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  • Gerald_H/python-programming
  • franziska.niemeyer/python-programming
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Excercises/Python_course_exercises_F.ipynb 0 → 100644
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%% Cell type:markdown id: tags:
# Python course 2021 - Exercises F
%% Cell type:markdown id: tags:
## Part1 - DNA, RNA and peptide sequences
%% Cell type:markdown id: tags:
---
1.1) Write a function to get the reverse complement (upper case letters) of a DNA sequence given in upper case letters!
%% Cell type:code id: tags:
```
```
%% Cell type:markdown id: tags:
---
1.2) Write a function to convert a DNA sequence into a RNA sequence!
%% Cell type:code id: tags:
```
```
%% Cell type:markdown id: tags:
---
1.3) Write a function to translate a DNA sequence into amino acids (first frame only)!
* Tip: [wiki - codon tables](https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables)
%% Cell type:code id: tags:
```
```
%% Cell type:markdown id: tags:
---
1.4) Write a function to translate DNA sequences in all 6 frames into peptide sequences! The longest peptide sequence per DNA sequence should be returned!
%% Cell type:code id: tags:
```
```
Exercises/Python_course_2021_exercises_B.ipynb deleted 100644 → 0
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%% 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 deleted 100644 → 0
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%% 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:
```
```
Syllabus_Python_Programming_for_Life_Scientists_WS2021_2022.pdf deleted 100644 → 0
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Vorbesprechung_2022.pdf deleted 100644 → 0
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data/.gitkeep 0 → 100644
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data/AtCol0_Exons.fasta 0 → 100644
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data/exerciseF_task1_4_sequence.fasta.txt 0 → 100644
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>SduTW12_06g132610.v1 mRNA Similar to THI1-1: Thiamine thiazole synthase 1, chloroplastic (Vitis vinifera) chr06:1951696-1954502(-)
TTCTTTGTTAAATATTTAAATAGAATATGTTGATAAATCTTAAAGGCAGAGAGTACTGCA
TGCTTTACAAGTGTTACTTATGGAGATAGATGTACATGATATTTTTCTCTCGCTCTCCAT
ACTTGTCACTCGAGCCCCTATATAAATCCTTCCTCTTCCCCTTCCACTTGCTCACTCAAA
AATCTCCGCTCTATTCCCAATTCCCAATTCTTCGAGCTTTCTCTATCAATGGCAACAATG
