mdshw5

# This file contains pin mappings for the Wanhao Duplicator 9 MK1,
# also sold as the Monoprice Maker Pro MK1. To use this config,
# the firmware should be compiled for the AVR atmega2560.

# See the example.cfg file for a description of available parameters.

[stepper_x]
step_pin: PF7
dir_pin: !PK0
enable_pin: !PF6

mdshw5

title <- "Kinds of sunscreen I get to use:"
names <- c("SunSport Waterproof SPF30", 
           "The organic zinc kids one",
           "The moisturizing one",
           "The expensive one",
           "The one I like")
colors <- c("#EFD8B5", "#F9EDD4", "#CDE2CE", "#82C6BD", "#5BB6CC")
data <- data.frame(values=c(80,12,5,2,1), names=factor(names, levels=names))
library(ggplot2)
library(xkcd)

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from Spotfire.Dxp.Application.Visuals import VisualContent

vc = vis.As[VisualContent]()

dataTable=vc.Data.DataTableReference
marking=vc.Data.MarkingReference
marking.SetSelection(marking.GetSelection(dataTable),dataTable)

mdshw5

import gffutils
import os.path
from pyfaidx import Fasta

gtf_path = "/path/to/gencode.gtf"
gtf_db = gtf_path + ".db"
fasta_path = "/path/to/hg38.fasta"

if os.path.exists(gtf_db):
  db = gffutils.FeatureDB(gtf_db)

mdshw5

rule screenshot_config:
    input: bam="{dataset}.sort.bam", bai="{dataset}.sort.bam.bai", calls="{dataset}.calls"
    output: batch="{dataset}.igv.batch"
    params: runtime="600", memory="1G", filename="{dataset}.alignments.png"
    run:
        import os.path
        batch_template = """load {bam}
preference SAM.SHOW_CENTER_LINE false
snapshotDirectory {directory}
genome hg38

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import vcf

file = ''
with open('outfile.txt', 'w') as out:
  for variant in vcf.Reader(open(file)):
    if len(variant.FILTER) == 0:
      if variant.is_snp:
        for sample in variant.samples:
          ref, alt = sample.gt_bases.replace('|', '/').split('/')
          print(variant.CHROM, str(variant.POS), ref, alt, sep='\t', file=out) 

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from simplesam import Reader

with Reader(open("input.sam")) as sam, open("output.fastq", "w") as fastq:
  for read in sam:
    fastq.write("@%s\n" % read.qname)
    fastq.write("%s\n" % read.seq)
    fastq.write("+\n")
    fastq.write("%s\n" % read.qual)

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from Bio import bgzf
with bgzf.open('Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz') as fasta:
  fasta.tell()
  for line in fasta:
    if line.startswith('>'):
      fasta.tell()

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from pyfaidx import Fasta

# positions.txt:
# chr1 1 T
# chr1 100 C
# chr2 10 G
# ...

with open('positions.txt') as mut_table:
  # mutable Fasta modifies input file in-place

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import gffutils
import pyfaidx

db = gffutils.create_db('input.gff')
fasta = pyfaidx.Fasta('input.fa')

for cds in db.features_of_type('cds', order_by='start'):
  print(cds.sequence(fasta))