rec3141

ps -axeo pid,etime,command | awk '$2~/^0[1234]-/ && $0~/COMMAND/ { print $1 }' | xargs kill

rec3141

for FILE in *.tsv; do 
  LI=`grep -v '^#' $FILE | wc -l`; 
  SEQS=`gunzip -c ./../NPRB/$F1.faa.gz | grep -c '^>'`; 
  BP=`gunzip -c ./../NPRB/$F1.faa.gz | grep -v '^>' | wc -b`; 
  echo -e "$FILE\t$LI" >> target_hits.txt; 
done

rm target_hits2.txt;

for FILE in *.tsv; do 

rec3141

#!/bin/bash

Search=$1

grep -i $Search FOAM-onto_rel1.tsv > $Search.ont
grep -i $Search FOAM-onto_rel1.tsv | cut -f5 > $Search.ko
wc -l $Search.ko
rm $Search.acc
	grep -A1 -f $Search.ko ./../FOAM/FOAM-hmm_rel1a_switch.hmm | grep NAME | tr -s ' ' | cut -f2 -d' ' | sort -u > $Search.acc
wc -l $Search.acc

rec3141

head -n1000 18*R1.fastq | grep -v -e '==> 18' -e '^$' | paste - - - - | cut -f2 | sort | uniq -c | sort -rn | head -n1000 | catg > 18s-top1000f.fa

rec3141

#!/bin/bash
NODE=bio
THREADS=7 #7 for bio, 24 for t1small
MEM=200 #128 max for t1small, 200+ for bio

mkdir -p spades-assembly
DIR='.'

#NPRB_meta_TBS.04.MEIO.R1.trimmed.fastq.gz
for PREFIX in `ls *.trimmed.fastq.gz | cut -f1-3 -d'.' | sort -u `; do

rec3141

#!/bin/sh
# run hmmer using hmm files
#INDIR=$1 #directory to search for .fastq.gz files

INDIR=~/work/NPRB

cd ~/work/hmm

for hmmfile in *.hmm; do
	hmm=`basename $hmmfile .hmm`;

rec3141

while read line; do curl -s "https ://api.crossref.org/works?query=`echo $line | tr -sC '[^a-zA-Z]' '+'`" | tr "," "\n" | tr -d '"\' | grep ^DOI | cut -f2- -d':' | head -n1 | xargs -I{} curl -sLH "Accept: application/x-bibtex" https ://doi.org/{} | grep -v '^\s*[<"]'; done < file

rec3141

while read line; do curl -LH "Accept: application/x-bibtex" https://doi.org/$line    | grep -v '^\s*[<"]'; done < dois.txt > dois.bib

rec3141

while read line; do title=`echo $line | sed 's/ /+/g'`; curl -s https://api.crossref.org/works?query.title=$title&rows=1 | tr ',' '\n' | tr -d '"\' | grep ^DOI | cut -f2- -d':'; done < titles.txt > titles.bib

rec3141

Q&A