https://sourceforge.net/p/snowyowl/activity/Recent activity for SnowyOwlenFri, 12 May 2017 14:36:16 -0000https://sourceforge.nethttps%3A//sourceforge.net/projects/snowyowl/files/SnowyOwl_2.1.0.tar.gz/downloadSnowyOwlFri, 12 May 2017 14:36:16 -0000https://sourceforge.net/projects/snowyowl/files/SnowyOwl_2.1.0.tar.gz/downloadhttps://sourceforge.net/p/snowyowl/code/ci/99a609e36ae3003d36a853f03a38663e0c7217f7/Converted and debugged SnowyOwl to use strand-specific RNA-Seq dataIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/99a609e36ae3003d36a853f03a38663e0c7217f7/https://sourceforge.net/p/snowyowl/code/ci/3c500a067e9c475d0b073f55b42d6adb600cdcd7/Fixed "Coordinate out of range error" in find_longest_ORFs.pyIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/3c500a067e9c475d0b073f55b42d6adb600cdcd7/https://sourceforge.net/p/snowyowl/code/ci/0fd11ec811671dd5d26b5897c23d6eed65e57149/Merge remote-tracking branch 'origin/strand_specific' into strand_specificIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/0fd11ec811671dd5d26b5897c23d6eed65e57149/https://sourceforge.net/p/snowyowl/code/ci/19f3c32413f2319e108e78f2001e55cbc4eb8cc1/Removed stray importIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/19f3c32413f2319e108e78f2001e55cbc4eb8cc1/https://sourceforge.net/p/snowyowl/code/ci/5dcd4f0992e1d6971f590ee1c97f2244855bc1cb/Merge branch 'direct_training' of compute2.fungalgenomics.ca:GIT/SnowyOwl into direct_trainingIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/5dcd4f0992e1d6971f590ee1c97f2244855bc1cb/https://sourceforge.net/p/snowyowl/code/ci/9dbe1c9c3559b0c31823fcbbf987993908dc8ee6/debugged GFF3mRNA.addExonIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/9dbe1c9c3559b0c31823fcbbf987993908dc8ee6/https://sourceforge.net/p/snowyowl/code/ci/17296d684e08d33711f41f86c4e1b92646ceb958/Added test for TrainingModels type to check_project_filesIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/17296d684e08d33711f41f86c4e1b92646ceb958/https://sourceforge.net/p/snowyowl/code/ci/c5011cce04475084fcbb05f27920f3e5f4fee910/Changed External_Training_Set.gb to Consensus_Training_set.gb for compatibility with file dependenciesIanFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/c5011cce04475084fcbb05f27920f3e5f4fee910/https://sourceforge.net/p/snowyowl/code/ci/7cd30eb737dbfcc27cc73ca0d5c4722efa057cab/Removed extra . from protein filenames in task_Complete_Score_Splice_hinted_Augustus_models_Software_BlastIanFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/7cd30eb737dbfcc27cc73ca0d5c4722efa057cab/https://sourceforge.net/p/snowyowl/code/ci/8b5d3f8a90f56de837ffe57a012c61eaf9f7445e/Modified simplifyIDs.py to give unique IDs to exonsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/8b5d3f8a90f56de837ffe57a012c61eaf9f7445e/https://sourceforge.net/p/snowyowl/code/ci/b479e63955802cbd7e0524dbf191da02e2447da7/Fixed conflicts between transcript and exon boundsIanFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/b479e63955802cbd7e0524dbf191da02e2447da7/https://sourceforge.net/p/snowyowl/code/ci/4afa271b127058adaed6059dcd0bb75b5da67ff4/Fixed bug in scoring of bogus intronsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/4afa271b127058adaed6059dcd0bb75b5da67ff4/https://sourceforge.net/p/snowyowl/code/ci/beb2ee8bb1f0062cec9826c076664aaf46f7d83a/Fixed mistaken mergeian_reidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/beb2ee8bb1f0062cec9826c076664aaf46f7d83a/https://sourceforge.net/p/snowyowl/code/ci/309bb75e6e57c51c3388542bb1fa5697341c8242/Fixed