Write a Python script
$30-250 USD
Betales ved levering
The program will do the following:
1. Input a file: .AB1 format
2. Parse the files so the data can be manipulated. [login to view URL]
3. At base #171 in the attached file, there are two high peaks, rather than one. (You can view this visually on the attached picture.) The double peak is a duplication of the previous peak. The program should scan the file, identify double peaks, and then clean them from the file. It should also identify where these double peaks start and end in the file. They will never be at the same spot in the file. (In the attached file, they end at base #257.
4. The program will save a clean file with "-cleaned" appended to the end of the original filename.
The right freelancer will get additional work along these same lines, cleaning up other types of errors in the file.
I would note there are likely existing free software dependencies that could be utilized to read trace files (.AB1).
http://biopython.org/wiki/SeqIO
http://biopython.org/wiki/ABI_traces
https://github.com/lh3/seqtk
It may be possible to parse the double peaks after conversion to FASTQ format. That would be preferable if it is possible.
NOTE: A double peak does not always mean that one of the peaks needs to be removed. It only should be removed if there is a repeating pattern that goes on for more than one base.
The final task for this project is to join two cleaned files into a single file known as a contig. Examples for testing are the FF94 files. One is a "forward" file and one is a "reverse" file. The reverse file will need to have the reverse-complement taken in order to get the two files to line up. There are sofware packages that can automate this, such as CAP3. http://seq.cs.iastate.edu/cap3.html or EMBOSS.
Prosjekt-ID: #16621503
Om prosjektet
8 frilansere byr i gjennomsnitt $118 for denne jobben
I am a full time developer and have high skills in python so I can complete this project. My price and time is negotiable. Let's discuss details via chat. I'll provide best service.
Hi sir AS python expert I am very glad to see your post. Python is my main skill, I have read your job description carefully and feel very confident on your project. 100% possible for me I can help you well. Plea Mer
I have high proficiency in , Mathematics, Python,Algorithm, C programming, Machine learning . Once you share the project, I will have a look & confirm if I can do it. I’m honest, creative and a unique person to carry Mer
Hello my name is Fares, i can get it done perfectly as you want let's chat when you are online. Thanks
I'm a quick-learner who can find solution quickly and implement them in "regle de l'art" fashion, I'm experienced with Python and C.
Will provide fast and efficient delivery of project. Have previous experiences also. Pay only if project will be completed on time.
