johnsolk

# makes all files read only
chmod -w *

# renames files with underscores 
for i in *.fastq; do j=$(echo $i | cut -d_ -f1-3 ); k=$(echo $i | cut -d_ -f5); echo mv $i "$j-$k"; done

# adds pwd to $PATH in .bashrc
echo export PATH=$(pwd):$PATH >> ~/.bashrc

# renames files

johnsolk

johnsolk

import screed
import os
from os import path
import subprocess
from subprocess import Popen, PIPE

def make_dir(dirname):
    if os.path.isdir(dirname) == False:
        os.mkdir(dirname)
        print("Directory created:", dirname)

johnsolk

# MaSuRCA 3.2.6 installation on MSU hpcc
ssh dev-intel14
cd bin
wget https://github.com/alekseyzimin/masurca/releases/download/3.2.6/MaSuRCA-3.2.6.tar.gz
tar -xvzf MaSuRCA-3.2.6.tar.gz
cd MaSuRCA-3.2.6
module load GNU/4.8.3
BOOST_ROOT=install ./install.sh

johnsolk

johnsolk

>DNA_CS
GCCATCAGATTGTGTTTGTTAGTCGCTTTTTTTTTTTGGAATTTTTTTTTTGGAATTTTTTTTTTGCGCTAACAACCTCCTGCCGTTTTGCCCGTGCATATCGGTCACGAACAAATCTGATTACTAAACACAGTAGCCTGGATTTGTTCTATCAGTAATCGACCTTATTCCTAATTAAATAGAGCAAATCCCCTTATTGGGGGTAAGACATGAAGATGCCAGAAAAACATGACCTGTTGGCCGCCATTCTCGCGGCAAAGGAACAAGGCATCGGGGCAATCCTTGCGTTTGCAATGGCGTACCTTCGCGGCAGATATAATGGCGGTGCGTTTACAAAAACAGTAATCGACGCAACGATGTGCGCCATTATCGCCTAGTTCATTCGTGACCTTCTCGACTTCGCCGGACTAAGTAGCAATCTCGCTTATATAACGAGCGTGTTTATCGGCTACATCGGTACTGACTCGATTGGTTCGCTTATCAAACGCTTCGCTGCTAAAAAAGCCGGAGTAGAAGATGGTAGAAATCAATAATCAACGTAAGGCGTTCCTCGATATGCTGGCGTGGTCGGAGGGAACTGATAACGGACGTCAGAAAACCAGAAATCATGGTTATGACGTCATTGTAGGCGGAGAGCTATTTACTGATTACTCCGATCACCCTCGCAAACTTGTCACGCTAAACCCAAAACTCAAATCAACAGGCGCCGGACGCTACCAGCTTCTTTCCCGTTGGTGGGATGCCTACCGCAAGCAGCTTGGCCTGAAAGACTTCTCTCCGAAAAGTCAGGACGCTGTGGCATTGCAGCAGATTAAGGAGCGTGGCGCTTTACCTATGATTGATCGTGGTGATATCCGTCAGGCAATCGACCGTTGCAGCAATATCTGGGCTTCACTGCCGGGCGCTGGTTATGGTCAGTTCGAGCATAAGGCTGACAGCCTGATTGCAAAATTCAAAGAAGCGGGCGGAACGGTCAGAGAGATTGATGTATGAGCAGAGTCACCGCGATTATCTCC

johnsolk

johnsolk

johnsolk

#outputs top 20 barcodes in file, if there are any
zcat lane1_sample_L001_R1_001.fastq.gz | head -400000 | grep '^@HWI' | cut -d : -f 10 | sort | uniq -c | sort -nr | head -20

johnsolk

###################################################################
"""Function: Take in a dammit gff3, dammit fasta, dammit namemap.
Output gff3 and fasta with trinity names.
by Dr. Tessa Pierce
"""
###################################################################

import sys
import os
import argparse