conflicts between transcript and exon boundsIanFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/309bb75e6e57c51c3388542bb1fa5697341c8242/https://sourceforge.net/p/snowyowl/code/ci/623698a40cb7d0570ad52cc9c943ba3f5b4fbffc/Bump version to 2.1.0Ian ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/623698a40cb7d0570ad52cc9c943ba3f5b4fbffc/https://sourceforge.net/p/snowyowl/code/ci/6f279ac5c94ec3e4d0c453011ab4757c7413cf41/Modified task_Blat_hits_to_hints to switch sign of hints files relative to blat alignmentsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/6f279ac5c94ec3e4d0c453011ab4757c7413cf41/https://sourceforge.net/p/snowyowl/code/ci/48ab9a717fd2bbb0bfee5d7279710cef871d9c27/Debugged merge_strand_representatives and pool_gene_modelsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/48ab9a717fd2bbb0bfee5d7279710cef871d9c27/https://sourceforge.net/p/snowyowl/code/ci/3acec3b99d4d221ae2a4a25a2646508a4ef5f9a4/Added docstrings from master branchIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/3acec3b99d4d221ae2a4a25a2646508a4ef5f9a4/https://sourceforge.net/p/snowyowl/code/ci/97a9ab3761f41a41442cad0b732470b2d9678a4b/Accept 3-field coverage profiles from samtools depthIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/97a9ab3761f41a41442cad0b732470b2d9678a4b/https://sourceforge.net/p/snowyowl/code/ci/bfdf52d86be1c2814b3b50deab245823c5a72c9f/Merge branch 'strand_specific' of /home/ian_reid/GIT/SnowyOwl into strand_specifician_reidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/bfdf52d86be1c2814b3b50deab245823c5a72c9f/https://sourceforge.net/p/snowyowl/code/ci/37308eb122b41615ed6a86940488d798a97aaf49/moved AugustusConfigParser code inside run_ss_SnowyOwlIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/37308eb122b41615ed6a86940488d798a97aaf49/https://sourceforge.net/p/snowyowl/code/ci/b182dfe45da7b41de987bdf2ac23cf599454047f/Started converting SnowyOwl to use strand-specific RNA-Seq dataIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/b182dfe45da7b41de987bdf2ac23cf599454047f/https://sourceforge.net/p/snowyowl/code/ci/9dbe1c9c3559b0c31823fcbbf987993908dc8ee6/debugged GFF3mRNA.addExonIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/9dbe1c9c3559b0c31823fcbbf987993908dc8ee6/https://sourceforge.net/p/snowyowl/code/ci/0fd11ec811671dd5d26b5897c23d6eed65e57149/Merge remote-tracking branch 'origin/strand_specific' into strand_specificIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/0fd11ec811671dd5d26b5897c23d6eed65e57149/https://sourceforge.net/p/snowyowl/code/ci/3eabed6913f935bcd7553a7b9de17f39e122f73f/Modified islands2genes.py to force --singlestrand to False for strand-specific predictionsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/3eabed6913f935bcd7553a7b9de17f39e122f73f/https://sourceforge.net/p/snowyowl/code/ci/2d666220f1015378122c3e568a699af48d7a5995/Fixed setting of stopCodonExcludedFromCDSIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/2d666220f1015378122c3e568a699af48d7a5995/https://sourceforge.net/p/snowyowl/code/ci/759e25f42d9ce1abb76d0e0938d06ecfeed75dfc/Merge branch 'direct_training' into strand_specificIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/759e25f42d9ce1abb76d0e0938d06ecfeed75dfc/https://sourceforge.net/p/snowyowl/code/ci/715501298e8f54dfd54954d8ca51a70ce0d72509/Modified score_models.py to taper required coverage at transcript endsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/715501298e8f54dfd54954d8ca51a70ce0d72509/https://sourceforge.net/p/snowyowl/code/ci/7180f7254db19b764eb413830cccebfedf09fae4/Fixed conflicts between transcript and exon boundsIanFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/7180f7254db19b764eb413830cccebfedf09fae4/https://sourceforge.net/p/snowyowl/code/ci/d714ae096a5e0946346a15719d8482a3be5bcbd8/Wrapped GFF3Record.