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Now handling sequences with Uracil (U) nucleotides by converting to

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Thymine (T)
This commit is contained in:
Celine Mercier
2020-10-30 10:46:17 +01:00
parent 112e12cab0
commit 2e191372d7
2 changed files with 29 additions and 21 deletions
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6
src/encode.c
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@ -36,10 +36,12 @@ bool only_ATGC(const char* seq)
{ {
if (!((*c == 'A') || \ if (!((*c == 'A') || \
(*c == 'T') || \ (*c == 'T') || \
(*c == 'U') || \
(*c == 'G') || \ (*c == 'G') || \
(*c == 'C') || \ (*c == 'C') || \
(*c == 'a') || \ (*c == 'a') || \
(*c == 't') || \ (*c == 't') || \
(*c == 'u') || \
(*c == 'g') || \ (*c == 'g') || \
(*c == 'c'))) (*c == 'c')))
{ {
@ -182,6 +184,8 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
break; break;
case 't': case 't':
case 'T': case 'T':
case 'u':
case 'U':
seq_b[i/4] |= NUC_T_2b; seq_b[i/4] |= NUC_T_2b;
break; break;
default: default:
@ -288,6 +292,8 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
break; break;
case 't': case 't':
case 'T': case 'T':
case 'u': // discussable
case 'U':
seq_b[i/2] |= NUC_T_4b; seq_b[i/2] |= NUC_T_4b;
break; break;
case 'r': case 'r':

44
src/encode.h
View File

@ -64,7 +64,7 @@ enum
/** /**
* @brief Checks if there are only 'atgcATGC' characters in a * @brief Checks if there are only 'atgcuATGCU' characters in a
* character string. * character string.
* *
* @param seq The sequence to check. * @param seq The sequence to check.
@ -129,12 +129,13 @@ byte_t get_nucleotide_from_encoded_seq(byte_t* seq, int32_t idx, uint8_t encodin
/** /**
* @brief Encodes a DNA sequence with each nucleotide coded on 2 bits. * @brief Encodes a DNA sequence with each nucleotide coded on 2 bits.
* *
* A or a : 00 * A or a : 00
* C or c : 01 * C or c : 01
* T or t : 10 * T or t or U or u : 10
* G or g : 11 * G or g : 11
* *
* @warning The DNA sequence must contain only 'atgcATGC' characters. * @warning The DNA sequence must contain only 'atgcuATGCU' characters.
* @warning Uracil ('U') bases are encoded as Thymine ('T') bases.
* *
* @param seq The sequence to encode. * @param seq The sequence to encode.
* @param length The length of the sequence to encode. * @param length The length of the sequence to encode.
@ -169,23 +170,24 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
/** /**
* @brief Encodes a DNA sequence with each nucleotide coded on 4 bits. * @brief Encodes a DNA sequence with each nucleotide coded on 4 bits.
* *
* A or a : 0001 * A or a : 0001
* C or c : 0010 * C or c : 0010
* G or g : 0011 * G or g : 0011
* T or t : 0100 * T or t or U or u : 0100
* R or r : 0101 * R or r : 0101
* Y or y : 0110 * Y or y : 0110
* S or s : 0111 * S or s : 0111
* W or w : 1000 * W or w : 1000
* K or k : 1001 * K or k : 1001
* M or m : 1010 * M or m : 1010
* B or b : 1011 * B or b : 1011
* D or d : 1100 * D or d : 1100
* H or h : 1101 * H or h : 1101
* V or v : 1110 * V or v : 1110
* N or n : 1111 * N or n : 1111
* *
* @warning The DNA sequence must contain only IUPAC characters. * @warning The DNA sequence must contain only IUPAC characters.
* @warning Uracil ('U') bases are encoded as Thymine ('T') bases.
* *
* @param seq The sequence to encode. * @param seq The sequence to encode.
* @param length The length of the sequence to encode. * @param length The length of the sequence to encode.