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Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 19 21:47:27 2011 UTC (9 years ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_dev_05262011
Changes since 1.67: +17 -20 lines
Diff to previous 1.67
fixed correct abundances when doing grouping for table and barchart

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 16 20:23:14 2011 UTC (9 years ago) by tharriso
Branch: MAIN
Changes since 1.66: +5 -8 lines
Diff to previous 1.66
updated protein hits table and read tbale.  more user friendly and is based on selectred sources only.  can now annotate downloaded seqs from a source

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Fri May 6 21:17:04 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.65: +28 -22 lines
Diff to previous 1.65
fixed m5nr source for organisms, now allows m5nr and rna sources mixed

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 2 21:41:02 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.64: +14 -52 lines
Diff to previous 1.64
cleaned up workbench buttons, added links to protein ids

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 29 18:09:45 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.63: +13 -19 lines
Diff to previous 1.63
expanded function

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 29 11:35:33 2011 UTC (9 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.62: +44 -1 lines
Diff to previous 1.62
added function get_md5s_for_tax_level to MetagenomeAnalysis2.pm
added download of fasta sequences to rank abundance plot

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 28 22:03:38 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.61: +26 -33 lines
Diff to previous 1.61
added recruitment plot table, optimized workbench hits table

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 27 18:18:44 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.60: +59 -3 lines
Diff to previous 1.60
added functions to get analysis data and sims lines for set of md5s

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 25 19:38:40 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.59: +4 -5 lines
Diff to previous 1.59
fixed error in protein filtering

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 21 20:50:34 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
Changes since 1.58: +129 -22 lines
Diff to previous 1.58
1. fixed broken links for group selection
2. added Functional Annotation table
3. fixed M5NR source to show collapsed annotation with correct abundances / proteins

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 13 15:48:43 2011 UTC (9 years, 1 month ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_dev_04132011, mgrast_release_3_0_4
Changes since 1.57: +73 -4 lines
Diff to previous 1.57
added functions to get length and gc histogram data from job dirs

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 12 08:34:22 2011 UTC (9 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.56: +1 -1 lines
Diff to previous 1.56
fixed quoting in get_organisms_for_md5s query

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 11 14:42:20 2011 UTC (9 years, 1 month ago) by paczian
Branch: MAIN
Changes since 1.55: +14 -5 lines
Diff to previous 1.55
added option to set jobs with job_ids or metagenome_ids
fixed md5s_to_read_sequences

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 5 16:50:48 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_dev_04052011, mgrast_dev_04082011, mgrast_release_3_0_3
Changes since 1.54: +1 -2 lines
Diff to previous 1.54
changed source name from 'M5NR' to real name

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 1 03:20:05 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_dev_04012011
Changes since 1.53: +5 -7 lines
Diff to previous 1.53
fixed math bug

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 31 21:38:11 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_dev_03312011
Changes since 1.52: +57 -17 lines
Diff to previous 1.52
added functions for domain stats

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 31 18:31:23 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
Changes since 1.51: +86 -93 lines
Diff to previous 1.51
changed e-value, identity, and length filtering to be based on the avg value in the database and not the binned cutoffs

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 29 20:38:54 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
Changes since 1.50: +42 -58 lines
Diff to previous 1.50
changed to only use one cutoff filter at a time

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 28 19:15:21 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
Changes since 1.49: +74 -32 lines
Diff to previous 1.49
fixed issue with 'max_locks_per_transaction' error for too many jobs selected, added function to get abundance counts for a specific taxonomic level

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 09:55:39 2011 UTC (9 years, 2 months ago) by paczian
Branch: MAIN
CVS Tags: mgrast_dev_03252011, mgrast_release_3_0_2
Changes since 1.48: +3 -1 lines
Diff to previous 1.48
put in WHERE / AND check in md5s_to_read_sequences

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 17:34:41 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
fixed overview page to display hit distribution and rank abundance for rna only jobs, all sources merged together

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 16:55:53 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
Changes since 1.46: +82 -114 lines
Diff to previous 1.46
code changes to reflect DB changes: protein and rna md5s and organism data are merged into same tables (tagged by source) and not into seperate tables. fixed workbench and qiime export to work with rna

