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Statistical-Genetics
jass_preprocessing
Commits
92a461de
Commit
92a461de
authored
Nov 29, 2019
by
hjulienne
Browse files
add filter imputation quality
parent
8f85b369
Pipeline
#19045
passed with stages
in 57 seconds
Changes
31
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config:
7890896c7cf0d3614ade393a5c103246
config:
f0cd103aab646a141229409df671f02e
tags: 645f666f9bcd5a90fca523b33c5a78b7
doc/_build/html/_autosummary/jass_preprocessing.html
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doc/_build/html/_autosummary/modules.html
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@@ -17,32 +17,34 @@
<script
type=
"text/javascript"
src=
"../_static/js/modernizr.min.js"
></script>
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../"
src=
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></script>
<script
type=
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src=
"../_static/jquery.js"
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<script
type=
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type=
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<script
type=
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src=
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></script>
<script
type=
"text/javascript"
src=
"../_static/js/theme.js"
></script>
<link
rel=
"stylesheet"
href=
"../_static/css/theme.css"
type=
"text/css"
/>
<link
rel=
"stylesheet"
href=
"../_static/pygments.css"
type=
"text/css"
/>
<link
rel=
"index"
title=
"Index"
href=
"../genindex.html"
/>
<link
rel=
"search"
title=
"Search"
href=
"../search.html"
/>
<script
src=
"../_static/js/modernizr.min.js"
></script>
</head>
<body
class=
"wy-body-for-nav"
>
<div
class=
"wy-grid-for-nav"
>
<nav
data-toggle=
"wy-nav-shift"
class=
"wy-nav-side"
>
<div
class=
"wy-side-scroll"
>
<div
class=
"wy-side-nav-search"
>
<div
class=
"wy-side-nav-search"
>
...
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@@ -154,9 +156,7 @@
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"jass_preprocessing.html#module-jass_preprocessing.map_gwas"
>
jass_preprocessing.map_gwas module
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"jass_preprocessing.html#module-jass_preprocessing.map_reference"
>
jass_preprocessing.map_reference module
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"jass_preprocessing.html#module-jass_preprocessing.save_output"
>
jass_preprocessing.save_output module
</a></li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"jass_preprocessing.html#module-jass_preprocessing"
>
Module contents
</a><ul
class=
"simple"
>
</ul>
</li>
<li
class=
"toctree-l2"
><a
class=
"reference internal"
href=
"jass_preprocessing.html#module-jass_preprocessing"
>
Module contents
</a></li>
</ul>
</li>
</ul>
...
...
@@ -191,25 +191,16 @@
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../"
src=
"../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/js/theme.js"
></script>
<script
type=
"text/javascript"
>
jQuery
(
function
()
{
SphinxRtdTheme
.
Navigation
.
enable
(
true
);
});
</script>
</script>
</body>
</html>
\ No newline at end of file
doc/_build/html/_modules/index.html
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@@ -17,32 +17,34 @@
<script
type=
"text/javascript"
src=
"../_static/js/modernizr.min.js"
></script>
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../"
src=
"../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/language_data.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/js/theme.js"
></script>
<link
rel=
"stylesheet"
href=
"../_static/css/theme.css"
type=
"text/css"
/>
<link
rel=
"stylesheet"
href=
"../_static/pygments.css"
type=
"text/css"
/>
<link
rel=
"index"
title=
"Index"
href=
"../genindex.html"
/>
<link
rel=
"search"
title=
"Search"
href=
"../search.html"
/>
<script
src=
"../_static/js/modernizr.min.js"
></script>
</head>
<body
class=
"wy-body-for-nav"
>
<div
class=
"wy-grid-for-nav"
>
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data-toggle=
"wy-nav-shift"
class=
"wy-nav-side"
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"wy-side-scroll"
>
<div
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"wy-side-nav-search"
>
<div
class=
"wy-side-nav-search"
>
...
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@@ -171,25 +173,16 @@
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../"
src=
"../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../_static/js/theme.js"
></script>
<script
type=
"text/javascript"
>
jQuery
(
function
()
{
SphinxRtdTheme
.
Navigation
.
enable
(
true
);
});
</script>
</script>
</body>
</html>
\ No newline at end of file
doc/_build/html/_modules/jass_preprocessing/compute_score.html
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92a461de
...
