assignment5

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 assignment5 [2018/10/18 09:01]dokuroot assignment5 [2018/10/20 17:37] (current)dokuroot Both sides previous revision Previous revision 2018/10/20 17:37 dokuroot 2018/10/18 09:01 dokuroot 2018/10/18 08:59 dokuroot 2018/10/18 08:56 dokuroot 2018/10/18 08:55 dokuroot 2018/10/18 08:51 dokuroot created 2018/10/20 17:37 dokuroot 2018/10/18 09:01 dokuroot 2018/10/18 08:59 dokuroot 2018/10/18 08:56 dokuroot 2018/10/18 08:55 dokuroot 2018/10/18 08:51 dokuroot created Line 20: Line 20: \\ \\ + + **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==== Line 60: Line 70: 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'​)''​).