GCTTCCACCTTGGCTTCCTCTGTTATTTCCAAGACTAATTTCCTTGACACACACAAATCA
TCTTTCTATGGAGTACCAATTTCATCACAAGCTAGATTGAAAATTGTGAAATCAACCCCA
CAGAATATGGCTGTTTCCATGTCTGCTGATGCTTCTCCTCCTCCTTACGATCTCGGAAGT
TTCAGTTTTAATCCGATTAAGGAATCGATTGTTGCTCGGGAAATGACACGTAGGTACATG
ACGGATATGATCACTTATGCGGATACTGATGTTGTTATTGTTGGTGCTGGATCTGCTGGT
CTATCTTGTGCTTATGAGCTCAGCAAGAACCCTGATGTTCAGGTATGCCTTTTTTCTATA
AAAAAAATTTATTTTATATATATATATGCATAGATATCGAAATTTAAGTTTGGTCGATTT
GAAGTCTAAGAGTGATAAATCGCGATTTTAAACTAATATACAATAAAAATTGGGTGAACC
Atagatatcagacttttatctgcaactgggatgtgatcccagtgttgatacatcatatgt
tgcgctcttaacactagatcaaggCTCGGGAGACATGTCAATTAAATTTTAAAAGCAGAG
ACGGGAAATTTTGCAGTTTGTGTTCTGTCGTCAATTGTGCTTCATATGTGTTACTGTTTG
ATTTGACATGATTCGTGAGAAAAAACGAAGATTTTTAAAATTTGTTAATATAAAAATGCA
ACCTTTTTTGGGGCTGAATTAAAAAATTGATAGATACTGTTTTACTTGTTTTTGATAGAT
TATTGGCACATAGGTTTCCTATTAAAAGTATTTGCAACTTTACTCGTACCCATAAATCAT
GTGACACTTTTTCCCTTAGGATTATTTGCTATTTGAGTGGGACCATTCAAGAGACAAAAG
TATATATTAATTGGGAAAGTTGTTTATATGCTTGTGAACCAGTGAAATTGCTTTTAAGAA
GTTGAGCTGATAACAATGAGTTTAATTGAATACACAGAGCCCGTCCTAGATCTGACTGTG
TACACACATTCACGATTACAATGAAGTCAATTGATGTTCTAATTGCTATAATTGTCGTTG
ATTGCAATATCAATGTTCTCCAATTTGAACTTGTGAGTTGTTTATGTGAATTGACTTTAT
ATGTGTAGGTTGCCATCCTTGAGCAATCTGTGAGCCCTGGTGGAGGTGCCTGGCTAGGTG
GACAACTCTTCTCAGCCATGGTTGTGCGTAAGCCAGCACATCTTTTCTTGAACGAGCTAG
GCATTGATTACGACGAGCAAGACAACTACGTGGTCATTAAACACGCTGCCTTGTTCACCT
CAACCATCATGAGCAAGCTTTTGGCCAGGCCAAATGTGAAGCTCTTTAATGCTGTTGCAA
CAGAGGACCTTATCGTGAAGAACGGAAGAGTCGGTGGTGTTGTCACTAACTGGTCTTTAG
TTTCCCAGAACCACGACACACAATCCTGCATGGACCCCAATGTTATGGAGGCTAAGGTTG
TGGTCAGCTCCTGTGGCCACGATGGTCCCATGGGAGCCACTGGTGTTAAGAGGCTCAGGA
GCATTGGCATGATCAACAGTGTTCCTGGAATGAAAGCTTTGGACATGAACGCTGCTGAGG
ACGCGATTGTTAGACTTACCAGAGAAGTTGTACCTGGAATGATTGTTACAGGAATGGAAG
TTGCTGAAATTGACGGAGCACCAAGAATGGTGAGTATATTTGTCACCACTCTTACTACTA
TAAAGTAGTTGCACGTCTGTATTCTATGAACTCCTAATTTGCCTTACAACAAACAAGGCC
AACTGTGCCTCAATCAGTCTCAAACAAGTTTGGGAGAAACTCCTAATTTTGCCTTAATAT
AGCAAAATGGACACAAATGTTTCATACAGCCGATCTAATTTAGTTTTGCTAGTATAACTA
ATTGGAAATGTTTTATATTGTTCAGGGTCCAACTTTTGGAGCCATGATGATATCAGGGCA
GAAGGCAGCACACCTTGCCCTACGAGCGTTGGGATTGCCTAACGCCCTTGACGGAACTGC
AGAAACAAGCATCCACCCGGAGCTTATGTTGGCTGCAGCTGATGAAGCTGAAACTGCTGA
TGCTTGAATGTAATTTATAGTTTTCTAAGAAAGGATATGAAAAATATTAGTTTTTCCTAG
ATGAGTATGGTTATGTGGTGGAGAGATAAATTGGCAAGGGGATGATTAATATAAGATCAG
CAAGATGAATGTCTCTGTGTGCTTTGGTTGTCATGTCAATTCTTCTTTCTCTTTTGATTT
AGTGAAACTTCTATGTGAAAAAAGTGGTAGATTGTTATTTTGGTCGTTGAATAATCCTAT
GGGCCTTTTGGACTTTGTTTTGGTACTTGATGTGGTTTGGGTGAATGAACATTGTGATTG
GGCCAAGATCTTTCTTTCTCGTATATATTGGGCATTTGCTCAATTGGTAAAAGGACTCTA