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@@ -17,32 +17,34 @@
<script
type=
"text/javascript"
src=
"../../_static/js/modernizr.min.js"
></script>
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../../"
src=
"../../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/language_data.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/js/theme.js"
></script>
<link
rel=
"stylesheet"
href=
"../../_static/css/theme.css"
type=
"text/css"
/>
<link
rel=
"stylesheet"
href=
"../../_static/pygments.css"
type=
"text/css"
/>
<link
rel=
"index"
title=
"Index"
href=
"../../genindex.html"
/>
<link
rel=
"search"
title=
"Search"
href=
"../../search.html"
/>
<script
src=
"../../_static/js/modernizr.min.js"
></script>
</head>
<body
class=
"wy-body-for-nav"
>
<div
class=
"wy-grid-for-nav"
>
<nav
data-toggle=
"wy-nav-shift"
class=
"wy-nav-side"
>
<div
class=
"wy-side-scroll"
>
<div
class=
"wy-side-nav-search"
>
<div
class=
"wy-side-nav-search"
>
...
...
@@ -147,7 +149,7 @@
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
seaborn
</span>
<span
class=
"k"
>
as
</span>
<span
class=
"nn"
>
sns
</span>
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
matplotlib.pyplot
</span>
<span
class=
"k"
>
as
</span>
<span
class=
"nn"
>
plt
</span>
<span
class=
"n"
>
perSS
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"mf"
>
0.7
</span>
<div
class=
"viewcode-block"
id=
"compute_z_score"
><a
class=
"viewcode-back"
href=
"../../_autosummary/jass_preprocessing.html#jass_preprocessing.compute_score.compute_z_score"
>
[docs]
</a><span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
compute_z_score
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
mgwas
</span><span
class=
"p"
>
):
</span>
<span
class=
"sd"
>
"""
</span>
...
...
@@ -168,7 +170,7 @@
<span
class=
"k"
>
return
</span>
<span
class=
"n"
>
mgwas
</span></div>
<div
class=
"viewcode-block"
id=
"compute_sample_size"
><a
class=
"viewcode-back"
href=
"../../_autosummary/jass_preprocessing.html#jass_preprocessing.compute_score.compute_sample_size"
>
[docs]
</a><span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
compute_sample_size
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
mgwas
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
diagnostic_folder
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
trait
</span><span
class=
"p"
>
):
</span>
<div
class=
"viewcode-block"
id=
"compute_sample_size"
><a
class=
"viewcode-back"
href=
"../../_autosummary/jass_preprocessing.html#jass_preprocessing.compute_score.compute_sample_size"
>
[docs]
</a><span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
compute_sample_size
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
mgwas
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
diagnostic_folder
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
trait
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
perSS
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"mf"
>
0.7
</span><span
class=
"p"
>
):
</span>
<span
class=
"k"
>
if
</span>
<span
class=
"s1"
>
'
n
'
</span>
<span
class=
"ow"
>
in
</span>
<span
class=
"n"
>
mgwas
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
columns
</span><span
class=
"p"
>
:
</span>
<span
class=
"n"
>
myN
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
mgwas
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
n
</span>
...
...
@@ -192,7 +194,7 @@
<span
class=
"n"
>
warnings
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
warn
</span><span
class=
"p"
>
(
</span><span
class=
"s2"
>
"
Some snp had an infinite sample size
"
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
myW_thres
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
np
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
percentile
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
myN
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
dropna
</span><span
class=
"p"
>
(),
</span>
<span
class=
"mi"
>
90
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
ss_thres
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n
"
>
perSS
</span>
<span
class=
"o"
>
*
</span>
<span
class=
"n"
>
myW_thres
</span>
<span
class=
"n"
>
ss_thres
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n
b"
>
float
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
perSS
</span><span
class=
"p"
>
)
</span>
<span
class=
"o"
>
*
</span>
<span
class=
"n"
>
myW_thres
</span>
<span
class=
"n"
>
mgwas
</span><span
class=
"p"
>
[
</span><span
class=
"s2"
>
"
computed_N
"
</span><span
class=
"p"
>
]
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
myN
</span>
<span
class=
"n"
>
plt
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
clf
</span><span
class=
"p"
>
()
</span>
<span
class=
"n"
>
p1
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
sns
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
distplot
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
mgwas
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
computed_N
</span><span
class=
"p"
>
[
</span><span
class=
"o"
>
~
</span><span
class=
"n"
>
mgwas
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
computed_N
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
isna
</span><span
class=
"p"
>
()])
</span>
...
