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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Tue, 23 Oct 2012 17:06:30 +0000 (17:06 +0000)]
fixed nasty bug in classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1970
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martinahansen [Mon, 22 Oct 2012 13:07:55 +0000 (13:07 +0000)]
fixed nasty bug in classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1969
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martinahansen [Tue, 16 Oct 2012 14:12:34 +0000 (14:12 +0000)]
removed raise from classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1965
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martinahansen [Mon, 15 Oct 2012 17:11:42 +0000 (17:11 +0000)]
removed raise from classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1964
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martinahansen [Fri, 12 Oct 2012 08:49:09 +0000 (08:49 +0000)]
fixed classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1963
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martinahansen [Wed, 10 Oct 2012 13:20:55 +0000 (13:20 +0000)]
added some file locking to biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1962
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martinahansen [Wed, 10 Oct 2012 12:49:35 +0000 (12:49 +0000)]
added some file locking to Biopieces.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1961
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martinahansen [Wed, 10 Oct 2012 12:36:09 +0000 (12:36 +0000)]
added flock to biostat
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1960
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martinahansen [Wed, 10 Oct 2012 12:28:52 +0000 (12:28 +0000)]
removed stale file crap from biostat
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1959
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martinahansen [Wed, 10 Oct 2012 12:21:21 +0000 (12:21 +0000)]
added dynamic mem allocation to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1958
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martinahansen [Wed, 10 Oct 2012 12:20:38 +0000 (12:20 +0000)]
added dynamic mem allocation to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1957
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martinahansen [Tue, 9 Oct 2012 09:22:51 +0000 (09:22 +0000)]
changed default values for findsim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1954
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martinahansen [Tue, 9 Oct 2012 09:16:17 +0000 (09:16 +0000)]
cleanup of findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1953
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martinahansen [Tue, 9 Oct 2012 08:56:00 +0000 (08:56 +0000)]
cleanup of findsim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1952
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martinahansen [Tue, 9 Oct 2012 08:54:17 +0000 (08:54 +0000)]
cleanup of findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1951
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martinahansen [Thu, 27 Sep 2012 13:10:04 +0000 (13:10 +0000)]
upgraded kmer_freq test
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1950
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martinahansen [Thu, 27 Sep 2012 13:08:48 +0000 (13:08 +0000)]
polished kmer_freq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1949
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martinahansen [Thu, 27 Sep 2012 13:02:11 +0000 (13:02 +0000)]
removed kmer_freq test files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1947
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martinahansen [Thu, 27 Sep 2012 12:58:17 +0000 (12:58 +0000)]
clearning up kmer_stats and kmer_freq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1945
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martinahansen [Thu, 27 Sep 2012 12:40:13 +0000 (12:40 +0000)]
finishing work on match.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1943
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martinahansen [Tue, 25 Sep 2012 13:07:13 +0000 (13:07 +0000)]
work kmer_stats biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1941
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martinahansen [Tue, 25 Sep 2012 07:58:07 +0000 (07:58 +0000)]
added kmer_stats biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1938
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martinahansen [Fri, 21 Sep 2012 09:27:34 +0000 (09:27 +0000)]
added parser for phred qual to fasta.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1937
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martinahansen [Fri, 21 Sep 2012 09:10:48 +0000 (09:10 +0000)]
added qual_base(33|64)? methods to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1936
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martinahansen [Fri, 21 Sep 2012 09:09:50 +0000 (09:09 +0000)]
slight polish of read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1935
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martinahansen [Thu, 20 Sep 2012 15:10:47 +0000 (15:10 +0000)]
added bases_per_file option to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1933
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martinahansen [Wed, 19 Sep 2012 11:19:11 +0000 (11:19 +0000)]
fixed database type guess for blast_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1932
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martinahansen [Thu, 13 Sep 2012 13:19:26 +0000 (13:19 +0000)]
pair.rb now working correctly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1930
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martinahansen [Wed, 12 Sep 2012 19:43:13 +0000 (19:43 +0000)]
worked on pair aligner
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1929
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martinahansen [Tue, 11 Sep 2012 10:04:45 +0000 (10:04 +0000)]
working on pair.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1921
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martinahansen [Tue, 11 Sep 2012 09:58:37 +0000 (09:58 +0000)]
added align/match.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1920
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martinahansen [Tue, 11 Sep 2012 09:54:08 +0000 (09:54 +0000)]
worked on pair.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1919
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martinahansen [Mon, 10 Sep 2012 09:50:07 +0000 (09:50 +0000)]
fixed unit tests for seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1916
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martinahansen [Tue, 4 Sep 2012 14:51:00 +0000 (14:51 +0000)]
