Skip to content
Snippets Groups Projects

Compare revisions

Changes are shown as if the source revision was being merged into the target revision. Learn more about comparing revisions.

Source

Select target project
No results found

Target

Select target project
  • Gerald_H/python-programming
  • franziska.niemeyer/python-programming
  • ggp_python/python-programming
3 results
Show changes
Commits on Source (22)
Showing
with 840 additions and 0 deletions
File added
File added
File added
File added
File added
File added
File added
File added
File added
File added
File added
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
%% 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:
```
```
%% Cell type:markdown id: tags:
# Python course 2021 - Exercises E
%% Cell type:markdown id: tags:
## Part1 - modules
%% Cell type:markdown id: tags:
---
1.1) Write all AGIs of AtCol0_exons.fasta into a new file!
%% Cell type:code id: tags:
```
```
%% Cell type:markdown id: tags:
---
1.2) Some IDs occur multiple times. Add a filter step to reduce the results to unique IDs!
%% Cell type:code id: tags:
```
```
%% Cell type:markdown id: tags:
---
1.3) Calculate the frequency of each AGI and construct a histogram (matplotlib)!
```
plt.hist(<list_of_values>) #tip
```
%% Cell type:code id: tags:
```
```
%% 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:
```
```
>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
\ No newline at end of file