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assignment5 [2018/10/18 08:59]
dokuroot
assignment5 [2018/10/20 17:37] (current)
dokuroot
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 \\ \\
 +
 +**Additional Hints** (avoid reading these until you get stuck)\\
 +\\
 +1) Your code will likely have a nested for loop. Use the length of the nested list within the matrix (''​len(matrix[0])''​) for the number of iterations in the outer for loop.\\
 +\\
 +2) Use the length of the matrix (''​len(matrix)''​) for the number of iterations in the nested for loop.\\
 +\\
 +3) Append each element from the original nested lists within the matrix (''​matrix[n][i]'',​ where n and i are the two iteration variables in the for loops - but which order?) to a new list within the nested for loop and then append the new list to a second new list in the outer for loop.
 +\\
 +
 ====Exercise 2==== ====Exercise 2====
  
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 fastq file: [[ http://​rna.colostate.edu/​dokuwiki/​doku.php?​id=sample_data | small_RNAs.fastq]]\\ fastq file: [[ http://​rna.colostate.edu/​dokuwiki/​doku.php?​id=sample_data | small_RNAs.fastq]]\\
-fasta file: [[ http://​rna.colostate.edu/​dokuwiki/​doku.php?​id=sample_data | cel_miRNA.fa]]+fasta file: [[ http://​rna.colostate.edu/​dokuwiki/​doku.php?​id=sample_data | c_elegans_miRNAs.fa]]
  
 The function should: The function should:
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   let-7 1   let-7 1
   lin-4 0   lin-4 0
 +
 +**Additional Hints** (avoid reading these until you get stuck)\\  ​
 +1) Your first for loop should loop through the fastq file creating a dictionary with the sequence lines (''​if (line_number + 3) % 4 == 1''​) as the keys and the numbers of times each sequence appears as the values. You can increment the values using get (''​fastq_dictionary[sequence] = fastq_dictionary.get(sequence,​ 0) + 1''​).\\
 +\\
 +2) The second for loop should loop through the fasta file and retrieve the number of reads for each sequence and should write the miRNA name and reads to a new file (''​outfile.write(mirna_name[1:​] + '​\t'​ + str(fastq_dictionary.get(line,​ 0)) + '​\n'​)''​).
assignment5.1539874756.txt.gz ยท Last modified: 2018/10/18 08:59 by dokuroot