yangwu91

#!/bin/bash

if [ -f $1 ]; then
	for SRA in `grep -o "SRR[0-9]\{7\}" $1`; do
		echo $SRA
		fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files $SRA &
	done
else
	fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files $1
fi

yangwu91

#!/usr/bin/env python
# -*- coding:utf-8 -*-
# Written by Wu, Yang <wuyang@vt.edu>

'''
Usage:
python stringtie_FPKM.py <stringtie_output_dir>|<sample_list>

For example:
  python stringtie_FPKM.py /foo/stringtie_output/

yangwu91

import matplotlib
# To solve remote session issues:
matplotlib.use("Agg")

# To make fonts editable (Type 3 to Type 2):
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42
plt.savefig("foo.pdf", transparent = True) # PDF is the best.

# subplots settings:

yangwu91

import datetime
start_time = datetime.datetime.now()
end_time = datetime.datetime.now()
cost_time = (end_time - start_time).seconds
print "Done in %ss." % cost_time