{"action":"closed","issue":{"url":"https://api.github.com/repos/dereneaton/ipyrad/issues/41","labels_url":"https://api.github.com/repos/dereneaton/ipyrad/issues/41/labels{/name}","comments_url":"https://api.github.com/repos/dereneaton/ipyrad/issues/41/comments","events_url":"https://api.github.com/repos/dereneaton/ipyrad/issues/41/events","html_url":"https://github.com/dereneaton/ipyrad/issues/41","id":124879873,"number":41,"title":"Step7 - progress tix","user":{"login":"isaacovercast","id":5974975,"avatar_url":"https://avatars.githubusercontent.com/u/5974975?v=3","gravatar_id":"","url":"https://api.github.com/users/isaacovercast","html_url":"https://github.com/isaacovercast","followers_url":"https://api.github.com/users/isaacovercast/followers","following_url":"https://api.github.com/users/isaacovercast/following{/other_user}","gists_url":"https://api.github.com/users/isaacovercast/gists{/gist_id}","starred_url":"https://api.github.com/users/isaacovercast/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/isaacovercast/subscriptions","organizations_url":"https://api.github.com/users/isaacovercast/orgs","repos_url":"https://api.github.com/users/isaacovercast/repos","events_url":"https://api.github.com/users/isaacovercast/events{/privacy}","received_events_url":"https://api.github.com/users/isaacovercast/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-01-05T02:03:44Z","updated_at":"2016-01-11T18:18:56Z","closed_at":"2016-01-11T18:18:56Z","body":"notes on progress for step7 just to keep my head straight. Here \"fixed\" means assemble.write_outfiles.make_outfiles() has a function to call this, and the concordant file_conversion/loci2*.py file has been mod'd to suit.\r\n\r\n- loci2phynex: fixed, needs testing\r\n- loci2gphocs: ~~not~~ fixed, needs testing\r\n- loci2SNP: ~~not~~ fixed, needs testing (also needs to resolve the 'seed' issue)\r\n- loci2mig: ~~not~~ fixed, needs testing\r\n- loci2treemix: ~~not~~ fixed, needs testing\r\n- loci2vcf: ~~not~~ fixed, needs testing\r\n\r\n~~Treemix relies on .usnps already being output. Maybe .snps/.usnps can be included in the \"always output\" category with .loci/.alleles/.vcf. Part of me just wants to write all possible output formats to the outfiles/ directory and just not ask, might save a lot of coding heartache for the cost of a few handfuls of cycles.~~ I updated the loci2treemix.make() function to test for .usnps file, if it doesn't find it it calls loci2SNP to make it, if _that_ fails, then it bails out."}}