This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Verifying my Blockstack ID is secured with the address 1KFPYC3FE9BhSKfwy5KYfThJbcZaxEDUm3 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
multmerge = function(mypath){ | |
filenames=list.files(path=mypath, full.names=TRUE) | |
datalist = lapply(filenames, function(x){read.delim(file=x,header=T)}) | |
} | |
multmerge = function(mypath){ | |
filenames=list.files(path=mypath, full.names=TRUE) | |
datalist = lapply(filenames, function(x){read.table(pipe("cut -f1,2,3,4,5,6 myFile.txt"))}) | |
Reduce(function(x,y) {merge(x,y)}, datalist) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# .bash_profile | |
# Get the aliases and functions | |
if [ -f ~/.bashrc ]; then | |
. ~/.bashrc | |
fi | |
# User specific environment and startup programs | |
# Set colors | |
export CLICOLOR=1 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
hit_total=`awk '{total += $3} END {print total}' *fastsummary.species` | |
nohit_total=`awk '{total += $2} END {print total}' *nomatchsum` | |
total=(($hit_total + $nohit_total)) | |
human=`awk '{if ($4==9606) {print $3} }' *fastsummary.species` | |
echo (($human / $total)) | |
hit_total=`awk '{total += $3} END {print total}' *fastsummary.species`; nohit_total=`awk '{total += $2} END {print total}' *nomatchsum`; total=(($hit_total + $nohit_total)); human=`awk '{if ($4==9606) {print $3} }' *fastsummary.species`; echo (($human / $total)) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import argparse | |
import logging | |
parser = argparse.ArgumentParser() | |
parser.add_argument('-d','--debug', | |
help='Print lots of debugging statements', | |
action="store_const",dest="loglevel",const=logging.DEBUG, | |
default=logging.WARNING | |
) | |
parser.add_argument('-v','--verbose', |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
132585322 (100.00%) were unpaired; of these: | |
4790404 (3.61%) aligned 0 times | |
98633353 (74.39%) aligned exactly 1 time | |
29161565 (21.99%) aligned >1 times | |
N50: 10038 | |
N90: 100 | |
total contigs: 2097980 | |
average length: 282 bp | |
trimmed average length: 281 bp | |
greater than or equal to 100: 1437022 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/python2.7 | |
'''USAGE: quicksubmit.py "command -l parameter" [options] | |
This script submits your one line command as a job to the pbs job scheduler. | |
''' | |
import subprocess as s | |
import sys | |
import argparse | |
def submitjob(job_name, command, subtype = "qsub", walltime = "10:00:00", cput = "10:00:00", pm = "nodes=1:ppn=1:mem=2gb", mailto = "", afterok = "", verbose = False): | |
'''USAGE: submitjob('my_job', 'echo "hello world!"') |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
import sys | |
def get_next_fasta (fileObject): | |
'''usage: for header, seq in get_next_fasta(fileObject): | |
''' | |
header = '' | |
seq = '' | |
#The following for loop gets the header of the first fasta | |
#record. Skips any leading junk in the file | |
for line in fileObject: |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#multi k velvet | |
seq_file=$1 | |
fq=$(basename $seq_file .trimmed.fq.keep.abundfilt) | |
for k in {19..51..2}; | |
do | |
quicksubmit "velveth && velvetg" | |
name=$(basename $i .pe.fq.gz); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/sh | |
#script to run digital normalization | |
##### | |
#files | |
R1=$1 #"R1_001" forward fastq reads | |
R2=$2 #"R2_001" reversed fastq reads | |
COM=$3 #"combined_001" interleaved reads | |
#paths |
NewerOlder