CS计算机代考程序代写 python database Bioinformatics Java c++ algorithm Programming assignment 3

Programming assignment 3
Released on Tuesday 2021-10-26 00:00:00 +0000

Due Date: 2021-11-09 11:59:00 +0000 11:59Due

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CMSC 423 Project 3 (The FM-index) : Overview
This assignment deals with the construction and querying of the FM index. As

we saw in class, having a useful FM index relies upon having (at least

sampled) su�x array entries to recall the actual positions of the matching

patterns. Thus, this project assumes that you have a working su�x array

construction implementation.

If you completed project 2 and implemented your own su�x array

construction routines, I strongly encourage you to use those. However, if you

didn’t complete project 2 successfully and are therefore in need of an

e�cient su�x array construction implementation, you can �nd a starter

project in Java here and in C++ here.

Much like project 2, your project will consist of 3 executables buildfm ,

inspectfm , and queryfm which are described in more detail below. Though

you will implement 3 programs, you can think of the project as being broken

into two parts.

In the �rst part of the project, you will implement a program to read a

reference sequence from a FASTA �le, to construct the su�x array and FM

index on this sequence, and then to write the su�x array and FM index to �le

in a binary format. You will also implement a program to read the saved �le

University of Maryland

Bioinformatics Algorithms, Databases, and Tools

Fall 2021

 HOME  LECTURES  ASSIGNMENTS

 SYLLABUS / COURSE MATERIALS

https://github.com/rob-p/cmsc423_f21_project3_java_sample
https://github.com/rob-p/cmsc423_f21_project3_cpp_sample
http://www.cs.umd.edu/
https://rob-p.github.io/CMSC423_F21/
https://rob-p.github.io/CMSC423_F21/
https://rob-p.github.io/CMSC423_F21/lectures/
https://rob-p.github.io/CMSC423_F21/assignments/
https://rob-p.github.io/CMSC423_F21/course-materials/

from disk, produce a textual representation of the FM index, and write that

representation to an output �le.

In the second part of the project, you will implement a program to read your

serialized index from �le, as well as to read an input FASTA �le containing

many queries and an execution mode. Your program will then produce an

output �le with the query results in a well-speci�ed output format.

NOTE : The timeout for all tests for the gradescope server will be 30 minutes

Overall structure
You will submit your assignment as a tarball named CMSC423_F21_A3.tar.gz .

When this tarball is expanded, it should create a single folder named

CMSC423_F21_A3 . This folder must be created in the directory where the

decompression (i.e. tar xzvf ) is done, and must not be nested inside any

other folders. The details of how you structure your “source tree” are up to

you, but the following must hold (to enable proper automated testing of your

programs).

There should be a script at the top-level of CMSC423_F21_A3 called

build.sh . This should do whatever is necessary to create 3 executables at

the top level (one called buildfm and one called inspectfm and one called

queryfm ). If you’re comfortable with Make�les, this can just call make , or it

could simply run the commands necessary to compile your programs and

copy them to the top-level directory. You can assume this script is run in a

bash shell.

There should be a README.md �le in the top level directory. This README

�le should contain the following information.

What language have you written your solution in?

What did you �nd to be the hardest part of this assignment?

What resources did you consult in working on this assignment (view

this as a form of citation; you shouldn’t copy code directly from

anywhere in your assignment, but if you consulted other sources

please list them here).

Turnin : The assignment turnin will be handled using Gradescope. We intend

to have the infrastructure for this set up by the end of this week.

Part (a), constructing and inspecting the
In this part of the assignment, you will write two programs. The �rst program

will be called buildfm ; it will read in a “genome” (in FASTA ) format, build the

su�x array and FM index on this reference, and write the su�x array and FM

index to a binary �le. The second program will be called inspectfm ; it will read

in the binary �le written by buildfm , and then it will compute a textual

representation of the FM index and write out a �le containing this

representation.

buildfm

buildfm : Input

The input consists of 2 arguments, given in this order:

reference – the path to a FASTA format �le containing the reference of

which you will build the su�x array.

output – the program will write a single binary output �le to a �le with this

name, that contains a serialized version of the su�x array and the FM

index.

buildfm : Output

Your program will output a �le with the name given by the output argument

above. This must be a binary �le holding everything necessary to perform

query using your FM index. Speci�cally, it should include an encoding of the

su�x array, the BWT of the string, the �rst column of the FM index and the

“tally” table used to perform occ queries during the backward search

procedure.

