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Accept to deal with sequence in lower case

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@217 60f365c0-8329-0410-b2a4-ec073aeeaa1d
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Eric Coissac
2009-05-13 13:21:10 +00:00
parent 1428cd7499
commit ad6f493d0f
9 changed files with 261 additions and 42 deletions
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122
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<name>ecoPCR</name>
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<?xml version="1.0" encoding="UTF-8"?>
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91
src/libecoPCR/ecoseq.c
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@ -4,6 +4,7 @@
#include <zlib.h> #include <zlib.h>
#include <string.h> #include <string.h>
#include <stdio.h> #include <stdio.h>
#include <ctype.h>
static FILE *open_seqfile(const char *prefix,int32_t index); static FILE *open_seqfile(const char *prefix,int32_t index);
@ -11,32 +12,32 @@ static FILE *open_seqfile(const char *prefix,int32_t index);
ecoseq_t *new_ecoseq() ecoseq_t *new_ecoseq()
{ {
void *tmp; void *tmp;
tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure"); tmp = ECOMALLOC(sizeof(ecoseq_t),"Allocate new ecoseq structure");
return tmp; return tmp;
} }
int32_t delete_ecoseq(ecoseq_t * seq) int32_t delete_ecoseq(ecoseq_t * seq)
{ {
if (seq) if (seq)
{ {
if (seq->AC) if (seq->AC)
ECOFREE(seq->AC,"Free sequence AC"); ECOFREE(seq->AC,"Free sequence AC");
if (seq->DE) if (seq->DE)
ECOFREE(seq->DE,"Free sequence DE"); ECOFREE(seq->DE,"Free sequence DE");
if (seq->SQ) if (seq->SQ)
ECOFREE(seq->SQ,"Free sequence SQ"); ECOFREE(seq->SQ,"Free sequence SQ");
ECOFREE(seq,"Free sequence structure"); ECOFREE(seq,"Free sequence structure");
return 0; return 0;
} }
return 1; return 1;
} }
@ -49,9 +50,9 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
ecoseq_t *tmp; ecoseq_t *tmp;
int32_t lstr; int32_t lstr;
tmp = new_ecoseq(); tmp = new_ecoseq();
tmp->taxid=taxid_idx; tmp->taxid=taxid_idx;
if (AC) if (AC)
{ {
lstr =strlen(AC); lstr =strlen(AC);
@ -97,12 +98,14 @@ ecoseq_t *readnext_ecoseq(FILE *f)
int32_t comp_status; int32_t comp_status;
unsigned long int seqlength; unsigned long int seqlength;
int32_t rs; int32_t rs;
char *c;
int32_t i;
raw = read_ecorecord(f,&rs); raw = read_ecorecord(f,&rs);
if (!raw) if (!raw)
return NULL; return NULL;
if (is_big_endian()) if (is_big_endian())
{ {
raw->CSQ_length = swap_int32_t(raw->CSQ_length); raw->CSQ_length = swap_int32_t(raw->CSQ_length);
@ -110,44 +113,48 @@ ecoseq_t *readnext_ecoseq(FILE *f)
raw->SQ_length = swap_int32_t(raw->SQ_length); raw->SQ_length = swap_int32_t(raw->SQ_length);
raw->taxid = swap_int32_t(raw->taxid); raw->taxid = swap_int32_t(raw->taxid);
} }
seq = new_ecoseq(); seq = new_ecoseq();
seq->taxid = raw->taxid; seq->taxid = raw->taxid;
seq->AC = ECOMALLOC(strlen(raw->AC) +1, seq->AC = ECOMALLOC(strlen(raw->AC) +1,
"Allocate Sequence Accesion number"); "Allocate Sequence Accesion number");
strncpy(seq->AC,raw->AC,strlen(raw->AC)); strncpy(seq->AC,raw->AC,strlen(raw->AC));
seq->DE = ECOMALLOC(raw->DE_length+1, seq->DE = ECOMALLOC(raw->DE_length+1,
"Allocate Sequence definition"); "Allocate Sequence definition");
strncpy(seq->DE,raw->data,raw->DE_length); strncpy(seq->DE,raw->data,raw->DE_length);
