cf910d9cc2
misc. useful updates to python library
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3683 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-30 16:33:32 +00:00
e7939f7036
Fixed error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3653 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-28 14:50:28 +00:00
1cb8f51f8c
Fixed -t arg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3634 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 23:44:10 +00:00
3cd0570c1e
Now can run with multiple processes, multiple threads, or both
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3633 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 23:25:01 +00:00
dae3ce2c0f
changed log dir
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3632 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 23:08:13 +00:00
fea8054e9e
Updated long name for -l to --run-locally
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3631 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 22:26:45 +00:00
72e669538e
Updated arg description for -s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3629 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-24 22:04:01 +00:00
cef12b45e1
Fixed typo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3561 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 21:17:14 +00:00
c0370f4d0a
Added both inclusive and exclusive filters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3538 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 18:40:41 +00:00
d1a4c4f0d3
Added -w filter option allowing user to specify chromosomes to be skipped.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3531 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:58:25 +00:00
6fd2d39a7d
Modified run_locally mode to use os.system(..) instead of popen
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3515 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:10:03 +00:00
a3ccf49f5b
Write error to stderr
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3514 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:09:10 +00:00
2b31975cb4
Added more options for coordinate systems - now you can add 1 to either the start coordinates, the end coordinates, or both
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3508 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:49:19 +00:00
410afcdf2c
Added parallelization options - when running locally, multiple processes can be spawned, or a -nt arg can be specified to run each TranscriptToInfo instance multi-threaded
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3507 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:48:07 +00:00
92c72d3361
Added back lines that update the *big-table-header.txt file before using it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3506 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:45:41 +00:00
3c24223d02
Script for concatenating 2 AnnotatorInputTables, and writing the result to standard out. Merge-sorts the 2 tables while concatenating them
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3505 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 22:44:16 +00:00
f32a32269c
minor change for eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3418 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 20:13:36 +00:00
d1098fa77b
Removing unnecessary dependences that were causing problems for Sendu
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3410 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-21 13:07:41 +00:00
886e9c1297
Now can take a VCF file as input
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3378 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 17:06:12 +00:00
2a212c497f
minor improvements and bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3376 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 15:54:42 +00:00
43544cfdf9
remote control of IGV to jump to any number of loci in a file and screenshot the locus to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3375 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 12:59:36 +00:00
04e14ef85a
Refactored so it could be used for knownGene and CCDS as well as refGene
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3373 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-18 02:45:11 +00:00
2a803e9044
simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3352 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 13:39:09 +00:00
d3c33d4b3f
more powerful management routines for my pipeline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3351 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-12 13:37:39 +00:00
f120a00433
Fixed bug so that the strand, alternate, and reference columns are now moved correctly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3342 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-10 17:59:39 +00:00
d6b036cdab
Minor improvements to simple python code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3330 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 21:34:46 +00:00
d5b675b3e6
Added - Q&D script to gather verbose bed files to a VCF.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3294 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 02:49:16 +00:00
a462b5e1e7
Changed a default path
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3291 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-03 17:07:21 +00:00
28f746b76a
Added option to generate UCSC or NCBI sequence
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3283 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:26:00 +00:00
c214056d88
Script for concatenating results of GenerateTranscriptToInfo.py into one big file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3279 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:47:08 +00:00
0069cb426d
Script for spawning LSF jobs that run the TranscriptToInfo.java walker on each of the 50 contigs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3277 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:27:52 +00:00
ba7fe7c4e1
Renamed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3276 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:25:07 +00:00
4937295a0b
Renamed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3275 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 15:24:56 +00:00
bf3dbd8401
some useful routines for working with project processing. madPipeline contains a bunch of useful routines for building pipelines that I finally put into one file. Let's just say that I'm really looking forward to the new pipeline system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3260 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-26 12:34:04 +00:00
c7b4f78316
Added -m arg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3233 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 22:38:47 +00:00
7902db616e
Marginally more useful output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3201 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 14:45:14 +00:00
4eba9bffc1
Grabs average SNP calls, mismatch rate, aligned reads, and other important lane metrics from a SQUID export and summarizes them across multiple margins (lane numbers, flowcells, samples, libraries)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3193 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-17 03:09:05 +00:00
7973806716
interim update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3173 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 14:25:02 +00:00
2e4377b1cf
Awesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3170 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 18:17:41 +00:00
04c22a6640
Added handling of UCSC and NCBI reference sequences
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3165 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 14:40:31 +00:00
2183f10a1d
Script for validating and converting text files into the tabular format required for GenomicAnnotator -B inputs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3156 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 13:35:10 +00:00
fab31e1d53
Check in so I don't lose this code -- spawning of jobs by genes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3137 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 16:18:40 +00:00
27fb6f7594
Make sure to convert non-integer chromosomes (M,X,Y) back from their corresponding integer representations (0,23,24) when writing in .bed format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3119 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-03 20:01:21 +00:00
687fd477ff
Just some code I want to freeze. If you ever need to estimate the % of bases covered by exon, given an interval list, give it to getTargetedGenes. Not the best name for this function, but I don't expect anyone to use it but me.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3111 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 20:21:50 +00:00
ac9c335cd2
This is a python job dispatcher I've been using, which builds on Mark's FarmJob utility, and an example script of how I'm using it. Basically I wrote it to smartly break up analysis over an interval list, givin a maximum number of bases per job, a list of available queues, and a limit on each queue. It handles going over these limits in three ways:
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1) [default]: Fail
- No jobs are actually spawned
2) Space
- User provides a string of the form A:B:C where A is the number of days to wait before scheduling jobs over
the queue limits; B the number of hours, C the number of minutes. Exceeding the queue limits again will
increment the space by another A:B:C
3) Stop-Resume
- Spawns the maximum number of jobs, and writes a file describing the next job, and a hash code of the remaining jobs.
The next time the script is run, it spawns the next set of jobs starting with what's written in the file. If the
hash code (and thus the command string) changes between runs, the dispatcher fails-fast.
The base job dispatcher class is also capable of dealing with dependencies if it is used correctly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3102 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 19:53:13 +00:00
dc802aa26f
Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 13:32:00 +00:00
08d9ae403d
better farm commands, and simple utility to convert ucsc repeat masks to interval lists
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3040 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 13:11:06 +00:00
4bdc3b2784
automatic generation of individual and individual set import files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3001 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 10:36:33 +00:00
d9b12b468f
Adding default filter info
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3000 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 10:05:46 +00:00
196bca6819
Script to split concordance files into their constituent sets and calculate summary stats from a concordance file - SNPs called and number in dbSNP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2992 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 22:20:44 +00:00
depristo
weisburd
chartl
andrewk