transpose | InforMedia Services (IMS)

shell job is a translator between the binory code, the middle name. several types of shells, with slight differences. one natively installed on MAC and Unix. born-again shell

bash commands: cd change director, ls – list; ls -F if it does not work: man ls (manual for LS); colon lower left corner tells you can scrool; q for escape; ls -ltr

arguments is colloquially used with different names. options, flags, parameters

cd .. – move up one directory . pwd : see the content cd data_shell/ – go down one directory

cd ~ – brings me al the way up . $HOME (universally defined variable

the default behavior of cd is to bring to home directory.

the core shall commands accept the same shell commands (letters)

$ du -h . gives me the size of the files. ctrl C to stop

$ clear . – clear the entire screen, scroll up to go back to previous command

man history $ history $! pwd (to go to pwd . $ history | grep history (piping)

$ cat (and the file name) – standard output

$ cat ../

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how to edit and delete files

to create new folder: $ mkdir . – make directory

text editors – nano, vim (UNIX text editors) . $ nano draft.txt . ctrl O (save) ctr X (exit) .
$ vim . shift esc (key) and in command line – wq (write quit) or just “q”

$ mv draft.txt ../data . (move files)

to remove $ rm thesis/: $ man rm

copy files $cp $ touch . (touches the file, creates if new)

remove $ rm . anything PSEUDO is dangerous Bash profile: cp -i

*- wild card, truncate $ ls analyzed (list of the analyized directory)

stackoverflow web site .

+++++++++++++++++

head command . $head basilisk.day (check only the first several lines of a large file

$ for filename in basilisk.dat unicorn.dat . (making a loop = multiline)

> do (expecting an action) do

> head -n 3 $filename . (3 is for the first three line of the file to be displayed and -n is for the number)

> done

for doing repetitive functions

also

$ for filename in *.dat ; do head -n 3$x; done

$ for filename in *.dat ; do echo $filename do head -n 3$x; done

$ echo $filename (print statement)

how to loop

$ for filename in *.dat ; do echo $filename ; echo head -n 3 $filename ; done

ctrl c or apple comd dot to get out of the loop

http://swcarpentry.github.io/shell-novice/02-filedir/

also

$ for filename in *.dat

> do

> $filename

> head -n 10 (first ten files ) $filename | tail -n 20 (last twenty lines)

$ for filename in *.dat

do
>> echo $filename
>> done

$ for filename in *.dat
>> do
>> cp $filename orig_$filename
>>done\

history > something else

$ head something.else

+++++++++++++

another function: word count

$ wc *.pdb (protein databank)

$ head cubane.pdb

if i don;t know how to read the outpun $ man wc

the difference between “*” and “?”

$ wc -l *.pdb

wc -l *.pdb > lenghts.txs

$ cat lenghts.txt

$ for fil in *.txt
>>> do
>>> wc -l $fil

by putting a $ sign use that not the actual text.

++++++++++++

$ nano middle.sh . The entire point of shell is to automate

$ bash (exectubale) to run the program middle.sh

rwx – rwx – rwx . (owner – group -anybody)

bash middle.sh

$ file middle.sh

$path .

$ echo $PATH | tr “:” “\n”

/usr/local/bin

/usr/bin

/bin

/usr/sbin

/sbin

/Applications/VMware Fusion.app/Contents/Public

/usr/local/munki

$ export PATH=$PWD:$PATH

(this is to make sure that the last version of Python is running)

$ ls ~ . (hidden files)

$ ls -a ~

$ touch .bach_profile .bashrc

$history | grep PATH

19 echo $PATH

44 echo #PATH | tr “:” “\n”

45 echo $PATH | tr “:” “\n”

46 export PATH=$PWD:$PATH

47 echo #PATH | tr “:” “\n”

48 echo #PATH | tr “:” “\n”

55 history | grep PATH

wc -l “$@” | sort -n ($@ – encompasses eerything. will process every single file in the list of files

$ chmod (make it executable)