...
@@ -235,25 +237,16 @@
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../../"
src=
"../../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/js/theme.js"
></script>
<script
type=
"text/javascript"
>
jQuery
(
function
()
{
SphinxRtdTheme
.
Navigation
.
enable
(
true
);
});
</script>
</script>
</body>
</html>
\ No newline at end of file
doc/_build/html/_modules/jass_preprocessing/dna_utils.html
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@@ -17,32 +17,34 @@
<script
type=
"text/javascript"
src=
"../../_static/js/modernizr.min.js"
></script>
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../../"
src=
"../../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/language_data.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/js/theme.js"
></script>
<link
rel=
"stylesheet"
href=
"../../_static/css/theme.css"
type=
"text/css"
/>
<link
rel=
"stylesheet"
href=
"../../_static/pygments.css"
type=
"text/css"
/>
<link
rel=
"index"
title=
"Index"
href=
"../../genindex.html"
/>
<link
rel=
"search"
title=
"Search"
href=
"../../search.html"
/>
<script
src=
"../../_static/js/modernizr.min.js"
></script>
</head>
<body
class=
"wy-body-for-nav"
>
<div
class=
"wy-grid-for-nav"
>
<nav
data-toggle=
"wy-nav-shift"
class=
"wy-nav-side"
>
<div
class=
"wy-side-scroll"
>
<div
class=
"wy-side-nav-search"
>
<div
class=
"wy-side-nav-search"
>
...
...
@@ -183,25 +185,16 @@
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../../"
src=
"../../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/js/theme.js"
></script>
<script
type=
"text/javascript"
>
jQuery
(
function
()
{
SphinxRtdTheme
.
Navigation
.
enable
(
true
);
});
</script>
</script>
</body>
</html>
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doc/_build/html/_modules/jass_preprocessing/map_gwas.html
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92a461de
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@@ -17,32 +17,34 @@
<script
type=
"text/javascript"
src=
"../../_static/js/modernizr.min.js"
></script>
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../../"
src=
"../../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/language_data.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/js/theme.js"
></script>
<link
rel=
"stylesheet"
href=
"../../_static/css/theme.css"
type=
"text/css"
/>
<link
rel=
"stylesheet"
href=
"../../_static/pygments.css"
type=
"text/css"
/>
<link
rel=
"index"
title=
"Index"
href=
"../../genindex.html"
/>
<link
rel=
"search"
title=
"Search"
href=
"../../search.html"
/>
<script
src=
"../../_static/js/modernizr.min.js"
></script>
</head>
<body
class=
"wy-body-for-nav"
>
<div
class=
"wy-grid-for-nav"
>
<nav
data-toggle=
"wy-nav-shift"
class=
"wy-nav-side"
>
<div
class=
"wy-side-scroll"
>
<div
class=
"wy-side-nav-search"
>
<div
class=
"wy-side-nav-search"
>
...
...
@@ -151,6 +153,9 @@
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
sys
</span>
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
pandas
</span>
<span
class=
"k"
>
as
</span>
<span
class=
"nn"
>
pd
</span>
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
numpy
</span>
<span
class=
"k"
>
as
</span>
<span
class=
"nn"
>
np
</span>
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
gzip
</span>
<span
class=
"kn"
>
import
</span>
<span
class=
"nn"
>
re
</span>
<div
class=
"viewcode-block"
id=
"walkfs"
><a
class=
"viewcode-back"
href=
"../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.walkfs"
>
[docs]
</a><span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
walkfs
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
startdir
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
findfile
</span><span
class=
"p"
>
):
</span>
<span
class=
"sd"
>
"""
</span>
...
...
