辅导讲解CS、CS辅导讲解、代作CS程序

Programming languages for Bioinformatics

1. Write a program to find differences between two files containing bioinformatics data.

Synopsis:

Biodiff [options] from-file to-file

If you have two files A (from-file) and B (to-file), you are expected to generate all lines in A-B,

A & B, and B-A in terms of the criteria you set. The file format of file A and B can be different.

There will be two styles for comparison: one is coordinate based (option –c ) and the other

is name based (option –n). You can set one of these two options as the default style. The

two styles were described as follows.

1). Coordinate-based diff. Two or more columns from file A and B will be selected and

compared to check if the two regions overlap. If two regions from the two files overlap, then

these two regions will be put into to A&B_A and A&B_B; those regions in A but not in A&B

will be put into A-B; and those in B but not in A&B will be put into B-A. Note, the comparison

is based on the coordinates specified by two columns set by the user, but the output result

contains whole lines in the original files.

For example, we have two example files A_ucsc_genes.txt and B_ucsc_gene.gtf. If you run

Biodiff –c –a 3,4 –b 3,4 A_ucsc_genes.txt B_ucsc_gene.gtf

Column 3 and 4 from A_uscs_genes.txt file will be selected to represent a region and column

3 and 4 from B_ucsc_gene.gtf file will be selected to represent a region, then they are

compared. If these two regions overlap, it should generate 4 result files corresponding to

A&B_A, A&B_B, A-B, and B-A, where A&B_A contains those lines from file A and overlap

with some entries in file B; A&B_B contains lines from file B and overlap with entries in file A;

A-B contains those lines from file A and have no overlapping entries in B; and B-A stands for

those lines from file B but have no overlapping entries in A.

2) Name-based diff. Two columns from file A and B will be selected and compared in terms

of string comparison. Users need to specify the column numbers in two files to be compared.

For example, two example track files (A_ucsc_genes.txt and B_ucsc_gene.gtf) were

downloaded from the WashU Genome Browser website (http://genomebrowser.wustl.edu ).

Both Files A_ucsc_genes.txt and B_ucsc_gene.gtf contain some UCSC genes with different

file formats. If you run

Biodiff –n –a 0 –b 8 A_ucsc_genes.txt B_ucsc_gene.gtf

The first column from A_uscs_genes.txt file and the 9th column from B_ucsc_gene.gtf file

will be selected and compared. If their names “overlap”, it should generate 4 result files

corresponding to A&B_A, A&B_B, A-B, and B-A, where A&B_A contains those lines from file

A and overlapping with some entries in file B; A&B_B contains lines from file B and

overlapping with entries in file A; A-B contains those lines from file A and with no

overlapping entries in B; and B-A stands for those lines from file B but with no overlapping

entries in A. Here, we call a string s “overlaps” with another string t, if s contains the whole

string t or t contains the whole string s.

Please write your program in C and test it thoroughly. Your program is expected to deal

with very large size files (the test files may be of hundred MBs). Both the accuracy and

speed will be evaluated for your program. (Hint: when you compare two files, first sort the

entries in each file based on the column of your pick; then compare them.)

In addition, please write your code as pretty as you can and put as much explanation as

you can.

You report should include at least 4 parts: 1). Design of the program; 2) implementation of the

program; 3). Usage of your program and test examples together with results. 4) Conclusions and

discussions. Part 2 should include the source code as the appendix.

Turning in your homework

Please hand in a hard copy and an electric copy of your project report. Please submit the electric

copy of your report through the course website at ou are strongly suggested to

test your code in a local machine or in the teaching server first before you submit your homework

to the submission website. The homework report should be handed in before the class start on