Stan implementation of the bayesian model Skelly et al 2011 Genome Research
Download cmdstan-2.9.0.tar.gz, https://github.com/stan-dev/cmdstan/releases/download/v2.9.0/cmdstan-2.9.0.tar.gz
tar xvzf cmdstan-2.9.0.tar.gz
cd cmdstan-2.9.0
Inti Pedroso inti
inti
/ gist:450303
Created
June 23, 2010 18:10
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| structure(list(ensembl = structure(c(11L, 11L, 11L, 11L, 11L, | |
| 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, | |
| 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, | |
| 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 28L, 28L, | |
| 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, 28L, | |
| 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, | |
| 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, | |
| 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, | |
| 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 4L, | |
| 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, |
inti
/ test_step_method.py
Last active
January 1, 2016 23:49
Example using custom step method on PyMC: - generate samples for a sum of gaussian variables with mean 0 and std 1.
- build a pymc model to fit a generative model to this set of observations. First declare all variables within the model context. The std of the (s variable) should be 1.4 as expected. Second try to update the variable p using a cu…
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| import pymc as mc | |
| import numpy as np | |
| import time | |
| import theano.tensor as T | |
| import theano | |
| theano.config.compute_test_value = 'off' | |
| ## generate some data | |
| N = 10000 |
inti
/ example_theano_scan.py
Last active
January 2, 2016 10:49
Example of using theano scan to update two variables on a loop
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| import theano | |
| import theano.tensor as T | |
| theano.config.compute_test_value = 'off' | |
| import numpy as np | |
| # routine to make some data up | |
| def makeup_data(n,p): | |
| X = np.memmap('test.memmap', dtype='float64', mode='w+', shape=(n,p)) |
inti
/ bcf_call_output.vcf
Created
October 14, 2014 13:37
example output generating error on BCF and VT normalise. command used was the following using an mpileup as piped output: /home/ipedroso/APP/bcbio-nextgen/bin/bcftools call -v -m -
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| ##fileformat=VCFv4.2 | |
| ##FILTER=<ID=PASS,Description="All filters passed"> | |
| ##samtoolsVersion=1.0+htslib-1.0 | |
| ##samtoolsCommand=samtools mpileup -f /home/ipedroso/APP/bcbio-nextgen/genomes/populus_trichicarpa/ptri_v3/seq/ptri_v3.fa -t DP -u -g -l /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work/samtools/scaffold_2499/GW-10958-scaffold_2499_0_3827-raw-regions.bed /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work/align/GW-10958/14_2014-09-26_populus_trichocarpa_diversity_1-sort.bam | |
| ##reference=file:///home/ipedroso/APP/bcbio-nextgen/genomes/populus_trichicarpa/ptri_v3/seq/ptri_v3.fa | |
| ##contig=<ID=Chr01,length=50495391> | |
| ##contig=<ID=Chr02,length=25263035> | |
| ##contig=<ID=Chr03,length=21816808> | |
| ##contig=<ID=Chr04,length=24267051> | |
| ##contig=<ID=Chr05,length=25890704> |
inti
/ bcbio-nextgen-debug.log
Created
December 23, 2014 17:13
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| [ipedroso@jimi log]$ cat bcbio-nextgen-debug.log | |
| [2014-12-17T14:05Z] Resource requests: bwa, sambamba, samtools; memory: 2.00; cores: 16, 1, 16 | |
| [2014-12-17T14:05Z] Configuring 3 jobs to run, using 16 cores each with 32.1g of memory reserved for each job | |
| [2014-12-17T14:05Z] Timing: organize samples | |
| [2014-12-17T14:05Z] multiprocessing: organize_samples | |
| [2014-12-17T14:05Z] Using input YAML configuration: /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/config/populus_trichocarpa_diversity_1.yaml | |
| [2014-12-17T14:05Z] Checking sample YAML configuration: /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/config/populus_trichocarpa_diversity_1.yaml | |
| [2014-12-17T14:05Z] Testing minimum versions of installed programs | |
| [2014-12-17T14:05Z] Timing: alignment preparation | |
| [2014-12-17T14:05Z] multiprocessing: prep_align_inputs |
inti
/ bcbio-nextgen.log
Created
December 23, 2014 17:14
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| [ipedroso@jimi log]$ cat bcbio-nextgen.log | |
| [2014-12-17T14:05Z] Timing: organize samples | |
| [2014-12-17T14:05Z] multiprocessing: organize_samples | |
| [2014-12-17T14:05Z] Using input YAML configuration: /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/config/populus_trichocarpa_diversity_1.yaml | |
| [2014-12-17T14:05Z] Checking sample YAML configuration: /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/config/populus_trichocarpa_diversity_1.yaml | |
| [2014-12-17T14:05Z] Testing minimum versions of installed programs | |
| [2014-12-17T14:05Z] Timing: alignment preparation | |
| [2014-12-17T14:05Z] multiprocessing: prep_align_inputs | |
| [2014-12-17T19:37Z] multiprocessing: disambiguate_split | |
| [2014-12-17T19:37Z] Timing: alignment |
inti
/ bcbio-nextgen-commands.log
Created
December 23, 2014 17:15
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| [ipedroso@jimi log]$ cat bcbio-nextgen-commands.log | |
| [2014-12-17T14:05Z] gunzip -c /media/TeraData/ipedroso/globus_endpoint/Ptrichocarpa_phytozome/v3.0/diversity/bam/BESC-015_1.fastq.gz | /home/shared/app/bcbio/tool/bin/bgzip -c /dev/stdin > /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work2/align_prep/tx/tmp2vQ808/BESC-015_1.fastq.gz | |
| [2014-12-17T14:05Z] gunzip -c /media/TeraData/ipedroso/globus_endpoint/Ptrichocarpa_phytozome/v3.0/diversity/bam/93-968_1.fastq.gz | /home/shared/app/bcbio/tool/bin/bgzip -c /dev/stdin > /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work2/align_prep/tx/tmpgNAsco/93-968_1.fastq.gz | |
| [2014-12-17T16:51Z] gunzip -c /media/TeraData/ipedroso/globus_endpoint/Ptrichocarpa_phytozome/v3.0/diversity/bam/BESC-015_2.fastq.gz | /home/shared/app/bcbio/tool/bin/bgzip -c /dev/stdin > /media/TeraData/ipedroso/ANALYSES/Populus/Diversity_1/populus_trichocarpa_diversity_1/work2/align_prep/tx/tmptFim84/BESC-015_2.fastq.gz | |
| [ |
inti
/ snakemake_output.txt
Created
June 10, 2015 13:53
SnakeMake: Unexpectedly present output files
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| Provided cores: 100 | |
| Provided resources: java_re=3 | |
| Ignored resources: large_n_io, gnu_parallel | |
| Job counts: | |
| count jobs | |
| 2240 index_vcf | |
| 2100 index_bam | |
| 2000 SplitNCigarReads_SampleRegionWise | |
| 2000 recode_CIGAR_N_to_D | |
| 100 freebayes_joint_regionwise |
inti
/ Populus_trichicarpa_example.bed
Created
March 10, 2016 18:08
Example bed file for VarDictJava issue #23
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| Chr03 1671030 1678847 | |
| Chr03 1680122 1683702 | |
| Chr03 1684822 1686872 | |
| Chr03 1689404 1693397 | |
| Chr03 1723476 1727153 | |
| Chr03 1774605 1776831 | |
| Chr03 1778862 1780912 | |
| Chr03 1796910 1798963 | |
| Chr03 1819329 1823273 | |
| Chr03 1828476 1831732 |
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