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Merge branch 'master' of https://git.wmi.amu.edu.pl/ahypki/bioinf-2023-2024-introduction-cpp

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Arkadiusz Hypki 2024-05-10 10:41:58 +02:00
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ex1-reading-fasta/description
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@ -6,12 +6,19 @@ https://en.wikipedia.org/wiki/FASTA_format
The FASTA format with one sequence for an elephant looks like this: The FASTA format with one sequence for an elephant looks like this:
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] >BTBSCRYR
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV tgcaccaaacatgtctaaagctggaaccaaaattactttctttgaagacaaaaactttca
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG aggccgccactatgacagcgattgcgactgtgcagatttccacatgtacctgagccgctg
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL caactccatcagagtggaaggaggcacctgggctgtgtatgaaaggcccaattttgctgg
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX gtacatgtacatcctaccccggggcgagtatcctgagtaccagcactggatgggcctcaa
IENY cgaccgcctcagctcctgcagggctgttcacctgtctagtggaggccagtataagcttca
gatctttgagaaaggggattttaatggtcagatgcatgagaccacggaagactgcccttc
catcatggagcagttccacatgcgggaggtccactcctgtaaggtgctggagggcgcctg
gatcttctatgagctgcccaactaccgaggcaggcagtacctgctggacaagaaggagta
ccggaagcccgtcgactggggtgcagcttccccagctgtccagtctttccgccgcattgt
ggagtgatgatacagatgcggccaaacgctggctggccttgtcatccaaataagcattat
aaataaaacaattggcatgc
The FASTA format has to separate parts: The FASTA format has to separate parts:
@ -20,7 +27,7 @@ The FASTA format has to separate parts:
2. sequence 2. sequence
Thus, the excercise for reading FASTA file briefly looks like this: Thus, the excercise for reading FASTA file, in C, briefly looks like this:
1. Select sequence and save it to a file, e.g. seq.fasta 1. Select sequence and save it to a file, e.g. seq.fasta
@ -28,4 +35,20 @@ Thus, the excercise for reading FASTA file briefly looks like this:
https://cplusplus.com/reference/cstdio/fopen/ https://cplusplus.com/reference/cstdio/fopen/
Tip: Use correct mode. Tip: Use correct mode.
3. Read the file, line by line, using e.g. snippet of code from here:
https://cplusplus.com/forum/beginner/22558/
4. Check if the lines starts with ';' or with '>', then skip such a line
If the line is OK, then count how many A, C, T, G are in the given line and
save that information.
In order to check if the line starts with a given character you can
simply use index of a string (line[0] - this is first character in the
array line).
The end.