@@ -214,46 +219,48 @@
<span
class=
"k"
>
return
</span>
<span
class=
"n"
>
df
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
replace
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
def_missing
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
nan_vec
</span><span
class=
"p"
>
)
</span></div>
<div
class=
"viewcode-block"
id=
"map_columns_position"
><a
class=
"viewcode-back"
href=
"../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.map_columns_position"
>
[docs]
</a><span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
map_columns_position
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
GWAS_labels
</span><span
class=
"p"
>
):
</span>
<div
class=
"viewcode-block"
id=
"map_columns_position"
><a
class=
"viewcode-back"
href=
"../../_autosummary/jass_preprocessing.html#jass_preprocessing.map_gwas.map_columns_position"
>
[docs]
</a><span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
map_columns_position
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
column_dict
</span><span
class=
"p"
>
):
</span>
<span
class=
"sd"
>
"""
</span>
<span
class=
"sd"
>
Find column position for each specific Gwas
</span>
<span
class=
"sd"
>
Args:
</span>
<span
class=
"sd"
>
gwas_internal_link (str): filename of the GWAS data (with path)
</span>
<span
class=
"sd"
>
GWAS_labels (
str): filename
of the
csv
information file
</span>
<span
class=
"sd"
>
GWAS_labels (
pd.DataFrame): corresponding row
of the information file
</span>
<span
class=
"sd"
>
Return:
</span>
<span
class=
"sd"
>
pandas Series with column position and column names as index
</span>
<span
class=
"sd"
>
"""
</span>
<span
class=
"n"
>
column_dict
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
read_csv
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
GWAS_labels
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
sep
</span><span
class=
"o"
>
=
</span><span
class=
"s1"
>
'
</span><span
class=
"se"
>
\t
</span><span
class=
"s1"
>
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
na_values
</span><span
class=
"o"
>
=
</span><span
class=
"s1"
>
'
na
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
index_col
</span><span
class=
"o"
>
=
</span><span
class=
"mi"
>
0
</span><span
class=
"p"
>
)
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
gwas_file
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
gwas_internal_link
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
split
</span><span
class=
"p"
>
(
</span><span
class=
"s1"
>
'
/
'
</span><span
class=
"p"
>
)[
</span><span
class=
"o"
>
-
</span><span
class=
"mi"
>
1
</span><span
class=
"p"
>
]
</span>
<span
class=
"n"
>
my_labels
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
column_dict
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
loc
</span><span
class=
"p"
>
[
</span><span
class=
"n"
>
gwas_file
</span><span
class=
"p"
>
]
</span>
<span
class=
"c1"
>
#Our standart labels:
</span>
<span
class=
"n"
>
reference_label
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
column_dict
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
columns
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
tolist
</span><span
class=
"p"
>
()
</span>
<span
class=
"c1"
>
# labels in the GWAS files
</span>
<span
class=
"n"
>
target_lab
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
Index
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
my_labels
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
values
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
tolist
</span><span
class=
"p"
>
())
</span>
<span
class=
"n"
>
f
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"nb"
>
open
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
reference_label
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
column_dict
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
index
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
tolist
</span><span
class=
"p"
>
()
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
reference_label
</span><span
class=
"p"
>
)
</span>
<span
class=
"c1"
>
# labels in the GWAS files
</span>
<span
class=
"n"
>
target_lab
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
Index
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
column_dict
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
values
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
tolist
</span><span
class=
"p"
>
())
</span>
<span
class=
"n"
>
is_gzipped
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
re
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
search
</span><span
class=
"p"
>
(
</span><span
class=
"sa"
>
r
</span><span
class=
"s2"
>
"
.gz$
"
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"k"
>
if
</span>
<span
class=
"n"
>
is_gzipped
</span><span
class=
"p"
>
:
</span>
<span
class=
"n"
>
f
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
gzip
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
open
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
line
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
f
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
readline
</span><span
class=
"p"
>
()
</span>
<span
class=
"n"
>
line
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
line
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
decode
</span><span
class=
"p"
>
(
</span><span
class=
"s1"
>
'
utf-8
'
</span><span
class=
"p"
>
)
</span>
<span
class=
"k"
>
else
</span><span
class=
"p"
>
:
</span>
<span
class=
"n"
>
f
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"nb"
>
open
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
line
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
f
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
readline
</span><span
class=
"p"
>
()
</span>
<span
class=
"n"
>
count_line
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"mi"
>
0
</span>
<span
class=
"n"
>
line
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
f
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
readline
</span><span
class=
"p"
>
()
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
line
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
header
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
Index
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
line
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
split
</span><span
class=
"p"
>
())
</span>
<span
class=
"n"
>
header
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
Index
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
line
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
split
</span><span
class=
"p"
>
())
</span>
<span
class=
"k"
>
def
</span>
<span
class=
"nf"
>
get_position
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
I
</span><span
class=
"p"
>
,
</span><span
class=
"n"
>
x
</span><span
class=
"p"
>
):
</span>
<span
class=
"k"
>
try
</span><span
class=
"p"
>
:
</span>
<span
class=
"k"
>
return
</span>
<span
class=
"n"
>
I
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
get_loc
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
x
</span><span
class=
"p"
>
)
</span>
<span
class=
"k"
>
