jergosh

class SklearnWrapper(object):
    
    def __init__(self, clf, params={}):
        self.clf = clf(**params)

    def __getattr__(self, name):
        return self.clf.__getattribute__(name)
        

jergosh

#!/usr/bin/env perl
# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
# Copyright [2016-2019] EMBL-European Bioinformatics Institute
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 

jergosh

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)

jergosh

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)

jergosh

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")

jergosh

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"),

jergosh

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

jergosh

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";)

jergosh

#!/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'
    );

jergosh

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