__init__() in try block in gff3Iterator,genes() to avoid abort on strange input lineian_reidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/d714ae096a5e0946346a15719d8482a3be5bcbd8/https://sourceforge.net/p/snowyowl/code/ci/bb02e255f2b37aac8a897917f94060258847547d/Added test for existence of non-empty files to task_Complete_Score_Augustus_ModelsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/bb02e255f2b37aac8a897917f94060258847547d/https://sourceforge.net/p/snowyowl/code/ci/e97ed58c02ce157e8ef84e2b9a34b5cc2db176d6/Removed extra . from filenames in task_Complete_Score_Splice_hinted_Augustus_modelsIanFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/e97ed58c02ce157e8ef84e2b9a34b5cc2db176d6/https://sourceforge.net/p/snowyowl/code/ci/507ce104b3395998d23ce410e967dc1c6bf9c4d4/Changes to help avoid redoing tasks when SnowyOwl restartsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/507ce104b3395998d23ce410e967dc1c6bf9c4d4/https://sourceforge.net/p/snowyowl/code/ci/af7f352061f1e14c279c3aede5c43b58be6a2830/Changed Alias stringIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/af7f352061f1e14c279c3aede5c43b58be6a2830/https://sourceforge.net/p/snowyowl/code/ci/b75e6b4fcd50e94873e452e51c7fc86193d863c3/Eliminated redundant re-addition of exons to transcriptsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/b75e6b4fcd50e94873e452e51c7fc86193d863c3/https://sourceforge.net/p/snowyowl/code/ci/e42ddae31929196223ebcc8ca13995a5aae0e6ca/Re-enabled score checking in score_models.check_exons_vs_splicesian_reidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/e42ddae31929196223ebcc8ca13995a5aae0e6ca/https://sourceforge.net/p/snowyowl/code/ci/169109ed033dffdfb11673c017c45b0faebe2e32/Corrected strand assignment in task_Blat_hits_to_hintsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/169109ed033dffdfb11673c017c45b0faebe2e32/https://sourceforge.net/p/snowyowl/code/ci/9397a03d8dbf6299978be7a8e1231d211659f8ee/Run Genemark even when TrainingModels are ExternalIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/9397a03d8dbf6299978be7a8e1231d211659f8ee/https://sourceforge.net/p/snowyowl/code/ci/b3a683ea0134272895905e261a41714bc352817f/Check that stopCodonExcludedFromCDS is set correctlyIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/b3a683ea0134272895905e261a41714bc352817f/https://sourceforge.net/p/snowyowl/code/ci/03b2cdc03dc22f576f3f3259fc97353948a8263e/Corrected failure to set status in transcripts with intron errorsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/03b2cdc03dc22f576f3f3259fc97353948a8263e/https://sourceforge.net/p/snowyowl/code/ci/36c60f3ce2d35372e8bbc5a735da7cd86b159081/Created direct_training branch of SnowyOwl_ssIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/36c60f3ce2d35372e8bbc5a735da7cd86b159081/https://sourceforge.net/p/snowyowl/code/ci/d2a189907763efc38038e1778cbb44b01b2267a8/Ensure that low_start and low_end have defined values in