ATTTAAAAAAACACACAGGTCAACTAGGCAATAAATAGGCAATAATACAACTGAGCAACG
GATAGCCCATCAAATTGATACGTACAAACTTAGTGCACATACTAACC
>SduTW12_06g132620.v1 mRNA Similar to GOS2: Protein translation factor SUI1 homolog (Oryza sativa subsp. japonica) chr06:1970033-1973436(-)
CTCTTTATTAGCTGATTTCACATTATATTTTCCTTTTTTCTTCTGTGCACTGACTTTTCT
GTATTTTGCTCAAGACTTATCCGGATTTTGGGGTCTGCTGTATTGCCACCGTCTTCAATC
TCTACAAACCCTAACCTTCGGATCAGGTAAATCTTCAATACCCACTTGTTTTATTGGTTG
ATAATCTTCAGATCTGGTGAATTAGCTTTGTTTGTTTGTCTAGTACTTGTTTTTGTTATA
AAGATCGGATTTTTAATCCAAGAATTGGTAGAATTTTGGGGATTTTAGGCTTGAGATGTT
GATTTATGATGCTTAGTGATAAAGATGGATTTTTATTCCAAGAATTGGTGGAATTTTGTG
GCTAGAGATGCTGATTTATGATTATTAGTGATAAAGATCGGAtttttatgatgtccgtgt
tgttccggtcagctttggctcacctggactaattccatggtatacctgccacctcatcac
ctagtattttgtctctgttgggatttgaaccTTGGGTGCTTTGGTTGTTCTATGCTTTCT
GTTATGATGCTTAGTGATAAATATTGGATTtttatgatgaccctgttgtttggatcagct
ttcgcacacctagactaattccacggtatatctgttacctctgaccagcaacaactatca
gataactctgtccatcaagtctaccaatgctagaatagatgggaaggatctcctaatgtt
ttttctctgctgggatttgaatcttgggtgctatggttGTTCTTTGCTTGCTATTGTGAT
GCTTATTGAATGATCTGGTTATATATTCATAGTAACTGGAACCGTTTTATGAAACTTTTA
TATCAAAGTTGTGATTGGTACTGTTTTTGAAGAAGTTACTCTAGAGCTATGTACTTTTTC
TGATGCAAGTTTTGATCTTTTTTCTTTTGGGTTGTTTTCTGTTGCAATAGTCTGGTCGTA
TTTCTCCAAGAGTTGGAATCATTTAAGATTTTTAAAGTAGAGTTGTCCGTTTCTGATGCC
TAGTTATTTTATTATGGGGGTGTGTTGTTTTGCTGAATTCTAGTTGTGTTTTCTCCAAGG
ATTTTGATATCACTTTGGGATTTGTATGCTGTTTTTTATACTTATTATAGAATATCTGTT
GTTTGTCTTACTCTGGTTGTTGGGGGGAACAAATGCGTGTGTAAGATTACCTTTCCAACC
CTATTTGTGGTGAAGGATTATTTTTTCTGATGAATAAGtttctgtatttgattctctacc
ttttttctttctttctttctgtttttGGTTTGGATATTGGATGGGCTTTTACCAGTTCTT
TTGCCTCCTGTTGCTCTTAATACTAAAACATATGTGGATCGCCTCTTTCTATTGTACATA
CGACATGCAAGATGATAATGGAATCTGTCGGAAGCTTTATCTTGTGTATTATGTTGTTGA
TAAAAATTGGAATTTTCTGAAAGACTAGTACTATGCTGGTACTTTACTGCAAGCTGTCTC
ATGTGTATTGTTTTGGTGATAAATAGAGTTGTTTTCTTTTCCAACTTTCTTGCTAATAAA
GGTTTCTTCTTTCATCTGTTTATGTTTATGTCCTATTTAGCTTTTGATTGTCCTGTTTTT
TAGACAGGGTGTTTGTATTGATAATCTGATACAGCTGCTTGTCTACTATATAGGATATTT
AGATAACTCCTTGTCATTGTATGTATGCAAAATGATTAAATAGTCTACGTTGATGTTTGT
CACTACTTGAGACGTGGAATTTGGTTTCTTGTTTATTCTTCTTGTTGTAATAGCTGCTGA
GCTCTTTTTCATTTGCCTAGGTCTGAGCATCCAAGTTTCGAGATCTGTGTGCTCCTGTTG
TCTTCTACTCTCAGCCAAGTTTCATGTCTGATCTCGACGTCCAAATTCCTACCGCTTTTG
GTATGGGCCTCTCCTTAAATCACATTCTGTTTTAGTGCAATTTCGTGTATTTCCTGTCTT
ATCAGATCAGTAAATCAGTTTCAGTTGAATGTTAAAAAAGTTCGGGTTCATGTTTTATAG
AGGTGATAGTTTAGATGCAAAGAAAGAAAAGGGTTGAGAAGAAAGCATGCTAGTTCAGAG
GATATGAATTATATTCTTATCTTCTATACCTGACCAGTCATGCTGCTTTATTATGCTTTA
