{"push_id":908810734,"size":36,"distinct_size":3,"ref":"refs/heads/experimental/lincRNA_dev","head":"914fe5751a937e583294ff451d60e3f517f8aae3","before":"1d690c835f3b1dae1497fbbb8a139315e9ae8ccc","commits":[{"sha":"471776749a6008cad8cff89f9dbadffd26769828","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to Hive_build_geneset_conf.pm\nPut in the allowed_input_sets parameter, which is needed by the clustering module to tell which genes to take from the input dbs. Also put in the single_exon_support_penalty parameter, which is how much is needed to add on to the support threshold in the case of single exon genes","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/471776749a6008cad8cff89f9dbadffd26769828"},{"sha":"c92a5b26516e67ef12edd7032c10fb6757507c3f","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveClusterSourceGenes.pm\nAdded in some code to work with cluster slices, to be used in cases where the location of a cluster has been predetermined. There are some issues with this at the moment, as test cases show more genes are being made than expected. Porbably due to the existence of sub clusters, as the API fetches the genes on overlap of the cluster slice so sub cluster genes are probably getting represented twice. Committing now anyway, but may remove later and instead just work with gene ids directly","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/c92a5b26516e67ef12edd7032c10fb6757507c3f"},{"sha":"38cef69241268bf28fee3db4318c57a15842b692","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveProcessGeneClusters.pm\nAdded in a bunch of code related to dealing with single exon genes in addition to some code to recluster the final set of candidate transcripts for any gene that is being output. The reason is that the candidate transcripts may no longer be fully connnected and a reclustering is needed to build the final set of gene models","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/38cef69241268bf28fee3db4318c57a15842b692"},{"sha":"615cf1c79133d8a2f1baf7ae007ba34d58019360","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveSubmitAnalysis.pm\nAdded in code to make this generate cluster slice style ids. It works by taking in a slice as input (usually toplevel) and then clustering all the genes on that slice. After clustering it goes through the clustered and unlcustered list and makes output ids defined by the borders of the slice. The output ids look like normal slice ids, with the expception that a 7th column is added, which contains the strand the cluster is on. I could have simple used the strand column already present in the slice, however if I had done that then there would be a risk of the code behaving in unexpected ways. This way any code that expects a cluster slice will have to parse out the regular slice and the strand explicitly, while code not designed to run on cluster slices will fail if they get one","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/615cf1c79133d8a2f1baf7ae007ba34d58019360"},{"sha":"da38f49594acaf08b24ce16125eaa101bd6aa4ee","author":{"email":"ab5e2bca84933118bbc9d48ffaccce3bac4eeb64@ebi.ac.uk","name":"Carlos"},"message":"Create output dir as part of the reports dir creation.","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/da38f49594acaf08b24ce16125eaa101bd6aa4ee"},{"sha":"e1e73c96566c3710bfd618d2e0e95db4261c62bc","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created HiveAugustus.pm\nThe module isn't fully working yet, but it is an initial conversion of the RunnableDB to hive","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/e1e73c96566c3710bfd618d2e0e95db4261c62bc"},{"sha":"ab82c911d14acc4693435e6431e7cf5daa36200d","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveDownloadUniProtFiles.pm\nAdded in a change to allow the use of an array ref for excluding multiple taxon ids","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/ab82c911d14acc4693435e6431e7cf5daa36200d"},{"sha":"9b32292497e6e28a95681b90d9bb609f4c24c09f","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveExonerate2Genes.pm\nAdded in some code to allow a feature region id to be passed in as an input id. Basically this allows a slice with an accession stuck on to the end of it to be passed in and then parsed. With the slice and the accession, a temporary query file and temporary db file based on the accession and the slice are created and exonerate is run on a drastically reduced search space ala genewise. This allows for large numbers of models be be created in a matter of minutes","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/9b32292497e6e28a95681b90d9bb609f4c24c09f"},{"sha":"a8e3aab88e2380b3576c421cb94f5d7a41898e06","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveGenBlast.pm\nChange to the supporting feature code to deal with exons of less than 3bp in length or 3bp exons that are not a complete codon. The API can't handle split codons, so don't make a supporting feature in the case of only having split codons on an exon","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/a8e3aab88e2380b3576c421cb94f5d7a41898e06"},{"sha":"37093cb26d73d6dbea352da8a7754b210d6cbee0","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveLoadSeqsPipeDB.pm\nJust changed it so that if you are outputting accessions as input ids for downstream analyses directly, then these are sent out as an array ref and not a string","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/37093cb26d73d6dbea352da8a7754b210d6cbee0"},{"sha":"860aba59f8f2377c1f6f01c2ac1bb8173330c5ba","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveSubmitAnalysis.pm\nAdded in code to