'] Amplicon
ERS2625756 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625756 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805846 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n9 b Litter Litter n9 b ['MGYS00002681'] Amplicon
ERS2625751 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625751 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805841 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n4 a Litter Litter n4 a ['MGYS00002681'] Amplicon
ERS2625730 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625730 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805820 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 9-2 Teku kana tek 9-2 ['MGYS00002681'] Amplicon
ERS2625740 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625740 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805830 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_HANENZY_4 Compost tea CT_HANENZY_4 ['MGYS00002681'] Amplicon
ERS2625755 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625755 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805845 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n9 a Litter Litter n9 a ['MGYS00002681'] Amplicon
ERS2625726 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625726 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805816 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 4-2 Teku kana tek 4-2 ['MGYS00002681'] Amplicon
ERS2625749 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625749 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805839 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n3 a Litter Litter n3 a ['MGYS00002681'] Amplicon
ERS2625754 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625754 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805844 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n4 d Litter Litter n4 d ['MGYS00002681'] Amplicon
ERS2625752 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625752 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805842 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n4 b Litter Litter n4 b ['MGYS00002681'] Amplicon
ERS2625743 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625743 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805833 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_SPADOLA_3 Compost tea CT_SPADOLA_3 ['MGYS00002681'] Amplicon
ERS2625748 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625748 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805838 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_GALLUCCI_4 Compost tea CT_GALLUCCI_4 ['MGYS00002681'] Amplicon
ERS2625745 2018-01-01/2018-12-31 0.0 Compost tea Compost tea Compost soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625745 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805835 2018-01-01 Compost tea Compost tea Compost Italy 2018-07-30T09:16:20 40.6493 14.8922 CT_GALLUCCI_1 Compost tea CT_GALLUCCI_1 ['MGYS00002681'] Amplicon
ERS2625727 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625727 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805817 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 4-3 Teku kana tek 4-3 ['MGYS00002681'] Amplicon
ERS2625722 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625722 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805812 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 3-2 Teku kana tek 3-2 ['MGYS00002681'] Amplicon
ERS2625760 2018-01-01/2018-12-31 0.0 Soil forest Litter Litter soil Italy 40.64934 14.892231 Illumina MiSeq metagenome ERS2625760 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805850 2018-01-01 Soil forest Litter Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 Litter n3 d Litter Litter n3 d ['MGYS00002681'] Amplicon
ERS2625724 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625724 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805814 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 3-4 Teku kana tek 3-4 ['MGYS00002681'] Amplicon
ERS2625728 2018-01-01/2018-12-31 0.0 Teku kana Teku kana Litter soil Italy 40.649334 14.892222 Illumina MiSeq metagenome ERS2625728 2018-07-30 root:Engineered:Solid waste:Composting SAMEA4805818 2018-01-01 Teku kana Teku kana Litter Italy 2018-07-30T09:16:20 40.6493 14.8922 tek 4-4 Teku kana tek 4-4 ['MGYS00002681'] Amplicon
Loading