A simple python script (preferably bioinformatics)
Budget: $10 – $30 USD
I seek a bioinformatician who could help me create a simply Python script or simply a Python code writer who is willing to have a brief zoom chat so that I could explain to you the jargon of this task.
In brief, the script should compare two similar input files (multiple RNA sequence alignments), both saved in .aln format: file_1.aln and file_2.aln.
Step 1:
The script should first calculate a consensus sequence for each of the input files, producing an output file, output_1.consensus. These output files should sum up a composition of each position in the multiple sequence alignment. For example:
Position 1 in the sequence of file_1.aln (this residue is variable and missing in 29% of RNA sequences):
A 30%
G 20%
U 12%
C 9%
- 29%
Position 2 in the sequence of file_1.aln (this residue is immutable and remains A in all sequences):
A 100%
G 0%
U 0%
C 0%
- 0%
Etc.
Step 2:
Then, the script should “substract” output_1.consensus and output_2.consensus for each RNA residue, producing composition_bias.consensus file. For instance,
If Position 1 in output_1.consensus looks like this:
A 30%
G 20%
U 12%
C 9%
- 29%
and Position 1 in output_2.consensus looks like this:
A 50%
G 0%
U 12%
C 9%
- 29%
Then the corresponding value for the position 1 in the composition_bias.csv output file should look like:
Position 1:
A 20%
G -20%
U 0%
C 0%
- 0%
This composition_bias.consensus file should have a table format with six columns:
Position number, A (%), G (%), C (%), U (%), -(%).
Hope this is clear. Please ask for more detail.
In brief, the script should compare two similar input files (multiple RNA sequence alignments), both saved in .aln format: file_1.aln and file_2.aln.
Step 1:
The script should first calculate a consensus sequence for each of the input files, producing an output file, output_1.consensus. These output files should sum up a composition of each position in the multiple sequence alignment. For example:
Position 1 in the sequence of file_1.aln (this residue is variable and missing in 29% of RNA sequences):
A 30%
G 20%
U 12%
C 9%
- 29%
Position 2 in the sequence of file_1.aln (this residue is immutable and remains A in all sequences):
A 100%
G 0%
U 0%
C 0%
- 0%
Etc.
Step 2:
Then, the script should “substract” output_1.consensus and output_2.consensus for each RNA residue, producing composition_bias.consensus file. For instance,
If Position 1 in output_1.consensus looks like this:
A 30%
G 20%
U 12%
C 9%
- 29%
and Position 1 in output_2.consensus looks like this:
A 50%
G 0%
U 12%
C 9%
- 29%
Then the corresponding value for the position 1 in the composition_bias.csv output file should look like:
Position 1:
A 20%
G -20%
U 0%
C 0%
- 0%
This composition_bias.consensus file should have a table format with six columns:
Position number, A (%), G (%), C (%), U (%), -(%).
Hope this is clear. Please ask for more detail.