-
Notifications
You must be signed in to change notification settings - Fork 0
This package is designed to pull annotations from PubChem via their PUGView API It iterates through JSON pages and retrieves the annotations. It is designed for Multi-threading and will work best with HPC systems with fast internet connections. Be aware the time required will vary wildly with each annotation type
License
demontrees/PubChem_Prospector
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
_ __ _,.----. ,--.-,,-,--, ,----. ___
.-`.' ,`. .--.-. .-.-. _..---. .' .' - \/==/ /|=| | ,-.--` , \ .-._ .'=.'\
/==/, - \/==/ -|/=/ | .' .'.-. \/==/ , ,-'|==|_ ||=|, ||==|- _.-`/==/ \|==| |,--.--------.
|==| _ .=. ||==| ,||=| -|/==/- '=' /|==|- | .|==| ,|/=| _||==| `.-.|==|, | / -/==/, - , -\
|==| , '=',||==|- | =/ ||==|-, ' |==|_ `-' \==|- `-' _ /==/_ , /|==| \/ ,\==\.-. - ,-./
|==|- '..' |==|, \/ - ||==| .=. \|==| _ , |==| _ |==| .-' |==|- , _ |`--`--------`
|==|, | |==|- , //==/- '=' ,\==\. /==| .-. ,\==|_ ,`-._|==| _| | |
/==/ - | /==/ , _ .'|==| - / `-.`.___.-'/==/, //=/ /==/ , //==/ /V/ , /
`--`---' `--`..---' `-._`.___,' `--`-' `-`--`--`-----`` `--`./ `--`
_ __ _,.---._ ,-,--. _ __
.-`.' ,`. .-.,.---. ,-.' , - `. ,-.'- _\ .-`.' ,`.
/==/, - \/==/ ` \ /==/_, , - \/==/_ ,_.'/==/, - \,--.--------.
|==| _ .=. |==|-, .=., |==| .=. \==\ \ |==| _ .=. /==/, - , -\
|==| , '=',|==| '=' /==|_ : ;=: - |\==\ -\ |==| , '=',\==\.-. - ,-./
|==|- '..'|==|- , .'|==| , '=' |_\==\ ,\|==|- '..' `--`--------`
|==|, | |==|_ . ,'. \==\ - ,_ //==/\/ _ |==|, |
/==/ - | /==/ /\ , ) '.='. - .' \==\ - , /==/ - |
`--`---' `--`-`--`--' `--`--'' `--`---'`--`---'
,----. _,.----. ,--.--------. _,.---._
,-.--` , \ .' .' - \/==/, - , -\,-.' , - `. .-.,.---.
|==|- _.-`/==/ , ,-'\==\.-. - ,-./==/_, , - \ /==/ ` \
|==| `.-.|==|- | . `--`\==\- \ |==| .=. |==|-, .=., |
/==/_ , /|==|_ `-' \ \==\_ \|==|_ : ;=: - |==| '=' /
|==| .-' |==| _ , | |==|- ||==| , '=' |==|- , .'
|==|_ ,`-._\==\. / |==|, | \==\ - ,_ /|==|_ . ,'.
/==/ , / `-.`.___.-' /==/ -/ '.='. - .' /==/ /\ , )
`--`-----`` `--`--` `--`--'' `--`-`--`--'
::::::::::
::::::: ::::::!!!!!!!!!!!/!
:::: !!!!!!!!!!!!!!!!!!!!
:::: !!!!!!!!!!!!!!!!!!!!!!!!!!!
:::: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
::: !!!!!!!!!!!!!!+!! !!!!!!!!!!!!!!
::: !!!!!!!!!!!!!! +! !!!!!!!!!!!!!!
:::: !!!!!!!!!!!! ; ! !!!!!!!!!!!
:::: !!!!!!!!!!! ;;;;; ;; ;;!!!!!!!!
:::: !!!!!!!!!!! ;;;;;;;; ;;;;;;;!!!!!!!!
::::!!!!!!!!!! ;;; + ;;;;!!!!!!!!
:::!!!!!!!!!! ;; ++++ ++ !!!!!!!
:::!!!!!!!!!!W ; ++@0 \ +0@ !!!!!!\\\\\\\\
:!!!!!!!!!!WWW +++@ \ @++!!!!!\\\\\\\\\\\\\\\\
:!!!!!!!!!WWWW | │ !!!!\\\\\\\\\\\\\\\\\\\\\
!!!!!!!!! WWWW W | | \ ! W\\\\\\\\\\\\ \\\\\\
!!!!!!!!!!WWWWWWWW WWWWW──|──| WWW\\\ \\\\\\\\ \\\\\
!!!!!!!!!!WWWWWWWWWWW WWWWWWWWWWWWWWWWWWW\ \\\\\\\ \\\\
!!!!!!!!!!WWWWWWWWW WWWW┌ W WWWWWWWWWWWWW \\ \ \\
!!!!!!!!!!WWWWWWWWWWWWWW \U\ ____/ WWWWWW W \ \\
!!!!!!!!!!WWWWWWW WWWWWW │ U UU │ WWWWWW \\ \
!!!!!!!!!!WWWWWWWWWWWWWW \ \ \ \│ WWWWW \\ \\
!!!!!!!!!WWWWWWWWWWWWWWWWW \nn_n__/WWWWW \ \/
!!!!!WWWWWWWWWWWWWWWWWWWWWWW W WWWWWWWW \\ / /
!!!!!WW!WWWWWWWWWWWWWWWWWWWWWWWWWWW / ─ - /
!!!!!!!!!!!WWWWWWWWWWWWWWWWWWWWWWWWW / /
!!!!!!!WWWW!WWWWWWWWWWWW WWWWWW ─ - /
!!!!!!!W!!WWW WWWWWWW WWWW - /
WWWW W WWW ── ─
PubChem Prospector: _
This pakcage is designed to pull annotations from PubChem via their PUGView API __ __|_|__
It iterates through JSON pages and retrieves the annotations. It is designed for / \ _|+.+|_
Multi-threading and will work best with HPC systems with fast internet connections \// |WWW|\\
Be aware the time required will vary wildly with each annotation type // \\
build_annotation_dict:
this function creates a dictionary of all possible annotations PubChem Prospector can access
just run "build_annotation_dict()" and access the dictionary by calling pc_annotations
it is structured {entry_type:[annotations]}
the available entry types are:
Taxonomy, Element, Cell, Protein, Assay, Gene, Compound, and Pathway
Usage:
prospector.build_annotation_dict()
prospector.pc_annotations
annotation_search:
this function is just a quick shortcut for searching annotations in the pc_annotations dictionary
just give it the entry_type and the string to search by and you can save the result(s) as a variable
Usage:
z = prospector.annotation_search({ENTRY_TYPE},{SEARCH_STRING})
get_dict
this is the main function of PubChem_Prospector. It calls a series of smaller functions to build a
dictionary containing all selected annotations for the given entry type. It collects each annotation
one at a time, so the more you ask for, the longer it will take, but it puts them all together in a
nice clean package, accesible by the numeric ids for that entry type in PubChem. You can use either
a string specifying a single annotation type, or a list of annotation types for the second argument
You can specify the number of threads as well. Default is 32
Usage:
pc_dict = prospector.get_dict({ENTRY_TYPE}, {ANNOTATION_TYPE}, threads = 32)
About
This package is designed to pull annotations from PubChem via their PUGView API It iterates through JSON pages and retrieves the annotations. It is designed for Multi-threading and will work best with HPC systems with fast internet connections. Be aware the time required will vary wildly with each annotation type
Resources
License
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published