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 10 21:42:18 2011 UTC (9 years, 2 months ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_release_3_0_1
Changes since 1.45: +18 -10 lines
Diff to previous 1.45
fixed issue with rna request

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 8 16:06:17 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_release_3_0
Changes since 1.44: +53 -51 lines
Diff to previous 1.44
fixed error checking if no table

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 21 17:34:43 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03052011
Changes since 1.43: +7 -6 lines
Diff to previous 1.43
fixed bug with retrieving job table names

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 18 22:12:17 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
Changes since 1.42: +3 -3 lines
Diff to previous 1.42
changed job data paths

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 18 17:49:58 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
Changes since 1.41: +13 -10 lines
Diff to previous 1.41
fixed counts for sub-abundance (md5 sum list)

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 15 16:20:53 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
Changes since 1.40: +7 -7 lines
Diff to previous 1.40
dded method for mapping source types

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 04:15:13 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
Changes since 1.39: +33 -10 lines
Diff to previous 1.39
added support for rna data in 'organism classification'

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 11 20:17:02 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
Changes since 1.38: +34 -28 lines
Diff to previous 1.38
modified to work with new JobDB

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Feb 11 15:18:50 2011 UTC (9 years, 3 months ago) by tharriso
Branch: MAIN
Changes since 1.37: +1 -1 lines
Diff to previous 1.37
updated to work with new JobDB

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jan 24 22:26:39 2011 UTC (9 years, 4 months ago) by tharriso
Branch: MAIN
Changes since 1.36: +13 -4 lines
Diff to previous 1.36
added code to only display 'M5NR' data if multiple dbs exist for a given job

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 19 15:27:29 2011 UTC (9 years, 4 months ago) by paczian
Branch: MAIN
Changes since 1.35: +10 -2 lines
Diff to previous 1.35
merged conflicts

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 15:24:55 2011 UTC (9 years, 4 months ago) by tharriso
Branch: MAIN
Changes since 1.34: +54 -25 lines
Diff to previous 1.34
code added to support alignment length filtering
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Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 10 15:40:45 2010 UTC (9 years, 5 months ago) by tharriso
Branch: MAIN
Changes since 1.33: +1 -1 lines
Diff to previous 1.33
text cleanup

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 1 18:21:48 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.32: +1 -1 lines
Diff to previous 1.32
fixed FIG_Config variable

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 22:58:03 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.31: +4 -6 lines
Diff to previous 1.31
minor bug fix

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 18:29:42 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.30: +7 -8 lines
Diff to previous 1.30
fixed bug with m5nr select

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 18:21:32 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.29: +16 -4 lines
Diff to previous 1.29
added return result for source 'M5NR' for organism data, returns non-redundent set from all sources

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 12:20:19 2010 UTC (9 years, 6 months ago) by paczian
Branch: MAIN
Changes since 1.28: +9 -1 lines
Diff to previous 1.28
fixed missing space bug in sequences_for_md5s

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 04:21:09 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.27: +48 -27 lines
Diff to previous 1.27
changed returns for organism and ontology data sets, return sub-abundance (abundance based on inputted set of md5s) instead of normalized abundace (removed)

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 9 20:57:13 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.26: +18 -18 lines
Diff to previous 1.26
cleanup

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 9 04:41:22 2010 UTC (9 years, 6 months ago) by tharriso
Branch: MAIN
Changes since 1.25: +94 -68 lines
Diff to previous 1.25
1. added % identity to filter options 2. now retreaving correct abundances for evaule and identity cutoffs 2. changed data return formats for organism and ontology searches - removed eval max/min - added identity avg/stdv, normalized abundance

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 5 02:46:14 2010 UTC (9 years, 7 months ago) by tharriso
Branch: MAIN
Changes since 1.24: +321 -294 lines
Diff to previous 1.24
big changes. operates on a list of jobs (based on inputed mg-ids), not one job object (based on inputed mg-ids). more optimization

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 3 17:06:55 2010 UTC (9 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.23: +1 -1 lines
Diff to previous 1.23
reverted to MGRAST_jobcache

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 3 13:31:27 2010 UTC (9 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.22: +4 -5 lines
Diff to previous 1.22
fixed ref check of job