seqlength = seq->SQ_length = raw->SQ_length; seqlength = seq->SQ_length = raw->SQ_length;
compressed = raw->data + raw->DE_length; compressed = raw->data + raw->DE_length;
seq->SQ = ECOMALLOC(seqlength+1, seq->SQ = ECOMALLOC(seqlength+1,
"Allocate sequence buffer"); "Allocate sequence buffer");
comp_status = uncompress((unsigned char*)seq->SQ, comp_status = uncompress((unsigned char*)seq->SQ,
&seqlength, &seqlength,
(unsigned char*)compressed, (unsigned char*)compressed,
raw->CSQ_length); raw->CSQ_length);
if (comp_status != Z_OK) if (comp_status != Z_OK)
ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data"); ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
for (c=seq->SQ,i=0;i<seqlength;c++,i++)
*c=toupper(*c);
return seq; return seq;
} }
/** /**
* Open the sequences database (.sdx file) * Open the sequences database (.sdx file)
* @param prefix name of the database (radical without extension) * @param prefix name of the database (radical without extension)
* @param index integer * @param index integer
* *
* @return file object * @return file object
*/ */
FILE *open_seqfile(const char *prefix,int32_t index) FILE *open_seqfile(const char *prefix,int32_t index)
{ {
@ -161,22 +168,22 @@ FILE *open_seqfile(const char *prefix,int32_t index)
"%s_%03d.sdx", "%s_%03d.sdx",
prefix, prefix,
index); index);
fprintf(stderr,"# Coucou %s\n",filename_buffer); fprintf(stderr,"# Coucou %s\n",filename_buffer);
if (filename_length >= 1024) if (filename_length >= 1024)
ECOERROR(ECO_ASSERT_ERROR,"file name is too long"); ECOERROR(ECO_ASSERT_ERROR,"file name is too long");
filename_buffer[filename_length]=0; filename_buffer[filename_length]=0;
input=open_ecorecorddb(filename_buffer,&seqcount,0); input=open_ecorecorddb(filename_buffer,&seqcount,0);
if (input) if (input)
fprintf(stderr,"# Reading file %s containing %d sequences...\n", fprintf(stderr,"# Reading file %s containing %d sequences...\n",
filename_buffer, filename_buffer,
seqcount); seqcount);
return input; return input;
} }
@ -186,38 +193,38 @@ ecoseq_t *ecoseq_iterator(const char *prefix)
static int32_t current_file_idx = 1; static int32_t current_file_idx = 1;
static char current_prefix[1024]; static char current_prefix[1024];
ecoseq_t *seq; ecoseq_t *seq;
if (prefix) if (prefix)
{ {
current_file_idx = 1; current_file_idx = 1;
if (current_seq_file) if (current_seq_file)
fclose(current_seq_file); fclose(current_seq_file);
strncpy(current_prefix,prefix,1023); strncpy(current_prefix,prefix,1023);
current_prefix[1024]=0; current_prefix[1024]=0;
current_seq_file = open_seqfile(current_prefix, current_seq_file = open_seqfile(current_prefix,
current_file_idx); current_file_idx);
if (!current_seq_file) if (!current_seq_file)
return NULL; return NULL;
} }
seq = readnext_ecoseq(current_seq_file); seq = readnext_ecoseq(current_seq_file);
if (!seq && feof(current_seq_file)) if (!seq && feof(current_seq_file))
{ {
current_file_idx++; current_file_idx++;
fclose(current_seq_file); fclose(current_seq_file);
current_seq_file = open_seqfile(current_prefix, current_seq_file = open_seqfile(current_prefix,
current_file_idx); current_file_idx);
if (current_seq_file) if (current_seq_file)
seq = readnext_ecoseq(current_seq_file); seq = readnext_ecoseq(current_seq_file);
} }
return seq; return seq;
} }