55 lines
1.7 KiB
Plaintext
55 lines
1.7 KiB
Plaintext
The job is to read FASTA file and count how many A, C, T, G letters are in an example sequence.
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FASTA one can get from the internet. We can use e.g. wiki page to get one sequence:
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https://en.wikipedia.org/wiki/FASTA_format
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The FASTA format with one sequence for an elephant looks like this:
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>BTBSCRYR
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tgcaccaaacatgtctaaagctggaaccaaaattactttctttgaagacaaaaactttca
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aggccgccactatgacagcgattgcgactgtgcagatttccacatgtacctgagccgctg
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caactccatcagagtggaaggaggcacctgggctgtgtatgaaaggcccaattttgctgg
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gtacatgtacatcctaccccggggcgagtatcctgagtaccagcactggatgggcctcaa
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cgaccgcctcagctcctgcagggctgttcacctgtctagtggaggccagtataagcttca
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gatctttgagaaaggggattttaatggtcagatgcatgagaccacggaagactgcccttc
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catcatggagcagttccacatgcgggaggtccactcctgtaaggtgctggagggcgcctg
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gatcttctatgagctgcccaactaccgaggcaggcagtacctgctggacaagaaggagta
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ccggaagcccgtcgactggggtgcagcttccccagctgtccagtctttccgccgcattgt
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ggagtgatgatacagatgcggccaaacgctggctggccttgtcatccaaataagcattat
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aaataaaacaattggcatgc
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The FASTA format has to separate parts:
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1. header
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2. sequence
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Thus, the excercise for reading FASTA file, in C, briefly looks like this:
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1. Select sequence and save it to a file, e.g. seq.fasta
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2. Open the file seq.fasta in C with fopen:
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https://cplusplus.com/reference/cstdio/fopen/
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Tip: Use correct mode.
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3. Read the file, line by line, using e.g. snippet of code from here:
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https://cplusplus.com/forum/beginner/22558/
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4. Check if the lines starts with ';' or with '>', then skip such a line
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If the line is OK, then count how many A, C, T, G are in the given line and
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save that information.
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In order to check if the line starts with a given character you can
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simply use index of a string (line[0] - this is first character in the
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array line).
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The end.
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