A D3 demonstration of SVG and Canvas intermingling. Blue circles are plotted in SVG, black circles in canvas. One force to rule them all. The plot is zoomable and pannable.
Inspired by M. Bostock's Canvas / SVG zoom comparison series and collision detection examples [1] [2] .
| import sys, random | |
| # board is defined as list of 19 land tiles: Forest (4), Sheep (4), Wheat (4), Brick (3), Rocks (3), Desert (1) | |
| def new_board(board=''): | |
| available = list('ffffsssswwwwbbbrrrd') | |
| for i in range(19): | |
| random.shuffle(available) | |
| board += available.pop() | |
| return board |
| import sys | |
| rows = [] | |
| for line in open('gene_names.csv'): | |
| a,b,c = line.replace('\n','').split(',') | |
| rows.append([a,c]) | |
| for file in sys.argv[1:]: | |
| for i, line in enumerate(open(file)): |
| # usage: | |
| # python 3reads.py /batch/dir1/ /batch/dir2/ # run all steps on two batches | |
| # python 3reads.py -2 -3 -loadAndKeep /batch/dir # run steps 2 and 3 and use STAR --loadAndKeep | |
| # python 3reads.py /batch/dir1 /batch/dir2/ -13 # run steps 1 and 3 on two batches | |
| import sys, os | |
| base_dir = '/home/sxv/code/s7s/' | |
| MAKE_FASTQ = '%s/make_fastq.sh' % base_dir | |
| ALIGN = '%s/align_smart-3seq.sh' % base_dir | |
| MAKE_EXPRESSION_TABLE = '%s/make_expression_table.R' % base_dir |
| gawk '//{x=tolower($0); gsub(/[aeiou]/,"",x); a[x]++; b[x]=$0;}END{for(i in a){ if(a[i]==1){print i, b[i]} }}' /usr/share/dict/words |
| import sys | |
| opts = { | |
| 'window': 100000, | |
| 'intrachrom': False | |
| } | |
| args = sys.argv[1:] | |
| for a, arg in enumerate(args): | |
| if arg.startswith('-'): | |
| if arg.startswith('-w') or arg.startswith('--window'): |
| # define input cases via master_key.txt | |
| # for each run, align fastq -> bam | |
| # if GATK specified, run GATK, variant calling, and annovar | |
| # run matricizer2 on tab output | |
| # todo: add R clustering scripts | |
| ## usage | |
| # python rnarunner.py --input-dir /path/to/fastqs | |
| ## NOTES: input-dir must contain master_key.txt, input fastq.gz files, matricizer2.py, UCSC_GENE_NAME3.txt |
| import sys | |
| from glob import glob | |
| if (len(sys.argv)<=1): match = '*n0*' | |
| else: match = sys.argv[1] | |
| file = glob(match)[0] | |
| counts = {} | |
| with open(file) as f: | |
| print f.readline() |
| #!/usr/bin/env bash | |
| for f in *.vcf; do \ | |
| gawk 'BEGIN{FS="\t"; OFS="\t"; } # separator=tab | |
| /CHROM/{ | |
| ## for(i=0; i<NF; i++){ if($i=="FORMAT"){ samples=(NF-i) } } # todo | |
| if($(NF-2)~/FORMAT/){ | |
| samples=2; # two samples? | |
| if($(NF)~/[nN]$/ || $(NF)~/normal$/){ swap=1 } # is order t/n? | |
| } |
| # define input cases via master_key.txt | |
| # for each run, align fastq -> bam | |
| # if GATK specified, run GATK, variant calling, and annovar | |
| # run matricizer2 on tab output | |
| # todo: add R clustering scripts | |
| ## usage | |
| # python rnarunner.py --input-dir /path/to/fastqs | |
| ## NOTES: input-dir must contain master_key.txt, input fastq.gz files, matricizer2.py, UCSC_GENE_NAME3.txt |