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acpipe_acjson is the python3 acjson base library. acjson - assay coordinate json - is a file format developed to log complicated biological wetlab experiment layouts.

Project description

About the acjson project ...

This is a python3 library to produce and process acjson objects.

Acjson (assay coordinate java script object notation) is in the big picture a json syntax (http://json.org/) compatible file format, that was developed to capture the most essential experimental annotations of a biological wetlab experiment, how ever simple or complicated the layout may be.

In the guts of this file format is each experimental condition described as a single coordinate.

Each coordinate is an adaptation of the input-processing-output (IPO) model from software engineering, which is used to describe the structure of an information processing program. In the biological experiment use-case, these are represented by (SPE) sample, perturbation, and assay endpoints, which are represented as three axes.

Each of this axis can hold as many sample or reagent records as needed to describe the experimental condition.

This library can produce and process such acjson objects.

Howto guide

How to install acpipe_acjson?

pip3 install acpipe_acjson

How to load the acpipe_acjson library?

import acpipe_acjson.acjson as ac

Howto get reference information about the implemented constants and functions?

import acpipe_acjson.acjson as ac

# basic constants
ac.ts_ABC
ac.ts_ACAXIS
ac.ts_NOTCOOR
ac.ts_COORSYS
ac.d_WELL
ac.d_RECORD
ac.d_RECORDLONG

# record dictionary add on constants
ac.d_SET
ac.d_EXTERNALID
ac.d_SAMPLE
ac.d_MICROSCOPE
ac.d_PRIMANTIBODY
ac.d_SECANTIBODY

# leaf constants
ac.leaf
ac.es_DATAFRAMELEAF

# 96 to 386 well constantes
ac.dii_96A1
ac.dii_96A2
ac.dii_96B1
ac.dii_96B2

# function
help(ac.retype)
help(ac.escoor)
help(ac.icoormax)
help(ac.ispotmax)
help(ac.ispot)
help(ac.xy2icoor)
help(ac.acrelabel)
help(ac.acbuild)
help(ac.acfuseaxisrecord)
help(ac.acfusewellrecord)
help(ac.acfuserepeat0011)
help(ac.acfuserepeat0101)
help(ac.acfuseobject)
help(ac.acfuse4to1)
help(ac.count_record)
help(ac.record_in_acjson)
help(ac.list_uniq_record)
help(ac.max_record)
help(ac.pop_record)
help(ac.pop_ac)
help(ac.xray)
help(ac.acjson2layouttsv)
help(ac.acjson2dataframetsv)

Project details


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