{"action":"opened","issue":{"url":"https://api.github.com/repos/cjfields/redmine-test/issues/79","labels_url":"https://api.github.com/repos/cjfields/redmine-test/issues/79/labels{/name}","comments_url":"https://api.github.com/repos/cjfields/redmine-test/issues/79/comments","events_url":"https://api.github.com/repos/cjfields/redmine-test/issues/79/events","html_url":"https://github.com/cjfields/redmine-test/issues/79","id":108470444,"number":79,"title":"AlignIO MSF writing","user":{"login":"cjfields","id":49265,"avatar_url":"https://avatars.githubusercontent.com/u/49265?v=3","gravatar_id":"","url":"https://api.github.com/users/cjfields","html_url":"https://github.com/cjfields","followers_url":"https://api.github.com/users/cjfields/followers","following_url":"https://api.github.com/users/cjfields/following{/other_user}","gists_url":"https://api.github.com/users/cjfields/gists{/gist_id}","starred_url":"https://api.github.com/users/cjfields/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjfields/subscriptions","organizations_url":"https://api.github.com/users/cjfields/orgs","repos_url":"https://api.github.com/users/cjfields/repos","events_url":"https://api.github.com/users/cjfields/events{/privacy}","received_events_url":"https://api.github.com/users/cjfields/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Category:%20Core%20Components","name":"Category: Core Components","color":"006699"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Priority:%20Normal","name":"Priority: Normal","color":"666600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Status:%20New","name":"Status: New","color":"FF6600"},{"url":"https://api.github.com/repos/cjfields/redmine-test/labels/Tracker:%20Bug","name":"Tracker: Bug","color":"FF0000"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-09-26T14:27:56Z","updated_at":"2015-09-26T14:27:56Z","closed_at":null,"body":"---\n\n\nAuthor Name: **Bernd W** (Bernd W)\nOriginal Redmine Issue: 3299, https://redmine.open-bio.org/issues/3299\nOriginal Date: 2011-10-04\nOriginal Assignee: Bioperl Guts\n\n---\n\nHi\n\nBioperl describes the MSF format: http://www.bioperl.org/wiki/MSF\\_multiple\\_alignment\\_format\nI found that writing MSF (version 1.5.2 to 1.61 and bioperl-live is different from this description.\nI am not sure what is all allowed in MSF, but the header is written like this:\n $self-\\>\\_print (sprintf(“\\\\n%s MSF: %d Type: %s %s Check: 00 ..\\\\n\\\\n”,\n $name, $aln-\\>num\\_sequences, $type, $date));\n\nThis means that we get lines like this:\nNoName MSF: 3 Type: P Tue Oct 4 21:34:51 2011 Check: 00 ..\n\nHowever, after MSF there should be the length, as in the Len: field.\nIn other descriptions I do find the alignment name preceding the MSF: and sometimes also column numbering as is written by BioPerl:\n\n1 50\nCYS1\\_DICDI/1-343 ——~~MKVIL LFVLAVFTVF VSS———~~ ————RG IPPEEQ——\nALEU\\_HORVU/1-362 MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG\nCATH\\_HUMAN/1-335 ———MWAT LPLLCAGAWL LGV———- -PVCGAAELS VNSLEK——\n\nHowever, most format description i see do not have numbers and alignment names.\nSee e.g.\nhttp://www.ebi.ac.uk/help/formats.html\\#MSF\nbut also http://tcoffee.vital-it.ch/Doc/doc3.html\nand http://bmerc-www.bu.edu/examples/output/seqlist.msf.html\n\nIn any case it seems that $aln-\\>num\\_sequences, is wrong and should be $aln-\\>length\n\n\n\n\n"}}