5th November 2012

The R function sweep
Working with a matrix, want to change each row or column.  Whether you operate by row or column is defined by MARGIN, as for apply..
E.g. add 1 to the 1st column, 2 to the 2nd, etc, of a matrix:
sweep(mymatrix,1,c(1:4), "+")

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find /path/to/files/ -name "session_*" -delete

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Type:

python

from Bio import SeqIO

SeqIO.convert("4788-1_S1_L001_R1_001_SISPA4_1.fastq", "fastq", "4788-1_S1_L001_R1_001_SISPA4_1.fasta", "fasta")

SeqIO.convert("4788-1_S1_L001_R1_001_SISPA4_1.fasta", "fastq", "4788-1_S1_L001_R1_001_SISPA4_1.qual", "quality")

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tar -zcvf archive_name.tar.gz directory_to_compress

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Reading in big files
library(sqldf)
f <- file="file" mybigfile="mybigfile" p="p">system.time(bigdf <- dbname="tempfile()," f="f" file.format="list(header=F," from="from" row.names="F)))<br" select="select" sqldf="sqldf">
See here