yuifu

#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''manipulate BAM/SAM file.'''
#import built-in modules
import os,sys
import re
import string
from optparse import OptionParser
import warnings
import string

yuifu

# Note: '2' indicates that the shuffled sequence preserves 2-mer frequency
./main.exe -s KTTTTCTTTTTTTTTTA -n 1 -k 2

# Repeat shuffling for 10 times
./main.exe -s KTTTTCTTTTTTTTTTA -n 10 -k 2

yuifu

# ref: https://github.com/guma44/ushuffle
# ref: https://www.python.org/dev/peps/pep-3112/
# ref: https://pypi.org/project/ushuffle/

from ushuffle import shuffle, Shuffler, set_seed

set_seed(12345)

seq = bytes('ATTTTCTTTTTTTTTTA', 'ascii')

yuifu

library(ComplexHeatmap)

# test data
list_ht <- list()

for(i in 1:8){

  mat1 = matrix(rnorm(80, 2), 8, 10)
  mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
  rownames(mat1) = paste0("R", 1:12)

yuifu

# tmux config options for mouse scroll
set-option -g mouse on
bind -n WheelUpPane if-shell -F -t = "#{mouse_any_flag}" "send-keys -M" "if -Ft= '#{pane_in_mode}' 'send-keys -M' 'copy-mode -e'"

bind -n WheelUpPane if-shell -F -t = "#{mouse_any_flag}" "send-keys -M" "if -Ft= '#{pane_in_mode}' 'send-keys -M' 'select-pane -t=; copy-mode -e; send-keys -M'"
bind -n WheelDownPane select-pane -t= \; send-keys -M

# Scroll History
set -g history-limit 30000

yuifu

Command

cwltool --debug "https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl" "job.yml"

job.yml

run_ids: # array of type "string"

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/home/harukao/anaconda3/bin/cwltool 1.0.20190228155703
https://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to serialize this will break.
html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" does not look like a valid URI, trying to serialize this will break.
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: RDFa parsing Error! mismatched tag: line 21, column 2
Workflow checker warning:
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl:12:5: Source 'nthreads'
                                                                                                                         of type ["null",
                                                                                                                         "int"] may be
                                                                                                                         incompatible
https://raw.githubuserc

yuifu

/home/harukao/anaconda3/bin/cwltool 1.0.20190228155703
https://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to serialize this will break.
html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" does not look like a valid URI, trying to serialize this will break.
Could not load extension schema https://schema.org/docs/schema_org_rdfa.html: RDFa parsing Error! mismatched tag: line 21, column 2
Workflow checker warning:
https://raw.githubusercontent.com/pitagora-network/pitagora-cwl/master/workflows/download-fastq/download-fastq.cwl:12:5: Source 'nthreads'
                                                                                                                         of type ["null",
                                                                                                                         "int"] may be
                                                                                                                         incompatible
https://raw.githubuserc

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テスト用GTFファイルの作成

wget -O - ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz | gunzip | head -n 1000 > test.gtf

GTFファイルから gene_id, gene_name のTSVを作る

yuifu

$ julia cli/run.jl relcov examples/data/RamDA_72h_A09.uniq.q40.bam examples/data/gencode.vM15.primary_assembly.annotation.protein_coding.head.bed zzz_experiments/_fire_test_relcov
Start calculating relative gene body coverage...
- bam: examples/data/RamDA_72h_A09.uniq.q40.bam
- bed12: examples/data/gencode.vM15.primary_assembly.annotation.protein_coding.head.bed
- output: zzz_experiments/_fire_test_relcov.geneBodyCoverage.txt
          zzz_experiments/_fire_test_relcov.geneBodyCoverage.pdf
- transcript_length_cut: 100
- max_depth: 0
- N_bin: 100