TAGATCCCTTTGCCGAGGCAAATGCTGATAACTCTGGTGCTGGGTCAAAAGATTACGTGC
ACATCCGTATACAACAAAGGAATGGTAGGAAAAGCCTGACAACTGTGCAGGGGTTGAAGA
AAGAATTCAGCTATAACAAGATACTGAAGGATCTTAAGAAAGAGTTCTGCTGCAATGGTA
CTGTCGTTCAGGATCCTGAATTAGGCCAGGTTTGTAACTTTGCATTCCAGTGCCTCGTCT
CTGTTATTGCAAGTTCTATGACTGATCTTATGTTTTTTGTTGTTTATGAAGGTTATTCAA
CTTCAGGGTGACCAGCGGAAGAACGTTTCTACATTTCTTGTCCAGGTGAGTGTGGTGCAG
ATTGAGCATGTCTTTTTGCTCGTTCAATATTAAGTTATCTTGCTATGATAAATAGATGCT
TAAAAAAATCTTATGTCATGCATTAACAGTCATTTGTGAATATCACTGTTTCAGTTAACT
TCTTCTGTCACTCCTGAATCGTGTCTTTTGAAGTGAAGTGGGTTAGTAATAGGCTGAGCT
GCTCATTAAGCAAAAAAAAGACACTCTTTTGGTTCAGTGTTCATTTCGATATTGAGTGTA
TGTACTGGAGTCACTTGTTACAGATTTACTGATCAAGGGCAGGAGGAGAGAATAGGCAAT
GACAGAACTAACAGCACTACTAATTCTGTAGCTTGACTTAAATTGATATCTTATGGGACT
CTCTGTTCCAAATTTTATAGTATTTATCTACTTTGTTGCTAATTTCTTCTTTTTGGATTT
GTTGAAGCAGGCTGGAATTGTGAAGAAAGAGCACATCAAAATTCATGGTTTCTGATTGCT
CTCATCAGCCTCAGCTGCACAGTTATCATACTTGTTATGTCAATGCCAGAGATAGGCTAT
CCAAACTCAGTTCTACTAAAACTTACTAGTGTTTAATTTCTGCTGGTTTGATATAAACAC
TGTATTTGCTTCTCTATGTTCCGTCTGAATATGAATCGTGTTATATTTTCGAGCACTTTA
CGAACCAATGATGATATTATTGAGTGCTCAAGAGACATGATCCTTGTCATTTTGGGTTGT
TGCTGATCGTCTAGTGCCGCTTAGAATTTACTGCATATGCAGCAGTTCTGGTTTACGTGC
TTCAATACCATTTGTATCATTTGGGATCATTCTTGATTTGGTGGTTCTTGAAAGGCTATT
GTTGGACTTTAGTATTGAGGAGTGGGGTTCATTCAATCTTTTAA
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data/expression_human_chr1.txt 0 → 100644
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data/expression_human_chr1_short.txt 0 → 100644
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#chrom chromStart chromEnd name strand geneId expScores
chr1 11868 14403 DDX11L1 + ENSG00000223972.5 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.166,0,0,0,0,
chr1 14409 29553 WASH7P - ENSG00000227232.5 4.064,3.371,2.686,4.048,3.901,3.64,5.164,1.438,1.693,1.566,4.992,5.721,2.483,2.147,1.686,1.748,1.539,1.442,2.73,1.742,4.439,2.494,1.679,5.629,7.098,4.648,3.595,4.326,3.117,4.103,6.134,1.52,0.925,2.771,2.215,1.765,4.508,3.527,1.417,6.685,6.634,1.808,5.425,7.083,5.933,6.133,4.194,5.926,3.062,4.703,6.273,7.19,5.745,2.647,
chr1 17368 17436 MIR6859-1 - ENSG00000278267.1 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
chr1 29570 31109 MIR1302-2HG + ENSG00000243485.5 0,0,0,0,0,0,0,0,0,0.024,0,0,0.027,0.03,0,0.025,0.031,0.023,0,0.02,0,0,0,0,0,0,0,0,0,0,0,0,0.018,0.018,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.054,0,0,0,0,
chr1 34553 36081 FAM138A - ENSG00000237613.2 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