Note: The speci�c binary encoding is up to you. You are allowed to use an

external serialization library for this component, but the serialization must be

to a binary (not text) format. In C++ you could use something like cereal or

bitsery; in Rust you could use soemthing like rkyv or serde with bincode. For

reasons mentioned previously (and for the sake of not running into

performance issues in future projects), I’d not recommend using Python for

this project.

inspectfm

https://uscilab.github.io/cereal/
https://github.com/fraillt/bitsery
https://github.com/rkyv/rkyv
https://github.com/serde-rs/serde
https://github.com/bincode-org/bincode

inspectfm : Input

The input consists of 3 arguments, given in this order:

index – the path to the binary �le containing your serialized FM index

array (as written by buildfm above).

sample_rate – the rate at which “tally table” entries will be sampled in your

output (see below).

output – the program will write output to this �le containing a textual

representation of your FM index.

inspectfm : Output

Your program will output a �le with the name given by the output argument

above. The output will consist of the following information:

first column : A tab-separated list of the counts of $ , A , C , G , T in the

text (in this order).

BTW(T) : The Burrows–Wheeler transform of the original text.

tally spot check A : This is a textual representation of certain values

within the tally array for the A character. Speci�cally, this line should

encode a list of tab-separated integers that consists of the following

entries of the tally array for the character A : [ sample_rate 0,

sample_rate 1, sample_rate 2, …, sample_rate �oor(text-length /

sample_rate )].

tally spot check C : This is a textual representation of certain values

within the tally array for the C character. Speci�cally, this line should

encode a list of tab-separated integers that consists of the following

entries of the tally array for the character C : [ sample_rate 0,

sample_rate 1, sample_rate 2, …, sample_rate �oor(text-length /

sample_rate )].

tally spot check G : This is a textual representation of certain values

within the tally array for the G character. Speci�cally, this line should

encode a list of tab-separated integers that consists of the following

entries of the tally array for the character G : [ sample_rate 0,

sample_rate 1, sample_rate 2, …, sample_rate �oor(text-length /

sample_rate )].

tally spot check T : This is a textual representation of certain values

within the tally array for the T character. Speci�cally, this line should

encode a list of tab-separated integers that consists of the following

entries of the tally array for the character T : [ sample_rate 0,

sample_rate 1, sample_rate 2, …, sample_rate �oor(text-length /

sample_rate )].

Part (b), querying the FM index
In the second part of the assignment, you will implement a program for

querying patterns in the text using your FM index. Your program for this part

should be called queryfm . This program will take as input 4 arguments, your

serialized FM index, a FASTA �le containing queries, a query mode parameter,

and an output �le name. It will perform query in the FM index and report the

results in the output �le speci�ed in the format speci�ed below.

queryfm : Input

index – the path to the binary �le containing your serialized su�x array

(as written by buildsa above).

queries – the path to an input �le in FASTA format containing a set of

records. Unlike project 1 you will need to care about both the name and

sequence of these FASTA records, as you will report the output using the

name that appears for a record. Note, query sequences can span more

than one line (headers will always be on one line).

query mode – this argument should be one of two strings; either complete

or partial . If the string is complete you should perform your queries

using the backward search algorithm and only report hits for a pattern if

it matches, in its entirety, in the text. If the string is partial you should

perform backward search and return the length and positions of the

longest matching su�x of the query pattern in the text.

output – the name to use for the resulting output.

queryfm : Output

output – the output �le of your program. This �le should contain the

results of your queries in the following format. Each line should contain a

tab-separated list containing the following information:

query_name , match_len , k , hit_1 , hit_2 , hit_k

University of

Maryland

Department of Computer Science

University of Maryland

College Park, MD

Here, the query_name is simply the header of the corresponding FASTA entry

(the string after the > — not including the > on the header line). The value

match_len is the length of the match. If your program was run with

query_mode of complete then match_len should be either the full length of

the query string (if there were hits) or 0 (if there were no hits). If your

program was run with query_mode of partial then match_len should be

the length of the longest mached su�x of the pattern. The value k is the

number of occurrences of the query string (or the longest matched su�x the

query string) in the underlying text on which the FM index is built. Finally,

hit_1 through hit_k are the positions in the original text (0-indexed) where

the query string (or the longest matched su�x of the query string) occurs. If

you are running in complete query mode and a query string does not occur

in the text, or if you are running in partial mode and the last character in

the query does not appear in the text, then you should report k = 0, and

there will be no hit_1 , … etc. entries for that query.