score_models.pyIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/d2a189907763efc38038e1778cbb44b01b2267a8/https://sourceforge.net/p/snowyowl/code/ci/e521fa936e2e5419dfad47361094d77af4ba3c55/Correct failure to set status in transcripts with intron errorsIan ReidFri, 12 May 2017 14:12:19 -0000https://sourceforge.net/p/snowyowl/code/ci/e521fa936e2e5419dfad47361094d77af4ba3c55/https://sourceforge.nethttp%3A//sourceforge.net/projects/snowyowl/files/SnowyOwl-2.0.4.tar.gz/downloadSnowyOwlWed, 01 Oct 2014 14:50:03 -0000http://sourceforge.net/projects/snowyowl/files/SnowyOwl-2.0.4.tar.gz/downloadhttps://sourceforge.net/p/snowyowl/code/ci/903dd2bafb387c8060b3ed1013188af41cc6c011/Added diagnostics for version and import errorsIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/903dd2bafb387c8060b3ed1013188af41cc6c011/https://sourceforge.net/p/snowyowl/code/ci/8e2ed26398b61aa6f4d679b6c34256963fdf22cb/Catch all exceptions in check_translatabilityIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/8e2ed26398b61aa6f4d679b6c34256963fdf22cb/https://sourceforge.net/p/snowyowl/code/ci/f5d654c92f036cfac5fbd04ebbaafec48c066eb4/Modified islands2genes and score_models to allo...Ian ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/f5d654c92f036cfac5fbd04ebbaafec48c066eb4/https://sourceforge.net/p/snowyowl/code/ci/99a4bc5b8c1f77ff62ea047d7de65b549fd09530/Modified islands2genes and score_models to allo...Ian ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/99a4bc5b8c1f77ff62ea047d7de65b549fd09530/https://sourceforge.net/p/snowyowl/code/ci/6a53b4019741eac62a71beda7bfc77cdbe4a1fd2/Handle models without a numeric scoreIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/6a53b4019741eac62a71beda7bfc77cdbe4a1fd2/https://sourceforge.net/p/snowyowl/code/ci/aafe6d1b5aee004a0386eb4cad3d83f5c965ff76/Added docstrings for functionsIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/aafe6d1b5aee004a0386eb4cad3d83f5c965ff76/https://sourceforge.net/p/snowyowl/code/ci/181835662bf7e0106c1d8cfd96b6893c182e895d/Addedget_predicted_protein_length_distribution.pyIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/181835662bf7e0106c1d8cfd96b6893c182e895d/https://sourceforge.net/p/snowyowl/code/ci/bb215cc99d03bf7b5eaab6cb86ef5213d792e13a/Reverted bad change in score_modelsIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/bb215cc99d03bf7b5eaab6cb86ef5213d792e13a/https://sourceforge.net/p/snowyowl/code/ci/5d8a8a7e1e21158904256b7fd16473abd2b088dd/Made pool-gene_models use the New ID as the gen...Ian ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/5d8a8a7e1e21158904256b7fd16473abd2b088dd/https://sourceforge.net/p/snowyowl/code/ci/f17f4a5da33f979c24e1e8b2ff532bb150a73d46/Declared global variables in run() methodIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/f17f4a5da33f979c24e1e8b2ff532bb150a73d46/https://sourceforge.net/p/snowyowl/code/ci/c3746a5b045086ee455c65382f787db6388fe144/Added docstrings for functionsIan ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/c3746a5b045086ee455c65382f787db6388fe144/https://sourceforge.net/p/snowyowl/code/ci/e388c02d1b03d5a03b98ef749c9d2442b267c938/Corrected bug in get-args that overwrote custom...Ian ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/e388c02d1b03d5a03b98ef749c9d2442b267c938/https://sourceforge.net/p/snowyowl/code/ci/0034a10f2d99e35f223fe054af207f8f74924c4c/Corrected erroneous test for altered configurat...Ian ReidWed, 01 Oct 2014 14:37:07 -0000https://sourceforge.net/p/snowyowl/code/ci/0034a10f2d99e35f223fe054af207f8f74924c4c/