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 2 19:16:23 2010 UTC (9 years, 7 months ago) by wilke
Branch: MAIN
Changes since 1.21: +1 -1 lines
Diff to previous 1.21
*** empty log message ***

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 29 14:51:30 2010 UTC (9 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.20: +6 -3 lines
Diff to previous 1.20
div by 0 error fixed in barchart
implemented multiple ontologies

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 29 03:56:56 2010 UTC (9 years, 7 months ago) by tharriso
Branch: MAIN
Changes since 1.19: +80 -5 lines
Diff to previous 1.19
updated / improved sequence retrieval

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 26 16:03:38 2010 UTC (9 years, 7 months ago) by tharriso
Branch: MAIN
Changes since 1.18: +61 -11 lines
Diff to previous 1.18
*** empty log message ***

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 24 17:40:53 2010 UTC (9 years, 7 months ago) by tharriso
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Changes since 1.17: +14 -26 lines
Diff to previous 1.17
*** empty log message ***

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 23 03:12:54 2010 UTC (9 years, 7 months ago) by tharriso
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Changes since 1.16: +4 -4 lines
Diff to previous 1.16
*** empty log message ***

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 23 02:47:54 2010 UTC (9 years, 7 months ago) by tharriso
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Changes since 1.15: +127 -223 lines
Diff to previous 1.15
*** empty log message ***

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 20 12:10:42 2010 UTC (9 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.14: +3 -0 lines
Diff to previous 1.14
get_md5_abundance now returns undef if the prot_tbl is not found

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 19 12:22:37 2010 UTC (9 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.13: +73 -6 lines
Diff to previous 1.13
new version

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 18 14:46:15 2010 UTC (9 years, 7 months ago) by wilke
Branch: MAIN
Changes since 1.12: +38 -0 lines
Diff to previous 1.12
*** empty log message ***

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 13 14:03:43 2010 UTC (9 years, 7 months ago) by paczian
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Changes since 1.11: +2 -0 lines
Diff to previous 1.11
dereferenced md5s in recently added functions

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 13 13:38:58 2010 UTC (9 years, 7 months ago) by paczian
Branch: MAIN
Changes since 1.10: +59 -3 lines
Diff to previous 1.10
added functions
get_functions_for_md5s
get_organisms_for_md5s

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 8 16:41:30 2010 UTC (9 years, 8 months ago) by tharriso
Branch: MAIN
Changes since 1.9: +5 -0 lines
Diff to previous 1.9
*** empty log message ***

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 8 14:11:34 2010 UTC (9 years, 8 months ago) by paczian
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Changes since 1.8: +18 -4 lines
Diff to previous 1.8
added get_md5_abundance

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 6 15:12:08 2010 UTC (9 years, 8 months ago) by tharriso
Branch: MAIN
Changes since 1.7: +14 -5 lines
Diff to previous 1.7
added job ids function

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 2 05:07:55 2010 UTC (9 years, 8 months ago) by tharriso
Branch: MAIN
Changes since 1.6: +31 -27 lines
Diff to previous 1.6
*** empty log message ***

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 1 19:46:37 2010 UTC (9 years, 8 months ago) by tharriso
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Changes since 1.5: +73 -8 lines
Diff to previous 1.5
merged Tobis stuff

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 30 19:35:20 2010 UTC (9 years, 8 months ago) by tharriso
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Changes since 1.4: +61 -179 lines
Diff to previous 1.4
fixed ach handle, added functions, cleanup

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 28 22:11:28 2010 UTC (9 years, 8 months ago) by tharriso
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Changes since 1.3: +2 -2 lines
Diff to previous 1.3
*** empty log message ***

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 28 21:31:18 2010 UTC (9 years, 8 months ago) by tharriso
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Changes since 1.2: +0 -1 lines
Diff to previous 1.2
*** empty log message ***

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 28 21:26:13 2010 UTC (9 years, 8 months ago) by tharriso
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Changes since 1.1: +160 -3 lines
Diff to previous 1.1
*** empty log message ***

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 28 16:33:05 2010 UTC (9 years, 8 months ago) by tharriso
Branch: MAIN
*** empty log message ***

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