added math_aux.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1913
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martinahansen [Tue, 4 Sep 2012 14:50:36 +0000 (14:50 +0000)]
added test_math_aux.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1912
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martinahansen [Tue, 4 Sep 2012 12:05:30 +0000 (12:05 +0000)]
fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1911
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martinahansen [Tue, 4 Sep 2012 12:04:21 +0000 (12:04 +0000)]
fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1910
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martinahansen [Mon, 3 Sep 2012 11:30:10 +0000 (11:30 +0000)]
revamped find_adaptor and clip_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1909
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martinahansen [Mon, 3 Sep 2012 11:29:11 +0000 (11:29 +0000)]
updated testing files for find_adaptor and clip_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1907
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martinahansen [Thu, 30 Aug 2012 12:10:27 +0000 (12:10 +0000)]
deleted old QA_454_report script
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1906
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martinahansen [Thu, 30 Aug 2012 12:09:53 +0000 (12:09 +0000)]
added nucleotide plot to QA_454_report
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1905
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martinahansen [Thu, 30 Aug 2012 11:18:48 +0000 (11:18 +0000)]
added plot_nucleotide_distribution biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1902
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martinahansen [Thu, 30 Aug 2012 08:23:27 +0000 (08:23 +0000)]
finally figured how to change plot color
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1900
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martinahansen [Thu, 16 Aug 2012 11:19:00 +0000 (11:19 +0000)]
did something to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1898
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martinahansen [Wed, 15 Aug 2012 13:34:14 +0000 (13:34 +0000)]
made find_orfs run on DNA or RNA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1896
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martinahansen [Tue, 14 Aug 2012 13:24:45 +0000 (13:24 +0000)]
fixed mean_scores to deal with 0 length seqs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1893
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martinahansen [Tue, 14 Aug 2012 13:23:10 +0000 (13:23 +0000)]
reverted trim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1892
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martinahansen [Tue, 14 Aug 2012 13:16:36 +0000 (13:16 +0000)]
changed trim_seq to omit outputting sequences with length 0
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1891
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martinahansen [Thu, 9 Aug 2012 11:15:37 +0000 (11:15 +0000)]
upgraded QA script to use new plot scores count feature
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1890
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martinahansen [Tue, 7 Aug 2012 17:50:02 +0000 (17:50 +0000)]
last fix on prodigal upgrade
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1888
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martinahansen [Tue, 7 Aug 2012 17:33:50 +0000 (17:33 +0000)]
upgraded prodigal
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1886
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martinahansen [Tue, 7 Aug 2012 13:41:32 +0000 (13:41 +0000)]
fixed typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1885
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martinahansen [Tue, 7 Aug 2012 11:48:20 +0000 (11:48 +0000)]
added assemble_seq_idba_ud
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1882
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martinahansen [Tue, 7 Aug 2012 09:34:18 +0000 (09:34 +0000)]
added relative count to plot_scores + rewrite for speed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1878
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martinahansen [Mon, 6 Aug 2012 14:43:28 +0000 (14:43 +0000)]
removed outdated installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1876
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martinahansen [Mon, 6 Aug 2012 14:42:46 +0000 (14:42 +0000)]
updated biopieces installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1875
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martinahansen [Fri, 13 Jul 2012 14:43:11 +0000 (14:43 +0000)]
fixed another bug in find orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1872
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martinahansen [Fri, 13 Jul 2012 14:32:53 +0000 (14:32 +0000)]
fixed bug in orf finder
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1871
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martinahansen [Fri, 13 Jul 2012 14:15:39 +0000 (14:15 +0000)]
fixed grave bug in find_orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1870
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martinahansen [Fri, 13 Jul 2012 13:54:49 +0000 (13:54 +0000)]
made orf finder case insensitive
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1868
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martinahansen [Fri, 13 Jul 2012 13:52:36 +0000 (13:52 +0000)]
added find_orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1867
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martinahansen [Fri, 13 Jul 2012 13:51:58 +0000 (13:51 +0000)]
added orf finder to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1866
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martinahansen [Tue, 10 Jul 2012 13:46:26 +0000 (13:46 +0000)]
ported align_pair_seq to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1865
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martinahansen [Tue, 10 Jul 2012 13:37:10 +0000 (13:37 +0000)]
added align/pair.rb to ruby trunk
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1864
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martinahansen [Tue, 10 Jul 2012 13:35:54 +0000 (13:35 +0000)]
fixed align.rb up a bit
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1863
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martinahansen [Tue, 10 Jul 2012 12:09:03 +0000 (12:09 +0000)]
minor fix to find_adaptor 2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1862
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martinahansen [Tue, 10 Jul 2012 12:06:09 +0000 (12:06 +0000)]
minor fix to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1861