$ find . -type d . (find only directories, recursively, )

$ find . -type f (files, instead of directories)

$ find . -name ‘*.txt’ . (find files by name, don’t forget single quotes)

$ wc -l $(find . -name ‘*.txt’) – when searching among direcories on different level

$ find . -name ‘*.txt’ | xargs wc -l – same as above ; two ways to do one and the same

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Saturday

Python

Link to the Python Plotting : https://swcarpentry.github.io/python-novice-gapminder

C and C++. scripting purposes in microbiology (instructor). libraries, packages alongside Python, which can extend its functionality. numpy and scipy (numeric and science python). Python for academic libraries?

going out of python $ quit () . python expect beginning and end parenthesis

new terminal needed after installation. anaconda 5.0.1

python 3 is complete redesign, not only an update.

http://swcarpentry.github.io/python-novice-gapminder/setup/

jupyter crashes in safari. open in chrome. spg engine maybe

https://swcarpentry.github.io/python-novice-gapminder/01-run-quit/

to start python in the terminal $ python

>> variable = 3

>> variable +10

several data types.

stored in JSON format.

command vs edit code. code cell is the gray box. a text cell is plain text

markdown syntax. format working with git and github . search explanation in https://swcarpentry.github.io/python-novice-gapminder/01-run-quit/

hackMD https://hackmd.io/ (use your GIthub account)

PANDOC – translates different data formats. https://pandoc.org/

print is a function

in what cases i will run my data trough Python instead of SPSS?

python is a 0 based language. starts counting with 0 – Java, C, P

atom_name = ‘helium ‘
print(atom_name[0]) string slicing and indexing is tricky

atom_name = ‘helium ‘
print(atom_name[0:6])

atom_name = ‘helium ‘
print(atom_name[7]) python does not know how to slice it

synthax of python is start : end : countby/step

string versus list . string is in a single quote, list will have brakets

strings allow me to work not only w values, revers the string

atom_name = ‘helium lithium beryllium’
print(atom_name[::-1])

muillyreb muihtil muileh

Atom_name = ‘helium’
len (atom_name) 6 . case sensitive

to clean the memory, restart the kernel

objects in Python have different types. adopt a class, value may have class inherent in its defintion

print (type(’42’)) . Python tells me that it is a string

print (type(42)) . tells e it is a string

LaTex

to combine integer and letter: print (str(1) + ‘A’)

converting a string to integer . : print (1 + int(’55’)) . all the same type

translation table. numerical representation of a string

float

print (‘half is’, 1 / 2.0)

built in functions and help

print is a function, lenght is a function (len); type, string, int, max, round,

Python does not explain well why the code breaks

ASCI character set – build in Python conversation

libraries – package: https://swcarpentry.github.io/python-novice-gapminder/06-libraries/

function “import”

Saturdady afternoon

reading .CSV in Python

http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip

**For windows users only: set up git https://swcarpentry.github.io/workshop-template/#git

python is object oriented and i can define the objects

python creates its own types of objects (which we model) and those are called “DataFrame”
method applied it is an attribute to data that already exists. – difference from function

data.info() . is function – it does not take any arguments

whereas

data.columns . is a method

print (data.T) . transpose. not easy in Excel, but very easy in Python

print (data.describe()) .

/Users/plamen_local/anaconda3/lib/python3.6/site-packages/pandas/__init__.py

%matplotlib inline teling Jupyter notebook

import pandas

data = pandas.read_csv(‘/Users/plamen_local/Desktop/data/gapminder_gdp_oceania.csv’ , index_col=’country’)
data.loc[‘Australia’].plot()
plt.xticks(rotation=10)

GD plot 2 is the most well known library.

xelatex is a PDF engine. reST restructured text like Markdown. google what is the best PDF engine with Jupyter

four loops . any computer language will have the concept of “for” loop. In Python: 1. whenever we create a “for” loop, that line must end with a single colon

2. indentation. any “if” statement in the “for” loop, gets indented

Posts Tagged ‘transpose’