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#!/usr/bin/perl | |
use strict; | |
use Bio::SeqIO; | |
use Bio::EnsEMBL::Registry; | |
Bio::EnsEMBL::Registry->load_registry_from_db( | |
-host => 'ensembldb.ensembl.org', | |
-user => 'anonymous' | |
); |
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JOB_DEP_CMD = echo $(DATASETS) | sed 's/ /"\) \&\& done("/g' | |
JOB_DEP = -w 'done("$(shell $(JOB_DEP_CMD))")' | |
@$(foreach DS,$(DATASETS), $(SUBMIT_JOB) -J $(DS) "samtools view -b -h $(ALN_DIR)/$(DS)/$(SPIKEIN_NVTR) $(SPIKEIN_NAMES) -o $(ALN_DIR)/$(DS)/spikeins.bam";) |
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library(biomaRt) | |
ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", | |
host="www.ensembl.org", path="/biomart/martservice") | |
attrs <- c("ensembl_gene_id", "upstream_flank") | |
gene_ann <- getBM(attributes=attrs, filters=list(ensembl_gene_id="ENSG00000165702", upstream_flank=100), mart=ensembl, checkFilters=F) | |
gene_ann |
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setwd("~/Documents/projects/paper-pat-seq/") | |
patsy_table <- read.table("Log/TEST_WT1_vs_MUT1_gcf.tab", header=T) | |
patsy_data <- patsy_table$runs_ma | |
names(patsy_data) <- as.character(patsy_table$transcripts) | |
pasta_table <- read.table("ExtData/PASTA_polyAranking.tab", header=T) | |
pasta_data <- pasta_table$weighted_length | |
names(pasta_data) <- as.character(pasta_table$transcripts) |
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seed used = 1386212133 | |
4 1644 | |
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import glob | |
for d in glob.glob("/nfs/research2/goldman/gregs/slr_pipeline/data/ens/78/trees/*"): | |
print "Directory name", d | |
# Probably more useful but would print a lot of stuff | |
# for f in glob.glob("/nfs/research2/goldman/gregs/slr_pipeline/data/ens/78/trees/*/*.nh"): | |
# print "File name", f |
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library(ggplot2) | |
library(grid) | |
library(gtable) | |
ex <- data.frame(xmin=1, xmax=100, ymin=0, ymax=15) | |
p <- ggplot(ex, aes(xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)) + | |
theme_minimal() + | |
theme(plot.margin=margin(l=2.0, unit="cm"), | |
panel.margin=margin(l=2.0, r=0, unit="cm"), |
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def make_layout(ann_dict): | |
def layout(node): | |
if node.is_leaf(): | |
labelFace = ete3.faces.TextFace(str(ann_dict[node.name])) | |
ete3.faces.add_face_to_node(labelFace, node, column=2, position="aligned") | |
esnFace = ete3.faces.RectFace(height=100*ann_dict[node.name], | |
width=10, | |
fgcolor="white", | |
bgcolor="red") |
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members <- read.table("~/Documents/group_members.txt", stringsAsFactors=F, header=F)$V1 | |
members_ordered <- sample(members, replace=F) | |
write.table(file="meeting_order.txt", data.frame(person=members_ordered), quote=F, row.names=F) |
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library("seqinr") | |
library("Biostrings") | |
library("MASS") | |
library("GenomicRanges") | |
library("dndscv") | |
## Helper methods copied from dndscv | |
nt = c("A","C","G","T") | |
compnt = setNames(rev(nt), nt) |
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