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martinahansen [Tue, 10 Jul 2012 09:38:29 +0000 (09:38 +0000)]
added -m hardcoded option to prodigal.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1860
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martinahansen [Tue, 10 Jul 2012 08:52:14 +0000 (08:52 +0000)]
fixed bug for missing sequence in genbank parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1858
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martinahansen [Mon, 2 Jul 2012 09:12:17 +0000 (09:12 +0000)]
added mum.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1857
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martinahansen [Mon, 2 Jul 2012 09:00:04 +0000 (09:00 +0000)]
updated order_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1856
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martinahansen [Mon, 2 Jul 2012 08:59:44 +0000 (08:59 +0000)]
updated order_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1855
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martinahansen [Fri, 29 Jun 2012 18:27:56 +0000 (18:27 +0000)]
clean-up of ruby code to remove rake warnings
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1852
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martinahansen [Fri, 29 Jun 2012 18:27:21 +0000 (18:27 +0000)]
rewrote mean_scores to fix bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1851
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martinahansen [Fri, 29 Jun 2012 13:44:59 +0000 (13:44 +0000)]
added scores_mean method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1850
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martinahansen [Thu, 28 Jun 2012 11:29:22 +0000 (11:29 +0000)]
cleanup of pair stuff in align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1849
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martinahansen [Wed, 27 Jun 2012 20:04:21 +0000 (20:04 +0000)]
fixed inline code warning
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1848
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martinahansen [Mon, 25 Jun 2012 11:36:40 +0000 (11:36 +0000)]
fixed bug in findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1847
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martinahansen [Mon, 25 Jun 2012 09:04:40 +0000 (09:04 +0000)]
added max_diversity swith to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1846
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martinahansen [Mon, 25 Jun 2012 09:02:40 +0000 (09:02 +0000)]
added max_diversity swith to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1845
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martinahansen [Mon, 25 Jun 2012 09:01:26 +0000 (09:01 +0000)]
added max_diversity swith to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1844
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martinahansen [Wed, 20 Jun 2012 11:19:35 +0000 (11:19 +0000)]
classify_taxonomy work
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1843
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martinahansen [Wed, 20 Jun 2012 09:38:04 +0000 (09:38 +0000)]
classify_taxonomy work
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1842
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martinahansen [Wed, 13 Jun 2012 13:50:15 +0000 (13:50 +0000)]
added classify_taxonomy (unfinished biopiece)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1841
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martinahansen [Fri, 8 Jun 2012 09:42:04 +0000 (09:42 +0000)]
fixed raw intput bug in read_fasta and read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1840
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martinahansen [Fri, 8 Jun 2012 09:14:16 +0000 (09:14 +0000)]
refactoring biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1839
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martinahansen [Fri, 8 Jun 2012 09:07:26 +0000 (09:07 +0000)]
fixed unit tests for test_trim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1838
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martinahansen [Fri, 1 Jun 2012 09:43:20 +0000 (09:43 +0000)]
added illumina 1.8 name scheme support to order pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1836
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martinahansen [Thu, 31 May 2012 14:22:57 +0000 (14:22 +0000)]
fixed bad error msg
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1835
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martinahansen [Wed, 30 May 2012 11:41:17 +0000 (11:41 +0000)]
fixed bug in sff.rb clip and mask methods
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1834
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martinahansen [Wed, 30 May 2012 11:39:48 +0000 (11:39 +0000)]
fixed bug in sff.rb to_seq method
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1833
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Wed, 30 May 2012 11:37:01 +0000 (11:37 +0000)]
added to_seq method to sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1832
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Fri, 25 May 2012 09:27:49 +0000 (09:27 +0000)]
fixed trim_seq tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1830
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 24 May 2012 20:49:05 +0000 (20:49 +0000)]
fixed ugly bug in trim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1829
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 24 May 2012 13:35:10 +0000 (13:35 +0000)]
moved patscan.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1828
74ccb610-7750-0410-82ae-
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martinahansen [Thu, 24 May 2012 13:32:20 +0000 (13:32 +0000)]
moved backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1827
74ccb610-7750-0410-82ae-
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martinahansen [Thu, 24 May 2012 13:30:02 +0000 (13:30 +0000)]
moved patternmatcher.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1826
74ccb610-7750-0410-82ae-
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martinahansen [Thu, 24 May 2012 13:09:11 +0000 (13:09 +0000)]
moving digest.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1825
74ccb610-7750-0410-82ae-
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martinahansen [Thu, 24 May 2012 09:00:48 +0000 (09:00 +0000)]
upgraded trim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1823
74ccb610-7750-0410-82ae-
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martinahansen [Wed, 23 May 2012 17:42:56 +0000 (17:42 +0000)]
refactored SeqError/TrimError
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1822
74ccb610-7750-0410-82ae-
013aeee3265d
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