{"action":"opened","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/2059","labels_url":"https://api.github.com/repos/biocore/qiime/issues/2059/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/2059/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/2059/events","html_url":"https://github.com/biocore/qiime/issues/2059","id":95655887,"number":2059,"title":"single_rarefaction.py bug?","user":{"login":"jtremblay","id":1168411,"avatar_url":"https://avatars.githubusercontent.com/u/1168411?v=3","gravatar_id":"","url":"https://api.github.com/users/jtremblay","html_url":"https://github.com/jtremblay","followers_url":"https://api.github.com/users/jtremblay/followers","following_url":"https://api.github.com/users/jtremblay/following{/other_user}","gists_url":"https://api.github.com/users/jtremblay/gists{/gist_id}","starred_url":"https://api.github.com/users/jtremblay/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jtremblay/subscriptions","organizations_url":"https://api.github.com/users/jtremblay/orgs","repos_url":"https://api.github.com/users/jtremblay/repos","events_url":"https://api.github.com/users/jtremblay/events{/privacy}","received_events_url":"https://api.github.com/users/jtremblay/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-07-17T13:24:58Z","updated_at":"2015-07-17T13:24:58Z","closed_at":null,"body":"Dear Qiime devs,\r\nWith the following command:\r\n```\r\nsingle_rarefaction.py -i otu_table.biom -o otu_table_rarefied.biom -d 1000\r\n```\r\nI get a biom table for which taxonomy lineages are not written appropriately in output hdf5 biom table. For instance the lineage I have for otu_table.biom is like this for a given OTU:\r\n```\r\n GROUP \"metadata\" {\r\n         DATASET \"taxonomy\" {\r\n            DATATYPE  H5T_STRING {\r\n               STRSIZE H5T_VARIABLE;\r\n               STRPAD H5T_STR_NULLTERM;\r\n               CSET H5T_CSET_ASCII;\r\n               CTYPE H5T_C_S1;\r\n            }     \r\n            DATASPACE  SIMPLE { ( 999, 148 ) / ( 999, 148 ) }\r\n            DATA {\r\n            (0,0): \"k__Eukaryota\", \"p__Streptophyta\", \"c__Liliopsida\",\r\n            (0,3): \"o__Poales\", \"f__Poaceae\", \"g__Zea\", \"s__Zea mays\", \"\",\r\n\r\n```\r\n\r\nAnd like this with the rarefied table:\r\n```\r\n GROUP \"metadata\" {\r\n         DATASET \"taxonomy\" {\r\n            DATATYPE  H5T_STRING {\r\n               STRSIZE H5T_VARIABLE;\r\n               STRPAD H5T_STR_NULLTERM;\r\n               CSET H5T_CSET_ASCII;\r\n               CTYPE H5T_C_S1;\r\n            }    \r\n            DATASPACE  SIMPLE { ( 997, 7 ) / ( 997, 7 ) }\r\n            DATA {\r\n            (0,0): \"['k__Eukaryota' 'p__Streptophyta' 'c__Liliopsida' 'o__Poales' 'f__Poaceae'\r\n            'g__Zea' 's__Zea mays']\",\r\n```\r\nWhen I convert back otu_table_rarefied.biom to otu_table_rarefied.tsv with:\r\n```\r\n biom convert -i otu_table_rarefied.biom -o otu_table_rarefied.tsv --table-type 'OTU table' --to-tsv --output-metadata-id='taxonomy' --header-key='taxonomy'\r\n```\r\nI get line returns and brackets in taxonomic lineages in my tsv otu table:\r\n```\r\n['k__Eukaryota' 'p__Streptophyta' 'c__Liliopsida' 'o__Poales' 'f__Poaceae'$\r\n 'g__Zea' 's__Zea mays']\r\n```\r\nConverting back and forth otu_table.tsv > otu_table.biom > otu_table.tsv is working fine, so I don't think this is a converting issue.\r\n\r\nCheers,"}}