Brad Chapman chapmanb
chapmanb
/ sacCer3.chrom.sizes
Created
November 20, 2018 10:06
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| chrI 230218 | |
| chrII 813184 | |
| chrIII 316620 | |
| chrIV 1531933 | |
| chrV 576874 | |
| chrVI 270161 | |
| chrVII 1090940 | |
| chrVIII 562643 | |
| chrIX 439888 | |
| chrX 745751 |
chapmanb
/ vagrant_pallet.clj
Created
June 20, 2011 11:26
Running pallet with manual specification of a server; example with vagrant virtualbox
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| (ns distblast-cluster.vagrant | |
| (:require [pallet.compute :as compute] | |
| [pallet.phase :as phase] | |
| [pallet.core :as core] | |
| [pallet.utils :as utils] | |
| [pallet.compute.node-list :as node-list] | |
| [pallet.action.exec-script :as exec-script])) | |
| (defn test-script [session] | |
| (-> session |
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| from Bio import Entrez | |
| def fetch_gene_coordinates(search_term): | |
| handle = Entrez.esearch(db="gene", term=search_term) | |
| rec = Entrez.read(handle) | |
| gene_id = rec["IdList"][0] # assuming best match works | |
| handle = Entrez.efetch(db="gene", id=gene_id, retmode="xml") | |
| rec = Entrez.read(handle)[0] | |
| gene_locus = rec["Entrezgene_locus"][0] |
chapmanb
/ arvados_add_update.py
Created
October 31, 2021 00:15
Example of adding and updating a sequence in Arvados, with required remove/save step to avoid certificate error
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| def simple_add_update(): | |
| """Test adding and updating a collection to reproduce certificate error. | |
| """ | |
| project_uuid = "pirca-j7d0g-h13mew3i5ya8cqq" | |
| name = "save_new_test" | |
| fname = "seqs.fa" | |
| avoid_an_error = True | |
| arvados_conn = get_connection_config() | |
| c = arvados.collection.Collection(apiconfig=arvados_conn) | |
| with c.open(fname, "wb") as writer: |
chapmanb
/ tcga_capture.R
Created
November 8, 2018 17:29
Query TCGA API for exome capture BED files -- thanks to Sehyun Oh
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| #!/usr/bin/env Rscript | |
| library(GenomicDataCommons) | |
| library(dplyr) | |
| manifest = GenomicDataCommons::files() %>% | |
| GenomicDataCommons::filter(~ cases.project.project_id == "TCGA-LUAD" & | |
| experimental_strategy == "WXS" & | |
| data_format == "BAM") %>% | |
| GenomicDataCommons::manifest() |
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| with open ("dna.txt", "r") as myfile: | |
| data=myfile.readlines() | |
| mRNA=data[1] | |
| def next_transcript(mRNA, cur_pos): | |
| initial=mRNA.find("AUG", cur_pos) | |
| for i in range(initial, len(mRNA),3): | |
| if mRNA[i:i+3] == "UAG": | |
| return initial, i |
chapmanb
/ omixon_optitype_hla_calls.csv
Created
November 15, 2015 11:29
Omixon test HLA calls (http://www.omixon.com/hla-typing-example-data/) with hg38 and OptiType (https://github.com/FRED-2/OptiType)
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| sample | locus | alleles | expected | validates | |
|---|---|---|---|---|---|
| NA12878 | A | HLA-A*01:01;HLA-A*11:01 | HLA-A*01:01;HLA-A*11:01 | yes | |
| NA12878 | B | HLA-B*56:01;HLA-B*08:01 | HLA-B*08:01;HLA-B*56:01 | yes | |
| NA12878 | C | HLA-C*07:01;HLA-C*01:02 | HLA-C*01:02;HLA-C*07:01 | yes | |
| NA12891 | A | HLA-A*24:02;HLA-A*01:01 | HLA-A*01:01;HLA-A*24:02 | yes | |
| NA12891 | B | HLA-B*08:01;HLA-B*07:02 | HLA-B*07:02;HLA-B*08:01 | yes | |
| NA12891 | C | HLA-C*07:01;HLA-C*07:02 | HLA-C*07:01;HLA-C*07:02 | yes | |
| NA18526 | A | HLA-A*24:02;HLA-A*33:03 | HLA-A*24:02;HLA-A*33:03 | yes | |
| NA18526 | B | HLA-B*40:01;HLA-B*58:01 | HLA-B*40:01;HLA-B*58:01;HLA-B*58:02 | no | |
| NA18526 | C | HLA-C*03:02;HLA-C*07:02 | HLA-C*03:02;HLA-C*07:02 | yes |
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| #!/bin/bash | |
| # snpEff executable shell script | |
| # http://snpeff.sourceforge.net/ | |
| # Extracts memory and system property Java arguments from the list of provided arguments | |
| # (ie -Xms 1g -Xmx 2g) | |
| jardir="$(cd "$(dirname "$0")" && pwd -P)" | |
| java=java | |
| if [ -e "$JAVA_HOME/bin/java" ] |
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| 2-584759 no MET | |
| 2-584751 MET (FISH and ddPCR) | |
| 2-584699 MET (FISH and ddPCR) |
chapmanb
/ bcbio_vm_install.sh
Created
January 29, 2019 15:54
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| #!/bin/bash | |
| set -eu -o pipefail | |
| export TARGETDIR=`pwd`/anaconda | |
| export BINDIR=`pwd` | |
| wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh | |
| bash Miniconda2-latest-Linux-x86_64.sh -b -p $TARGETDIR | |
| $TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen | |
| $TARGETDIR/bin/conda install --yes -c conda-forge -c bioconda bcbio-nextgen-vm | |
| mkdir -p $BINDIR/bin |
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