chr1 52472 53312 OR4G4P + ENSG00000268020.3 0,0,0.036,0,0,0,0.035,0.05,0.054,0.046,0.025,0.037,0.043,0.042,0.053,0.04,0.045,0.048,0.042,0.047,0.03,0,0,0,0.024,0.015,0.033,0.036,0,0,0,0.036,0.051,0.039,0,0.033,0,0,0.038,0,0,0,0,0.021,0.027,0,0.035,0,0.033,0,0,0,0,0,
chr1 62947 63887 OR4G11P + ENSG00000240361.1 0.041,0.041,0.054,0.029,0,0.039,0,0.064,0.068,0.072,0.047,0.05,0.07,0.073,0.077,0.064,0.059,0.065,0.057,0.066,0.039,0,0,0.051,0,0.043,0.045,0.041,0.023,0.043,0.036,0.06,0.073,0.058,0,0.043,0.039,0.033,0.054,0,0,0,0.029,0.042,0.043,0.042,0.04,0,0.047,0.054,0.039,0.016,0.027,0,
chr1 69090 70008 OR4F5 + ENSG00000186092.4 0.045,0.045,0.058,0,0.041,0.044,0.044,0.079,0.077,0.083,0.06,0.058,0.084,0.074,0.103,0.083,0.081,0.099,0.071,0.073,0.046,0.031,0,0.041,0,0.045,0.05,0.048,0.038,0.049,0,0.083,0.098,0.076,0.026,0.061,0.043,0.032,0.064,0.039,0,0.025,0.037,0.043,0.049,0.046,0.043,0.036,0.054,0.039,0.049,0,0.015,0,
chr1 89294 129223 RP11-34P13.7 - ENSG00000238009.6 0.018,0.021,0.016,0,0.008,0,0.015,0.019,0.021,0.019,0.022,0.023,0.024,0.025,0.02,0.019,0.02,0.016,0.017,0.019,0.023,0.009,0,0,0.024,0.016,0.016,0.018,0.024,0.016,0,0.016,0.016,0.017,0,0.017,0.035,0.02,0.014,0.019,0.03,0.015,0.025,0.029,0.019,0.019,0.017,0.083,0.017,0.334,0.023,0.026,0.025,0.096,
chr1 131024 134836 CICP27 + ENSG00000233750.3 0.019,0.038,0.015,0.024,0.021,0.012,0.016,0.015,0.018,0.018,0.029,0.036,0.02,0.019,0.014,0.024,0.022,0.015,0.024,0.016,0.028,0.017,0,0.055,0.07,0.013,0.018,0.022,0.116,0.018,0.035,0.014,0.011,0.019,0.088,0.023,0.132,0.046,0.005,0.015,0.099,0.029,0.085,0.064,0.026,0.026,0.03,0.454,0.025,0.277,0.058,0.039,0.072,0.795,
\ No newline at end of file
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data/genes_human_genenames_duplicates.txt 0 → 100644
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data/human_genes_alignment_identities.txt 0 → 100644
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gene_name alignment_identity
DDX11L1 76.4
NOC2L 32.4
PANK4 90.6
ADGRB2 56.9
IRF5 89.5
CPA1 75.0
CEP41 93.3
DGKI 44.4
HIPK2 39.7
TBXAS1 88.8
SLC37A3 47.9
BRAF 64.8
AGK 99.9
WEE2 100
SSBP1 58.3
CLEC5A 82.1
MGAM 56.9
TRBV7-7 99.8
EPHB6 96.0
TRPV6 65.5
TRPV5 87.0
LLCFC1 76.9
KEL 50.4
OR9A2 100
PIP 90.4
TAS2R39 99.1
GSTK1 84.2
TMEM139 77.7
CASP2 24.8
HINT1P1 68.9
CLCN1 90.7
FAM131B 92.3
MIR6892 88.5
ZYX 79.9
EPHA1 81.4
TTN 90.5
\ No newline at end of file
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