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def update_one_sample(gsmid, parse_fields=['other_ids', 'paper', 'name', 'species', 'description', 'antibody', 'factor', | |
'cell type', 'cell line', 'tissue', 'strain']): | |
"""Given a gsmid, tries to create a new sample--auto-filling in the | |
meta fields | |
If overwrite is True and there is the sample that has the same gsmid, this function will overwrite that sample | |
NOTE: will try to save the sample!! |
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CLASS1 = ["BMAL1-ZT10_rep1", "BMAL1-ZT10_rep2"] | |
CLASS1_PATHS = ["/mnt/Storage/data/exam_data/BMAL1/BMAL1-ZT10_rep1.bam", "/mnt/Storage/data/exam_data/BMAL1/BMAL1-ZT10_rep2.bam"] | |
CLASS2 = ["BMAL1-ZT22_rep1"] | |
CLASS2_PATHS = ["/mnt/Storage/data/exam_data/BMAL1/BMAL1-ZT22_rep1.bam"] | |
GTF = "/mnt/Storage/data/RefGene/mm9.gtf" | |
SAMPLES = CLASS1 + CLASS2 |
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def _bowtie(workflow, conf): | |
for target in conf.sample_targets: | |
bowtie = attach_back(workflow, | |
ShellCommand( | |
"{tool} -p {param[threads]} -S -m {param[max_align]} \ | |
{param[genome_index]} {input[fastq]} {output[sam]} 2> {output[bowtie_summary]}", | |
input={"genome_dir": os.path.dirname(conf.get_path("lib", "genome_index")), | |
"fastq": target + ".fastq"}, | |
output={"sam": target + ".sam", | |
"bowtie_summary": target + "_bowtie_summary.txt", }, |
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def _macs2(workflow, conf): | |
# merge all treatments into one | |
merge_bams_treat = ShellCommand( | |
"{tool} merge {output[merged]} {param[bams]}", | |
tool="samtools", | |
input=[target + ".bam" for target in conf.treatment_targets], | |
output={"merged": conf.prefix + "_treatment.bam"}) | |
merge_bams_treat.param = {"bams": " ".join(merge_bams_treat.input)} | |
if len(conf.treatment_targets) > 1: |
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def _macs2(workflow, conf): | |
# merge all treatments into one | |
merge_bams_treat = ShellCommand( | |
"{tool} merge {output[merged]} {param[bams]}", | |
tool="samtools", | |
input=[target + ".bam" for target in conf.treatment_targets], | |
output={"merged": conf.prefix + "_treatment.bam"}) | |
merge_bams_treat.param = {"bams": " ".join(merge_bams_treat.input)} | |
if len(conf.treatment_targets) > 1: |
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first_denom = {1:1,2:5,3:10,4:25,5:50} | |
def cc_rec(amount, kinds_of_coins = 5): | |
if amount == 0: | |
return 1 | |
elif amount < 0 or kinds_of_coins == 0: | |
return 0 | |
else: | |
return cc_rec(amount, kinds_of_coins - 1) + \ | |
cc_rec(amount - first_denom[kinds_of_coins], kinds_of_coins) |
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/* | |
* A white-list based PAC without regexp, by @janlay | |
* It's just simple and fast. | |
* Last update: Dec 9, 2013 | |
* Special thanks to @Paveo | |
*/ | |
function FindProxyForURL(url, host) { | |
var PROXY = "PROXY 127.0.0.1:8800;SOCKS 127.0.0.1:8801"; | |
var DEFAULT = "DIRECT"; |
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"""Library to interface with the GEO (GDS- GEO DataSets) repository""" | |
import os | |
import re | |
import sys | |
import urllib | |
import traceback | |
from datetime import datetime | |
import time | |
import enchant |
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SELECT st_geomfromtext('POINT(-1 38)', 4329); | |
select st_asewkt('0101000020E9100000000000000000F0BF0000000000004340'); | |
select st_geomfromtext('LINESTRING(-13 21,0 0,3 2') as mycheckmark; |
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SELECT st_geomfromtext('POINT(-1 38)', 4329); | |
select st_asewkt('0101000020E9100000000000000000F0BF0000000000004340'); | |
select st_geomfromtext('LINESTRING(-13 21,0 0,3 2') as mycheckmark; |