generate feature region ids. At the moment this works for genes, you specify a set of logic names and it will get all the genes. Then it looks at each gene, gets the coordinates and pads them with a specified amount (default is 10000). It makes a slice id based on the seq region. Then it gets the supporting features of the gene and extracts the hit name of each. It then sticks this onto the slice and outputs all unique slice/accession combos. This was designed with things like exonerate and genblast in mind, where the supporting evidence is just a single uniprot accession, so it will probably need to be expanded in future. Also added code for rechunking arrays of uniprot accessions. So if you run something like genblast on an array of accessions and it fails on a run limit you can pass in the array and it will output the individual accessions as new jobs.","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/860aba59f8f2377c1f6f01c2ac1bb8173330c5ba"},{"sha":"4dee93a288a0b9f82bedf6a939b9eb8ea913dadf","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created Hive_rodent_basic_conf.pm\nMade a rodent specific config. I have already changed this quite a bit during testing, so this is not as up to date as it could be. Essentially just a placeholder for now","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/4dee93a288a0b9f82bedf6a939b9eb8ea913dadf"},{"sha":"c69d6449e6951f077e64c36a829d49ac44a739a4","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveSubmitAnalysis.pm\nAdded in the feature strand to the output id.","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/c69d6449e6951f077e64c36a829d49ac44a739a4"},{"sha":"f9438ab1286ff94d2b02780c4b2fc510410fbe1d","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Created HiveGenewise.pm\nThis module is designed to run genewise based on an input id. At the moment this works off a feature region style input id, where it has a stranded slice and the hit name appended onto the end. It then runs genewise in that region. This worked on about 2/3 thirds of my test set but failed due to issues with feature pair lengths. I've decided to now change it so that I run Minigenewise instead of genewise and the input id will be a gene (say a genblast model), and the module will take the gene, get the supporting feature(s) and retrieve the corresponding proteins, then make a miniseq and align. This commit is to make sure I have a copy of the code before I change it to do this","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/f9438ab1286ff94d2b02780c4b2fc510410fbe1d"},{"sha":"e6a30bf07d6b1c89370be8dced3070ea81247c9f","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveExonerate2Genes.pm\nAdded some code to use the pid in the naming of the output file and also to handle multiple output files to delete (like when making a query file from a seq and making a db from a slice)","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/e6a30bf07d6b1c89370be8dced3070ea81247c9f"},{"sha":"5d3e304c1e12fb4c3ab4f94300760b9534a93158","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveGenBlast.pm\nAdded code to properly handle the rank of a transcript. Now this can be set to allow several transcripts to be returned for each query. Also now handles coverage and pid values that are stored directly on the transcript.","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/5d3e304c1e12fb4c3ab4f94300760b9534a93158"},{"sha":"de29f24feebcbe5ab14fd2c8e6c1a5641ea8d96d","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveGenewise.pm\nAdded code to make this work as minigenewise, since it's not working properly by using genewise directly. Now takes a transcript id from an input db as an input id. Then loads the transcript and extracts the supporting features, which act as the seed region for genewise","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/de29f24feebcbe5ab14fd2c8e6c1a5641ea8d96d"},{"sha":"1c2356a10c882969d4dc9f5b049fac0a00833356","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveSubmitAnalysis.pm\nAdded a new type, feature_id. Basically you ask for a feature type (transcript at the moment) and provide an input db and set of logic names and this will extract all the db ids for the features and output them as input ids for other jobs. Will probably extend in the future and add batching","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/1c2356a10c882969d4dc9f5b049fac0a00833356"},{"sha":"aaf28effaf40b4f401b4aeac0d64a06477c3a49b","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to GenBlastGene.pm\nAdded code to work with a max rank value to determine how many possibly transcripts to return. Also added in code to take in a percent identity from the runnabledb, this is used to post filter the transcripts. Anything not matching the pid will be removed","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/aaf28effaf40b4f401b4aeac0d64a06477c3a49b"},{"sha":"bdf67d76fc5508fbcb4ebc3a70b74f6ce588e822","author":{"email":"aa5ef0a84f95a8b352d9bda81a0c8ef099dcb88a@ebi.ac.uk","name":"fergalmartin"},"message":"Change to HiveGenBlast.pm\nPut in some code to empty the gene object before storing as there were some weird caching issues with the api. Disabled the supporting feature code (which I will soon remove) as I rewrote it from scratch and moved it to the runnable. Changed the way the logic name is set for entries that are not best in genome. Don't think this was actually needed, the issue I changed it for may have been a side effect of the caching issue","distinct":false,"url":"https://api.github.com/repos/Ensembl/ensembl-analysis/commits/bdf67d76fc5508fbcb4ebc3a70b74f6ce588e822"}]}