except
</span>
<span
class=
"ne"
>
KeyError
</span><span
class=
"p"
>
:
</span>
<span
class=
"k"
>
return
</span>
<span
class=
"n"
>
np
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
nan
</span>
<span
class=
"n"
>
label_position
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"p"
>
[
</span><span
class=
"n"
>
get_position
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
header
</span><span
class=
"p"
>
,
</span><span
class=
"n"
>
i
</span><span
class=
"p"
>
)
</span>
<span
class=
"k"
>
for
</span>
<span
class=
"n"
>
i
</span>
<span
class=
"ow"
>
in
</span>
<span
class=
"n"
>
target_lab
</span><span
class=
"p"
>
]
</span>
<span
class=
"n"
>
label_position
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"p"
>
[
</span><span
class=
"n"
>
get_position
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
header
</span><span
class=
"p"
>
,
</span><span
class=
"n"
>
i
</span><span
class=
"p"
>
)
</span>
<span
class=
"k"
>
for
</span>
<span
class=
"n"
>
i
</span>
<span
class=
"ow"
>
in
</span>
<span
class=
"n"
>
target_lab
</span><span
class=
"p"
>
]
</span>
<span
class=
"n"
>
mapgw
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
Series
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
label_position
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
index
</span><span
class=
"o"
>
=
</span><span
class=
"n"
>
reference_label
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
mapgw
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
mapgw
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
loc
</span><span
class=
"p"
>
[
</span><span
class=
"o"
>
~
</span><span
class=
"n"
>
mapgw
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
isna
</span><span
class=
"p"
>
()]
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
astype
</span><span
class=
"p"
>
(
</span><span
class=
"nb"
>
int
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
mapgw
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
sort_values
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
inplace
</span><span
class=
"o"
>
=
</span><span
class=
"kc"
>
True
</span><span
class=
"p"
>
)
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
mapgw
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
f
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
close
</span><span
class=
"p"
>
()
</span>
<span
class=
"k"
>
return
</span>
<span
class=
"n"
>
mapgw
</span></div>
...
...
@@ -269,18 +276,28 @@
<span
class=
"sd"
>
Return:
</span>
<span
class=
"sd"
>
a pandas dataframe with missing value all equal to np.nan
</span>
<span
class=
"sd"
>
"""
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"s2"
>
"
Reading file:
"
</span><span
class=
"p"
>
)
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
is_gzipped
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
re
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
search
</span><span
class=
"p"
>
(
</span><span
class=
"sa"
>
r
</span><span
class=
"s2"
>
"
.gz$
"
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
)
</span>
<span
class=
"k"
>
if
</span>
<span
class=
"n"
>
is_gzipped
</span><span
class=
"p"
>
:
</span>
<span
class=
"n"
>
compression
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"s1"
>
'
gzip
'
</span>
<span
class=
"k"
>
else
</span><span
class=
"p"
>
:
</span>
<span
class=
"n"
>
compression
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"kc"
>
None
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
column_map
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
values
</span><span
class=
"p"
>
)
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
column_map
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
index
</span><span
class=
"p"
>
)
</span>
<span
class=
"n"
>
fullGWAS
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
pd
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
read_csv
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
gwas_internal_link
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
delim_whitespace
</span><span
class=
"o"
>
=
</span><span
class=
"kc"
>
True
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
usecols
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
column_map
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
values
</span><span
class=
"p"
>
,
</span>
<span
class=
"c1"
>
#column_dict[
'
label_position
'
].keys(),
</span>
<span
class=
"n"
>
usecols
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
column_map
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
values
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
compression
</span><span
class=
"o"
>
=
</span><span
class=
"n"
>
compression
</span><span
class=
"p"
>
,
</span>
<span
class=
"c1"
>
#column_dict[
'
label_position
'
].keys(),
</span>
<span
class=
"n"
>
names
</span><span
class=
"o"
>
=
</span>
<span
class=
"n"
>
column_map
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
index
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
index_col
</span><span
class=
"o"
>
=
</span><span
class=
"mi"
>
0
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
header
</span><span
class=
"o"
>
=
</span><span
class=
"mi"
>
0
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
na_values
</span><span
class=
"o"
>
=
</span>
<span
class=
"p"
>
[
</span><span
class=
"s1"
>
''
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
#N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
#N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
#NA
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-1.#IND
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-1.#QNAN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-NaN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-nan
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
1.#IND
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
1.#QNAN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
header
</span><span
class=
"o"
>
=
</span><span
class=
"mi"
>
0
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
na_values
</span><span
class=
"o"
>
=
</span>
<span
class=
"p"
>
[
</span><span
class=
"s1"
>
''
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
#N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
#N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
N/A
'
</span><span
class=
"p"
>
,
</span><span
class=
"s1"
>
'
#NA
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-1.#IND
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-1.#QNAN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-NaN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-nan
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
1.#IND
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
1.#QNAN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
N/A
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
NA
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
NULL
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
NaN
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
nan
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
na
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
.
