- would be nice to be able to send kwargs to run_miso.py
- doesn't account for your paired-end samples at the moment
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import editdist | |
def distance(a, b): | |
""" | |
Find best edit distance between two strings of potentially uneven length. | |
>>> import editdist | |
>>> distance("abc", "abc") | |
0 | |
>>> distance("abc", "abcdef") |
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#!/usr/bin/env python | |
# coding=utf-8 | |
""" | |
Download the best resolution of the top <limit> video from subreddit 'videos' | |
to <out> directory. | |
""" | |
import multiprocessing | |
import os | |
import pafy |
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""" | |
qvality must be on the $PATH. | |
run on a file with pvalues in column 4: | |
$ python qvality.py --column 4 input.bed > output.bed | |
output file will have extra columns for PEP (posterior error prob) | |
and q-value. | |
if input.bed has a header, it is retained. |
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Hela_Pit1_T220A_0 | |
# Read Sequences: 1937152 | |
# Aligned: 535159 | |
# Unique Alignment: 396716 | |
# Gapped Alignment: 36685 | |
# Quality Filter: 342465 | |
# Homopolymer Filter: 285 | |
Hela_Pit1_T220A_1 | |
# Read Sequences: 3214272 |
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#! /usr/bin/env python | |
# encoding: utf-8 | |
import json | |
import urllib2 | |
# weather underground api key | |
api_key = '' | |
u = urllib2.urlopen("http://api.wunderground.com/api/%s/geolookup/q/autoip.json" % api_key) |
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#! /usr/bin/env python | |
# encoding: utf-8 | |
"""counts of mRNAs per sample where the reads have been aligned to mirbase.""" | |
import sys | |
import pybedtools | |
import pandas as pd | |
import os.path as op | |
from collections import Counter | |
def main(args): |
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#! /usr/bin/env bash | |
#BSUB -J align[1-12] | |
#BSUB -e gsnap.%J.%I.err | |
#BSUB -o gsnap.%J.%I.out | |
#BSUB -q normal | |
#BSUB -R "select[mem>16] rusage[mem=16] span[hosts=1]" | |
#BSUB -n 4 | |
<<DOC | |
align rnaseq samples using gsnap against mm9 |
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#!/usr/bin/env bash | |
#BSUB -J example | |
JOBIDS="" | |
# example loop | |
for (( i = 0; i < 10; i++ )); do | |
RUNSCRIPT=example.sh | |
echo "#! /usr/bin/env bash" > $RUNSCRIPT | |
echo "#BSUB -J example_slave" >> $RUNSCRIPT |
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# Usage: | |
# Rscript norm_count_table.R file_in.tab file_out.tab | |
# source("http://bioconductor.org/biocLite.R") | |
# biocLite("DESeq") | |
library(DESeq) | |
args <- commandArgs(TRUE) | |
filein <- args[1] | |
fileout <- args[2] |
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