Parsing files - Githubissues

MManee commented 8 years ago

the goal of these tasks is to learn different techniques to parse files!

MManee commented 8 years ago

I’ve uploaded a file (2taxa_tree.fas) in your data directory: https://github.com/kacst-bioinfo-lab/labwork/tree/master/data/abdulmalek
the file includes thousand groups of (Root, A and B) sequences in FASTA format starting from A
root represents the Root and A and B are the children of the root sequence
you need to parse this file to get the conserved elements (CNEs) and spacers of each sequence
you sould read from LOG file, every dataset includes the start and end location of CNE and spacer
slow model for CNE and fast for spacer
don’t consider dash (-) and star *()** signs in this stage
the output file should be in bed format (recommended) or text format as you wish, and should be located in your doc directory: https://github.com/kacst-bioinfo-lab/labwork/tree/master/doc/abdulmalek
the output file should look like this:

Run CA  CB  CR  CB-CA   CA-CR   CB-CR   SA  SB  SR  SB-SA   SA-SR   SB-SR
1   .   .   .   .   .   .   .   .   .   .   .   .
.
.
.
.
1000    .   .   .   .   .   .   .   .   .   .   .   .

they are 1000 groups, so you should have 1000 runs
CA is the the total CNE length of A, and CB is the the total CNE length of B and CR is the the total CNE length of Root
SA is the the total spacer length of A, and SB is the the total spacer length of B and SR is the the total spacer length of Root
and finally you should print the difference between the values as shown above

atalgarni commented 8 years ago

You can find the python code for parsing, counting the CNS & spacer in https://github.com/kacst-bioinfo-lab/labwork/tree/master/code/abdulmalek For the output file you can find it in https://github.com/kacst-bioinfo-lab/labwork/tree/master/doc/abdulmalek

MManee commented 8 years ago

you have to check your results again
to help you solve this issue, the first record should look like this:

Run CA  CB  CR  CB-CA   CA-CR   CB-CR   SA  SB  SR  SB-SA   SA-SR   SB-SR
1   1000    1000    1000    0   0   0   1012    985 1000    12  15  27

and you script should read form the input file where it is loctated (labwork/data/abdulmalek/2taxa_tree.fas) and write the output file where it should be located (labwork/doc/abdulmalek/CNS_SPACER_Counts.bed)

atalgarni commented 7 years ago

Please find the Python code at https://github.com/kacst-bioinfo-lab/labwork/tree/master/code/abdulmalek/CNS_SPACSER_1.py For the output file please check https://github.com/kacst-bioinfo-lab/labwork/tree/master/doc/abdulmalek/nucleotide_counts.bed

I have updated the result file. Sorry I took too long ,,,, just recalled it while sniffing around Github folder on my machine. @MManee

MManee commented 5 years ago

kacst-bioinfo-lab / labwork

Parsing files #5

New thread is now open to have a clean version of programming tasks for Training Purposes #22