Notes from Mangaging Project with GNU Make

Cited from the book "Managing Projects with GNU Make"

"The target is the file or thing that must be made. The prerequisites or dependants are those files that must exist before the target can be successfully created. And the commands are those shell commands that will exist before the target can be successfucreate the target from the prerequisites."

"When make is asked to evaluate a rule, it begins by finding the files indicated by the prerequisites and target. If any of the prerequisites has an associated rule, make attempts to update those first. Next, the target file is considered. If any prerequisite is newer than the target, the target is remade by executing the commands."

" To update a line: different target (or to update more than one target) include the target name with make. such as make target"

" --just-print (or -n) tells make to display the commands it would execute for a particular target without actually executing them."

" To set almost any makefile variable on the command line to override the default value or the value set in the makefile. For example:
make mytarget FOO=BAR"

"If no prerequisites are listed to the right, then only the target(s) that do not exist are updated."

"Each command must begin with a tab character. This (obscure) syntax tells make that the characters that follow the tab are to be passed to a subshell for execution. If you accidentally insert a tab as the first character of a noncommand line, make will interpret the following text as a command under most circumstances."

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Explicit Rules:

"Pattern rules use wildcards instead of explicit filenames. get file matching the pattern needs to updated. Implicit rule."

"Implicit rules are either pattern rules or suffix built-in database of rules makes writing makefile."

"A variable is either a dollar sign followed by a single character or a dollar sign followed by a word in."

Wildcards:

"Make's wildcards are identical to the Bourne shell's: ~, *, ?, [...], and [^...]."

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the automatic variable $?: the set of prerequisites that are newer than the target.

$@: the name of the current target.

"You can look at make's default set of rules (and variables) by running make --print-data-base."

"The percent character can be placed anywhere within the pattern but can occur only once."

XSLT Notes

Cited from the book "XSLT for Dummies"

"apply-templates doesn’t include the tags of the element—only what’s inside the tags"

"Namespaces were developed to avoid this name collision by linking a namespace identifier with a URI (Uniform Resource Identifier)."

"the primary purpose of xsl:copy is to carry over the element tags. However, if you combine it with xsl:apply-templates, you copy both the tags and its content"

"xsl:copy-of duplicates everything inside the current node. "

 "The select attribute of the xsl:copy-of element determines what is copied to the result tree."

"<xsl:value-of select="expression"/>"

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matching element nodes
<xsl:template match="*|/">
<xsl:apply-templates/>
</xsl:template>

matching text and attribute nodes

<xsl:template match="text()|@*">
<xsl:value-of select="."/>
</xsl:template>

matching processing instructions and comments
<xsl:template match="processing-instruction()|comment()"/>

"An XPath expression for matching a namespace node doesn’t exist."
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child axis: child:: or omitted by default.

attribute axis: attribute:: or @ by shorthand.

node() is a node test that matches any node whatever kind it is.

chapter[position()=1]

chapter[last()]
==================================================

Makefile Redirecting Input and Output

http://mirror.unl.edu/ctan/macros/latex/contrib/poetrytex/Makefile

MACS14 Usage Demonstration

Identifying ChIP-seq enrichment using MACS

Convert MACS Pileup BedGraph to BigWig: End Coordinate Bigger than Chr Size

End coordinate 155630142 bigger than chr4 size of 155630120 line 35753167

Create Venn Diagram for Biological Data

Visualization biological data using proportional venn diagrams

Create Pie Chart from Homer Output

Creating pie charts of binding from ChIP-seq data using HOMER

Pie Charts in ggplot2

ChIP-seq: Heatmap

Moving color key in R heatmap.2 (function of gplots package)

How to change the color key value in heatmap.2?

HeatMaps with R (Chip-Seq)

ChIP-seq heatmap example

Choose individual heatmaps for sorting/clustering

UCSC Coordinate Transformation

Coordinate Transforms

Python: OOP

Object Oriented Programming

Python: Static Method, Class Method and Instance Method

Cited from Really Understanding Python @staticmethod and @classmethod

Python: __slots__

Cited from Python __slots__

"The proper use of __slots__ is to save space in objects. Instead of having a dynamic dict that allows adding attributes to objects at anytime, there is a static structure which does not allow additions after creation."

