seq.c File Reference

Module to handle DNA and protein sequences. More...

#include "log.h"
#include "format.h"
#include "common.h"
#include "seq.h"
#include "numUtil.h"

Go to the source code of this file.

Functions
void	seq_aaFilter (char *in, DNA *out)
	Filter out non-aa characters and change to upper case.
Codon	seq_codonVal (DNA *start)
	Return value from 0-63 of codon starting at start.
void	seq_complement (DNA *dna, long length)
	Complement DNA (not reverse).
void	seq_dnaBaseHistogram (DNA *dna, int dnaSize, int histogram[4])
	Count up frequency of occurance of each base and store results in histogram.
void	seq_dnaFilter (char *in, DNA *out)
	Filter out non-DNA characters and change to lower case.
void	seq_dnaMixedCaseFilter (char *in, DNA *out)
	Filter out non-DNA characters but leave case intact.
int	seq_dnaOrAaScoreMatch (char *a, char *b, int size, int matchScore, int mismatchScore, char ignore)
	Compare two sequences (without inserts or deletions) and score.
void	seq_init ()
	Initialize the seq module.
int	seq_intronOrientation (DNA *iStart, DNA *iEnd)
	Given a gap in genome from iStart to iEnd, return 1 for GT/AG intron between left and right, -1 for CT/AC, 0 for no intron.
AA	seq_lookupCodon (DNA *dna)
	Returns one letter code for protein, 0 for stop codon, or X for bad input.
AA	seq_lookupMitochondrialCodon (DNA *dna)
	Returns one letter code for protein, 0 for stop codon, or X for bad input.
Bits *	seq_maskFromUpperCaseSeq (Seq *seq)
	Allocate a mask for sequence and fill it in based on sequence case.
void	seq_reverseComplement (DNA *dna, long length)
	Reverse complement DNA.
int	seq_seqIsLower (Seq *seq)
	Return 1 if sequence is all lower case, 0 otherwise.
void	seq_toRna (DNA *dna)
	Convert T's to U's.
aaSeq *	seq_translateSeq (dnaSeq *inSeq, unsigned offset, int stop)
	Return a translated sequence.
aaSeq *	seq_translateSeqN (dnaSeq *inSeq, unsigned offset, unsigned inSize, int stop)
	Return a translated sequence.
DNA *	seq_valToCodon (int val)
	Return codon corresponding to val (0-63).

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Detailed Description

Module to handle DNA and protein sequences.

Author:

Adapted by Lukas Habegger (lukas.habegger@yale.edu)

Definition in file seq.c.

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Function Documentation

Codon seq_codonVal

(

DNA *

start

)

Return value from 0-63 of codon starting at start.

Returns -1 if not a codon.

Definition at line 264 of file seq.c.

int seq_intronOrientation	(	DNA *	iStart,
		DNA *	iEnd
	)

Given a gap in genome from iStart to iEnd, return 1 for GT/AG intron between left and right, -1 for CT/AC, 0 for no intron.

Assumes DNA is lower cased.

Definition at line 615 of file seq.c.

aaSeq* seq_translateSeq	(	dnaSeq *	inSeq,
		unsigned	offset,
		int	stop
	)

Return a translated sequence.

Offset is position of first base to translate. If stop is 1 then stop at first stop codon. (Otherwise represent stop codons as 'Z').

Definition at line 505 of file seq.c.

aaSeq* seq_translateSeqN	(	dnaSeq *	inSeq,
		unsigned	offset,
		unsigned	inSize,
		int	stop
	)

Return a translated sequence.

Offset is position of first base to translate. If size is 0 then use length of inSeq.

Definition at line 463 of file seq.c.