Author:

Daniele Arosio

4. Old scripts#

4.1. fit_titration.py#

  • input ← csvtable and note _file

    • csvtable

    ../_images/csvtable.png

    • note _file

    ../_images/note_file.png

  • output → pK spK and pdf of analysis

It is a unique script for pK and Cl and various methods:

  1. svd

  2. bands

  3. single lambda

and bootstrapping

I do not know how to unittest TODO

  • average spectra

  • join spectra [‘B’, ‘E’, ‘F’]

  • compute band integral (or sums)

4.2. fit_titration_global.py#

A script for fitting tuples (y1, y2) of values for each concentration (x). It uses lmfit confint and bootstrap.

  • input ← x y1 y2 (file)

    • file

    ../_images/file.png

  • output →

    • params: K SA1 SB1 SA2 SB2

    • fit.png

    • correl.png

It uses lmfit confint and bootstrap. In global fit the best approach was using lmfit without bootstrap.

for i in *.dat; do gfit $i png2 --boot 99 > png2/$i.txt; done

4.3. IBF database uses#

Bash scripts (probably moved into prtecan) for:

  • fit_titration_global.py

  • fit_titration.py

    cd 2014-xx-xx

(prparser) pr.enspire *.csv

fit_titration.py meas/Copy_daniele00_893_A.csv A02_37_note.csv -d fit/37C | tee fit/svd_Copy_daniele00_893_A_A02_37_note.txt

w_ave.sh > pKa.txt

head pKa??/pKa.txt >> Readme.txt


# fluorimeter data
ls > list
merge.py list
fit_titration *.csv fluo_note

see: /home/dati/ibf/IBF/Database/Data and protocols_Liaisan/library after Omnichange mutagenesis/Readme_howto.txt

5. new#

  • Tit works for a plate organized with a pH-value for each row and a Cl conc value for each column.

  • Old fit works with a list of well and corresponding cl conc orpH value; the kind [“pH”, “Cl”] decides

Some measurements e.g. “A”, “C” and “D” are at T = 20 others (“B”, “E” and “F”) are taken at T = 37. This temp is present in each metadata. (e.g. measurements[“A”][“metadata”][“Temp”]).

A future note file format:

  • well, pH, Cl, T, mut, meas labels

    echo "Well,pH,Cl,Name,Temp,Labels" > v224H_note.csv
awk -F '\t' 'NR>1 {print $1 "," $2 "," $3 ",V224H,37.0,A B"}' v224H_note >> v224H_note.csv