Sorting samples in racks

Problem

Samples are sitting in a rack unsorted (with respect to their "externe Nummer"); they are scanned into an Excel file in that order

Objective

Sort the samples in the rack by

• A) placing them in a new rack in sorted order
• B) sort them in the same rack until they are in sorted order (in-place)

Usage

The script ("sort_samples.py") implements both of these methods. It can be run by placing it in the same directory as the Excel file and typing

./sample_sort.py <excel_filename>

on the command line (e.g. in the PowerShell on Windows). Alternatively, you can store the script in a different directory and additionally pass it the path to the directory where the Excel file sits:

./sample_sort.py <path/to/excelfile_directory/excel_filename>

By default, method A is used and the output will look something like this:

rack position <-- sample ID
1 <-- SE1403AA
2 <-- SE1404AA
3 <-- SE1405AA
.
.
.

old position --> new position
14 --> 1
16 --> 2
17 --> 3
2 --> 4
.
.
.

..., i.e. the sample on position 16 should be moved to position 1 on the new rack and so on.

For method B, run:

./sample_sort --inplace <excel_filename>

..., which will produce output looking like this:

rack position <-- sample number
1 <-- SE1403AA
2 <-- SE1404AA
3 <-- SE1405AA
.
.
.

old position --> new position
14 --> 1
1 --> 14
16 --> 2
2 --> 4
4 --> 15
.
.
.

Data

tobi_samples.xlsx (example Excel sheet to run the script on)

Requirements

pandas

Possible issues

• if pandas is not available, the script could be slightly adjusted to work with a .tsv instead of an .xlsx file
• if "externe Nummer" is in a different format, the script won't warn you about it and will just ignore this sample