'
</span><span
class=
"p"
>
])
</span>
<span
class=
"s1"
>
'
nan
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
na
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
.
'
</span><span
class=
"p"
>
,
</span>
<span
class=
"s1"
>
'
-
'
</span><span
class=
"p"
>
],
</span>
<span
class=
"n"
>
dtype
</span><span
class=
"o"
>
=
</span><span
class=
"p"
>
{
</span><span
class=
"s2"
>
"
snpid
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
str
</span><span
class=
"p"
>
,
</span>
<span
class=
"s2"
>
"
a1
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
str
</span><span
class=
"p"
>
,
</span><span
class=
"s2"
>
"
a2
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
str
</span><span
class=
"p"
>
,
</span><span
class=
"s2"
>
"
freq
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
float
</span><span
class=
"p"
>
,
</span>
<span
class=
"s2"
>
"
z
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
float
</span><span
class=
"p"
>
,
</span><span
class=
"s2"
>
"
se
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
float
</span><span
class=
"p"
>
,
</span>
<span
class=
"s2"
>
"
pval
"
</span><span
class=
"p"
>
:
</span><span
class=
"nb"
>
float
</span><span
class=
"p"
>
})
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
fullGWAS
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
head
</span><span
class=
"p"
>
())
</span>
<span
class=
"n"
>
fullGWAS
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
set_index
</span><span
class=
"p"
>
(
</span><span
class=
"s2"
>
"
snpid
"
</span><span
class=
"p"
>
,
</span>
<span
class=
"n"
>
inplace
</span><span
class=
"o"
>
=
</span><span
class=
"kc"
>
True
</span><span
class=
"p"
>
)
</span>
<span
class=
"nb"
>
print
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
fullGWAS
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
head
</span><span
class=
"p"
>
())
</span>
<span
class=
"n"
>
fullGWAS
</span>
<span
class=
"o"
>
=
</span>
<span
class=
"n"
>
fullGWAS
</span><span
class=
"p"
>
[
</span><span
class=
"o"
>
~
</span><span
class=
"n"
>
fullGWAS
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
index
</span><span
class=
"o"
>
.
</span><span
class=
"n"
>
duplicated
</span><span
class=
"p"
>
(
</span><span
class=
"n"
>
keep
</span><span
class=
"o"
>
=
</span><span
class=
"s1"
>
'
first
'
</span><span
class=
"p"
>
)]
</span>
<span
class=
"c1"
>
#fullGWAS = convert_missing_values(fullGWAS)
</span>
...
...
@@ -314,25 +331,16 @@
<script
type=
"text/javascript"
id=
"documentation_options"
data-url_root=
"../../"
src=
"../../_static/documentation_options.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/jquery.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/underscore.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/doctools.js"
></script>
<script
type=
"text/javascript"
src=
"../../_static/js/theme.js"
></script>
<script
type=
"text/javascript"
>
jQuery
(
function
()
{
SphinxRtdTheme
.
Navigation
.
enable
(
true
);
});
</script>
</script>
</body>
</html>
\ No newline at end of file
doc/_build/html/_modules/jass_preprocessing/map_reference.html
View file @
92a461de
...
...
@@ -17,32 +17,34 @@