A step-by-step 10-day Python3 tutorial especially for bioinformatician
Codes:
Day01_ReadInput_ExecutablePython.py
- Read input using ‘sys', and make the python script executable.
Day02_IfElse.py
- Solve the missing/extra input problem using if/else statement. Use internal function len(), print()
Day03_InputOutput.py
- Read a file, print, and write the first three columns of the first line to another new file.
Day04_TranslateFASTA.py
- Loop through a FASTA file containing CDS regions. Translate them into protein sequences using dictionary.
Day05_DebarcodeFASTQ_ByChuck.py
- Loop through a FASTQ file containing sequenced reads. Find the adapter and put them into the first line of the FASTQ, and use
yieldto be memory efficient.
Day06_JoinAndFunction.py
- Convert bed format containing RNA sequences to a FASTA format, saving the bed information in the FASTA header. Use
joinand self-defined function.
Day07_SplitAndDictionary.py
- Loop through a FASTA file converted from bed file in Day 6,
splitusing separator and count sequences based on the gnomonic 5´-end position (rather than the sequence itself), and report 5´-end positions and occurrence fromdictionary
Day08_TupleSet2DList.py
- Import ATACseq peaks and store chromosome and length information using
Tuple, then count unique chr appeared usingSet, and get a distribution of peak lengths using2D List (Matrix), finally format the Matirx into aPandas DataFrame
Day09_BioPython.py
- Import Genbank sequence record and process using Biopython package. Get familiar with
Seq,SeqRecord,SeqFeature,OrderedDictobjects and I/O methods
Day10_ClassAndPackages.py
- Implement Python class and other packages:
argparse,pandas,seaborn,matplotlibto build a small software that can take gene expression values as input, calculate fold changes and plot figures