Exercises/Project2/Primer_pairs.txt

-Name	Primer1	Primer2
-M01	22	23
-M02	26	27
-M03	30	31
-M05	42	43
-M06	46	47
-M07	NT12	NT13
-M09	130	131
-M11	NT10	NT11
-M12	206	207
-M13	03_NT04	03_NT05
-M14	03_NT22	03_NT23
-M15	03_NT26	03_NT27
-M16	03_NT56	03_NT57
-M20	424	425
-M21	426	427
-M22	430	431
-M23	NT18	NT19
-M24	NT34	NT35
-M25	504	505
-M26	606	607
-M27	622	623
-M29	628	629
-M30	704	705
-M31	708	709
-M32	710	711
-M33	712	713
-M34	800	801
-M36	NT16	NT17
-M37	900	901
-M38	1000	1001
-M39	1002	1003
-M41	1020	1021
-M42	1100	1101
-M44	1122	1123
-M45	1132	1133
-M46	1204	1205
-M47	1208	1209
-M48	1210	1211
-M49	NT06	NT07
-M50	1300	1301
-M51	1400	1401
-M52	1402	1403
-M53	1404	1405
-M55	1408	1409
-M56	1410	1411
-M57	1412	1413
-M60	1602	1603
-M62	1702	1703
-M64	1706	1707
-M66	1800	1801
-M67	1902	1903
-M68	2000	2001
-M69	2002	2003
-M70	2004	2005
-M72	2300	2301
-M74	2402	2403
-M77	822	823
-M78	2334	2335
-M81	2630	2633
-M81B	2630	2631
-M82	1502	1503
-M84	114a	114b
-M90	21C1	21C2
-M91	22C1	22C2
\ No newline at end of file

Exercises/Python_course_2021_exercises_B.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises B
-
-
-%% Cell type:markdown id: tags:
-
-## Part1 - control structures
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Write a script for guessing numbers!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Add tips (smaller/larger) during the guessing process!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-## Part2 - loops
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.1) Write a function counting to 100 and printing all numbers which can be divided by 4 without any residue!
-
-* Info: 10%2    #modulo division in Python
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.2) Write a function counting down from 1000 to 0 and printing all numbers!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.3) Generate a list of species names! Write a function printing all species names starting with "E"!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.4) Expand this function to limit the printing to species names which are additionally shorter than 10 characters!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.5) Expand this function to limit the printing to species names which are additionally ending with "a".
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-## Part3 - range & enumerate
-
-%% Cell type:markdown id: tags:
-
-
-
----
-3.1) Write a script to print 50x "here" and the current value of the control variable!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-3.2) Write a script to walk through the species list and to print the character from the species where the index corresponds to the current control variable value!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_C.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises C
-
-%% Cell type:markdown id: tags:
-
-## Part1 - file handling
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Count number of sequences (number of headers) in AtCol0_Exons.fasta!
-
-%% Cell type:code id: tags:
-
-``` 
-from google.colab import drive
-drive.mount('/content/drive')
-```
-
-%% Output
-
-    Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount("/content/drive", force_remount=True).
-
-%% Cell type:code id: tags:
-
-``` 
-datei = open("/content/drive/MyDrive/Python_course_2021_data/AtCol0_Exons.fasta", "r")
-lines = datei.readlines()
-datei.close()
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Count number of sequence lines!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.3) Count number of characters in document! (How many per line?)
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.4) How long are all contained sequences combined?
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.5) Calculate the average sequence length in this file!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_D.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises D
-
-%% Cell type:markdown id: tags:
-
-## Part1 - writing files
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Read the file AtCol0_Exons.fasta and write all headers (starting with '>') into a new file!
-
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Read the file AtCol0_Exons.fasta and write the following:
-* Line if it is a header
-* Length of line if it is a sequence line
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.3) Calculate the number of sequences, the cumulative length and the average length in a new file! Are they matching the values of the original file?
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.4) Write sequences into a new file if their length is a multiple of 10!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-## Part2 - characters
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.1) Read the file AtCol0_Exons.fasta and write the following:
-*   Only Arabidopsis Gene Identifier (e.g. AT1G01010)
-*   Gene Identifier, exon name, exon length (tab-delimited)
-
-
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_G.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises G
-
-%% Cell type:markdown id: tags:
-
-## Part1 - easygui
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Write a script to handle input of primer names and sequences! All information should be saved in a multiple FASTA file.
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Write a script to return a matching primer sequence from a FASTA file based on a given primer name.
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.3) Write a script to combine both functionalities: return primer sequence, if name is already present OR generate new entry if primer is novel.
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_H.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises H
-
-
-%% Cell type:markdown id: tags:
-
-## Operon structure plot
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Construct a figure to illustrate the order and orientation of genes in the gum gene cluster in *Xanthomonas campestris* pv. campestris!
-
-
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_I.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises I
-
-%% Cell type:markdown id: tags:
-
-## analyze the unknown data
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Construct a suitable visualization!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Analyze distribution and trends!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Apply statistical test to investigate difference!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_J.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises J
-
-%% Cell type:markdown id: tags:
-
-## construct heatmap
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Read data table and construct heatmap for the gene expression!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Display functional gene annotation!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```