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assignment4 [2018/10/10 16:29]
dokuroot
assignment4 [2018/10/10 21:56]
dokuroot
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 **Due date:​** ​ 10/16/18 at 10 am **Due date:​** ​ 10/16/18 at 10 am
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 +Follow the [[ script:​template | template]] shown in class for writing your code.  The "​main"​ segment of the module should prompt the user for the arguments and pass them to the functions and print the return values to the terminal.
  
 ====Exercise 1==== ====Exercise 1====
  
-Write a function, fastq_fasta(),​ that converts a fastq file to a new fasta formatted file.+Write a function, ​''​fastq_fasta(input_file, output_file)''​, that converts a fastq file to a new fasta formatted file.
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 The function should have the following attributes: The function should have the following attributes:
-  * Prompts the user for the input and output file names. 
   * Trims off the '​@'​ sign at the beginning of each ID line.   * Trims off the '​@'​ sign at the beginning of each ID line.
 +  * Writes to the output file only the ID lines and sequence lines, per fasta formatting rules.
 +  * Includes a '>'​ at the beginning of each ID line in the fasta output, per fasta formatting rules.
   * Exits gracefully if it can't open the the files.   * Exits gracefully if it can't open the the files.
-  * Prints to the terminal ​the number of reads that were processed ​(e.g. "Reads processed: 12345678").+  * Returns ​the number of reads that were processed. ​The return value can be printed from the "main" ​segment of the module.
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 The input and output files should have the following formats: The input and output files should have the following formats:
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 ====Exercise 2==== ====Exercise 2====
  
-Write a function, fastq_trimmer(),​ that trims any number of nucleotides from the 5' end of each read and any number of nucleotides from the 3' end of each read in a fastq file and writes the results to a new fastq formatted file.+Write a function, ​''​fastq_trimmer(input_file, output_file,​ trim_5p, trim_3p)''​, that trims any number of nucleotides from the 5' end of each read and any number of nucleotides from the 3' end of each read in a fastq file and writes the results to a new fastq formatted file. The quality score lines should be trimmed exactly as the sequence lines.
  
 The function should have the following attributes: The function should have the following attributes:
-  * Prompts the user for the input file name,  the output file name, the number of nucleotides to trim from the 5' end, and the number of nucleotides to trim from the 3' end. 
   * Exits gracefully if it can't open the the files.   * Exits gracefully if it can't open the the files.
-  * Prints to the terminal ​the number of reads that were processed ​and the original and resulting read length with the assumption that all reads are the same length. +  * Trims sequence lines and quality score lines as specified in the ''​trim_5p''​ and ''​trim_3p''​ arguments. 
- +  * Returns ​the number of reads that were processed. The return value can be printed from the "​main"​ segment of the module.
-  Reads processed: 12345678  +
-  Original read length: 50 nt +
-  Trimmed read length: 40 nt+
  
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 **Combine your functions into a single module and submit via Canvas for grading.** **Combine your functions into a single module and submit via Canvas for grading.**
assignment4.txt · Last modified: 2018/10/10 22:02 by dokuroot