{"action":"created","issue":{"url":"https://api.github.com/repos/meren/MED-Paper-Figure-6/issues/1","labels_url":"https://api.github.com/repos/meren/MED-Paper-Figure-6/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/meren/MED-Paper-Figure-6/issues/1/comments","events_url":"https://api.github.com/repos/meren/MED-Paper-Figure-6/issues/1/events","html_url":"https://github.com/meren/MED-Paper-Figure-6/issues/1","id":56125914,"number":1,"title":"Couple of small things","user":{"login":"neavemj","id":6932679,"avatar_url":"https://avatars.githubusercontent.com/u/6932679?v=3","gravatar_id":"","url":"https://api.github.com/users/neavemj","html_url":"https://github.com/neavemj","followers_url":"https://api.github.com/users/neavemj/followers","following_url":"https://api.github.com/users/neavemj/following{/other_user}","gists_url":"https://api.github.com/users/neavemj/gists{/gist_id}","starred_url":"https://api.github.com/users/neavemj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/neavemj/subscriptions","organizations_url":"https://api.github.com/users/neavemj/orgs","repos_url":"https://api.github.com/users/neavemj/repos","events_url":"https://api.github.com/users/neavemj/events{/privacy}","received_events_url":"https://api.github.com/users/neavemj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-01-31T14:06:02Z","updated_at":"2015-01-31T17:27:31Z","closed_at":null,"body":"Hi Meren! \r\n\r\nThanks again for these - I got it working on my dataset. I made a few changes that I thought you might be interested in:\r\n\r\n02_gen_MED_dict.py, line 39. \r\n\r\nThis line takes the header of the MED nodes, splits it by the pipe character '|' and takes the read ID as the first item. However, my MED output is in the format \">sample_readID\". So I changed this to split by '_' and take the second item as read ID. \r\n\r\nAlso, many of my read IDs (Illumina MiSeq) contain the '_' character so I had to sed these out to get it to run with MED, this then caused a key mismatch in the dictionaries. Fixed by changing the headers across all data sets. \r\n\r\n03_generate_heirarchy.py, line 10.\r\n\r\nThis line opens a file called '02_MED_nodes_by_freq.txt'. However, this doesn't appear to be created by the previous scripts. I thought that perhaps this is supposed to be the file with my nodes of interest - once changed it seemed to work ok. Is this correct?\r\n\r\nIf you're interested I also wrote a small python script to take a mothur 'bin.seqs' fasta file and turn it into a file similar to the output from Qiime's pick_otus.py, so mothur users can also use this pipeline.\r\n\r\nThanks again for this - diagram looks great!\r\n\r\nBest,\r\n\r\nMatt.\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/meren/MED-Paper-Figure-6/issues/comments/72327000","html_url":"https://github.com/meren/MED-Paper-Figure-6/issues/1#issuecomment-72327000","issue_url":"https://api.github.com/repos/meren/MED-Paper-Figure-6/issues/1","id":72327000,"user":{"login":"meren","id":197307,"avatar_url":"https://avatars.githubusercontent.com/u/197307?v=3","gravatar_id":"","url":"https://api.github.com/users/meren","html_url":"https://github.com/meren","followers_url":"https://api.github.com/users/meren/followers","following_url":"https://api.github.com/users/meren/following{/other_user}","gists_url":"https://api.github.com/users/meren/gists{/gist_id}","starred_url":"https://api.github.com/users/meren/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/meren/subscriptions","organizations_url":"https://api.github.com/users/meren/orgs","repos_url":"https://api.github.com/users/meren/repos","events_url":"https://api.github.com/users/meren/events{/privacy}","received_events_url":"https://api.github.com/users/meren/received_events","type":"User","site_admin":false},"created_at":"2015-01-31T17:27:31Z","updated_at":"2015-01-31T17:27:31Z","body":"Regarding the first point you made about \"02_gen_MED_dict.py, line 39\", my FASTA headers looked like this:\r\n\r\n    >158114885SUPP_GDNSLZP02JZXOX|Corynebacteriaceae;Corynebacterium\r\n    AGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCA(...)\r\n    >158114885SV_GDNSLZP02F0DICorynebacteriaceae;Corynebacterium\r\n    AGACTGGAATTCCTGGTGTAGCGGTGGAATGCGCAGATATCA(...)\r\n    >158114885SV_GDNSLZP02F25ZZ|Actinomycetaceae;Actinomyces\r\n    AGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCA(...)\r\n\r\nWhat that line tries to get is the '**158114885SUPP_GDNSLZP02JZXOX**' part. Read ID is the entire thing (which corresponds to sample_readID in your example)\r\n\r\nI hope this makes sense.\r\n\r\n\r\nThanks again,\r\n"}}