Python: *args and **kwargs

*args and **kwargs in python explained

Python Underscore "_" in Method and Variable Names

Cited from Python: Why do some functions have underscores “__” before and after the function name?

One underline in the beginning:

"Python doesn't have real private methods, so one underline in the start of a method or attribute means you shouldn't access this method."

Two underlines in the beginning:

"So, when you create a method starting with __ it means that you don't want to anyone can override it, it will be accessible only from inside the own class."

Two underlines in the beginning and in the end:

"When we see a method like __this__, don't call it. Because it means it's a method which Python calls, not by you."

ChIP-seq Plots

Metaseq

Data Structure in Python

Cited from What Are Linear Structures?

"What distinguishes one linear structure from another is the way in which items are added and removed, in particular the location where these additions and removals occur."

=================================================
Cited from What is a Stack?

'A stack (sometimes called a “push-down stack”) is an ordered collection of items where the addition of new items and the removal of existing items always takes place at the same end. This end is commonly referred to as the “top.” The end opposite the top is known as the "base."'

'The base of the stack is significant since items stored in the stack that are closer to the base represent those that have been in the stack the longest. The most recently added item is the one that is in position to be removed first.'

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Python: Pass Command Line Options

Argparse Tutorial

argparse option for passing a list as option

ArgumentParser

Differentail Gene Expression of Kallisto

Cited from Sleuth companion tool

Import abundance.txt files into an R matrix or list or Bioconductor SummarizedExperiment, follow read kallisto RNA-seq quantification into R / Bioconductor data structures

Analysis using Limma, follow How to run kallisto on NCBI SRA RNA-Seq data for differential expression using the mac terminal

Download mm9 Transcriptome Fasta

Mouse mm9 transcriptome fasta file, rna.fa.gz, is downloadable from ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.1/RNA/, according to the post Question: Reference Transcriptome From A Mouse

R Environment Variable for Maximum Number of Cores

SUGGESTION: Environment variable R_MAX_MC_CORES for maximum number of cores

Configure Custom Connection Options for SSH Client

Cited from How To Configure Custom Connection Options for your SSH Client

"The only difference is that depending on the option and value, using the equal sign with no spaces can allow you to specify an option on the command line without quoting."

Rsync Tutorial

How To Use Rsync to Sync Local and Remote Directories on a VPS

Peak Score for Macs Peaks

Cited from Question: What Is The Meaning Of The Score In Diffbind'S Occupancy/Overlap Analysis?

"The default peak score for macs peaks is the "=-10*LOG10(pvalue)" value. It is normalised to a 0..1 scale by dividing the scores by the maximum score (so the max score gets a value of 1)."

Integrating C++ with R

C++ for statisticians, with a focus on interfacing from R and R packages

DiffBind Official Tutorial

DiffBind Tutorial

Conversion Between Lowercase and Uppercase in Bash

Converting string to lower case in Bash shell scripting

Determine Whether RNA-seq Reads Are Stranded

Question: How To Determine If Paired–End Illumina Rnaseq Reads Are Strand–Specific

How to tell which library type to use (fr-firststrand or fr-secondstrand)? 

infer-experiment-py

Samtools Flagstat Results Explained

Question: What Does Samtools Flagstat Results Mean?

NCBI Programmatic Access to GEO

Programmatic access to GEO

NCBI E-utilities Tools

The E-utilities In-Depth: Parameters, Syntax and More

Aspera Connect Download and Install

aspera connect high-performance transfer plug-in can be downloaded from
http://downloads.asperasoft.com/connect2/

manual for installation can be found on http://download.asperasoft.com/download/docs/connect/3.6.0/user_linux/webhelp/index.html#dita/installation.html 

Loop Through Two arrays Deleting Overlaps in Perl

Loop through two arrays deleting overlaps in perl

Retrieve Data From Public Database

Accessing Public High-throughput Data Using R and Bioconductor