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Bio-IT Workshops
Intermediate Python
Commits
eb8154b7
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eb8154b7
authored
4 years ago
by
Toby Hodges
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add drafts for sections 2-4
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---
title
:
Working with Data
teaching
:
20
exercises
:
10
questions
:
-
"
How
should
I
work
with
numeric
data
in
Python?"
-
"
What's
the
recommended
way
to
handle
and
analyse
tabular
data?"
-
"
How
can
I
import
tabular
data
for
analysis
in
Python
and
export
the
results?"
objectives
:
-
"
handle
and
summarise
numeric
data
with
Numpy."
-
"
filter
values
in
their
data
based
on
a
range
of
conditions."
-
"
load
tabular
data
into
a
Pandas
dataframe
object."
-
"
describe
what
is
meant
by
the
data
type
of
an
array/series,
and
the
impact
this
has
on
how
the
data
is
handled."
-
"
add
and
remove
columns
from
a
dataframe."
-
"
select,
aggregate,
and
visualise
data
in
a
dataframe."
keypoints
:
-
"
Specialised
third-party
libraries
such
as
Numpy
and
Pandas
provide
powerful
objects
and
functions
that
can
help
us
analyse
our
data."
-
"
Pandas
dataframe
objects
allow
us
to
efficiently
load
and
handle
large
tabular
data."
-
"
Use
the
`pandas.read_csv`
and
`pandas.write_csv`
functions
to
read
and
write
tabular
data."
---
## plan
-
Toby currently scheduled to lead this session
-
Numpy
-
arrays
-
masking
-
aside about data types and potential hazards
-
reading data from a file (with note that more will come later on this topic)
-
link to existing image analysis material
-
Pandas
-
when an array just isn't enough
-
DataFrames - re-use material from
[
Software Carpentry
][
swc-python-gapminder
]
?
-
ideally with a more relevant example dataset...
-
include an aside about I/O - reading/writing files (pandas, numpy,
`open()`
, (?) bytes vs strings, (?) encoding)
-
Finish with example of
`df.plot()`
to set the scene for plotting section
{% include links.md %}
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---
title
:
Plotting Data
teaching
:
20
exercises
:
10
questions
:
-
"
How
can
I
create
publication-ready
figures
with
Python?"
objectives
:
-
"
plot
data
in
a
Matplotlib
figure."
-
"
create
multi-panelled
figures."
-
"
export
figures
in
a
variety
of
image
formats."
-
"
use
interactive
features
of
Jupyter
to
make
it
easier
to
fine-tune
a
plot."
keypoints
:
-
"
Matplotlib
is
a
powerful
plotting
library
for
Python."
-
"
It
can
also
be
annoyingly
fiddly.
Jupyter
can
help
with
this."
---
## plan
-
Renato currently scheduled to lead this session
-
Matplotlib
-
plotnine?
{% include links.md %}
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---
title
:
Parsing Command Line Arguments
teaching
:
20
exercises
:
10
questions
:
-
"
How
can
I
access
arguments
passed
to
my
Python
script
at
runtime?"
-
"
How
can
I
create
a
sophisticated
command
line
interface
for
my
script?"
-
"
How
can
I
provide
the
user
with
more
information
about
how
to
run
my
code?"
objectives
:
-
"
access
command
line
arguments
with
`sys.argv`."
-
"
parse
and
use
arguments
and
options
with
`argparse`."
-
"
create
a
comprehensive
usage
statement
for
their
script."
keypoints
:
-
"
Positional
command
line
arguments
can
be
accessed
from
inside
a
script
through
the
`sys.argv`
object."
-
"
The
`argparse`
module
allows
us
to
create
extensive
and
powerful
command
line
interfaces
for
our
scripts."
-
"
`argparse`
also
constructs
a
standardised
usage
statement
according
to
the
parser's
configuration."
---
## plan
-
Toby currently scheduled to lead this session
-
`sys.argv`
-
`argparse`
-
positonal arguments
-
options
-
capturing multiple items in a single argument
-
usage statements
{% include links.md %}
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...
...
@@ -46,6 +46,7 @@
[
rubygems
]:
https://rubygems.org/pages/download/
[
styles
]:
https://github.com/carpentries/styles/
[
swc-lessons
]:
https://software-carpentry.org/lessons/
[
swc-python-gapminder
]:
http://swcarpentry.github.io/python-novice-gapminder/
[
swc-releases
]:
https://github.com/swcarpentry/swc-releases
[
training
]:
https://carpentries.github.io/instructor-training/
[
workshop-repo
]:
{{
site.workshop_repo }}
...
...
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