obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

ecopcr: now printing a warning instead of interrupting with an error

Browse Source 
when a taxid is not found
This commit is contained in:
Celine Mercier
2020-04-10 11:22:04 +02:00
parent cd9cea8c97
commit 1218eed7fd
1 changed files with 26 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files

40
src/obi_ecopcr.c Executable file → Normal file
View File

@ -105,7 +105,8 @@ static int create_output_columns(Obiview_p o_view, bool kingdom_mode);
* @param o_temp1_column A pointer on the output column for the temperature for the first primer. * @param o_temp1_column A pointer on the output column for the temperature for the first primer.
* @param o_temp2_column A pointer on the output column for the temperature for the second primer. * @param o_temp2_column A pointer on the output column for the temperature for the second primer.
* *
* @retval 0 if the operation was successfully completed. * @retval 0 if the sequence was skipped (taxid not found, warning printed).
* @retval 1 if the sequence was successfully printed to the output.
* @retval -1 if an error occurred. * @retval -1 if an error occurred.
* *
* @since July 2018 * @since July 2018
@ -366,6 +367,17 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
// TODO add check for primer longer than MAX_PAT_LEN (32) // TODO add check for primer longer than MAX_PAT_LEN (32)
// Get sequence id
seq_id = obi_get_str_with_elt_idx_and_col_p_in_view(i_view, i_id_column, i_idx, 0);
// Get the taxon structure
main_taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);
if (main_taxon == NULL)
{
obidebug(1, "\nWarning: error reading the taxonomic information of a sequence. Seq id: %s, taxid: %d. Probably deprecated taxid. Skipping this sequence.", seq_id, taxid);
return 0;
}
ldelta = (pos1 <= keep_nucleotides)?pos1:keep_nucleotides; ldelta = (pos1 <= keep_nucleotides)?pos1:keep_nucleotides;
rdelta = ((pos2+keep_nucleotides)>=seq_len)?seq_len-pos2:keep_nucleotides; rdelta = ((pos2+keep_nucleotides)>=seq_len)?seq_len-pos2:keep_nucleotides;
@ -432,18 +444,9 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
tm2 = OBIFloat_NA; tm2 = OBIFloat_NA;
// Write sequence id // Write sequence id
seq_id = obi_get_str_with_elt_idx_and_col_p_in_view(i_view, i_id_column, i_idx, 0);
if (obi_set_str_with_elt_idx_and_col_p_in_view(o_view, o_id_column, o_idx, 0, seq_id) < 0) if (obi_set_str_with_elt_idx_and_col_p_in_view(o_view, o_id_column, o_idx, 0, seq_id) < 0)
{ {
obidebug(1, "\nError writing the sequence id (%s)", seq_id); obidebug(1, "\nError writing the sequence id");
return -1;
}
// Get the taxon structure
main_taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);
if (main_taxon == NULL)
{
obidebug(1, "\nError reading the taxonomic information of a sequence, sequence id: %s, taxid: %d", seq_id, taxid);
return -1; return -1;
} }
@ -629,7 +632,7 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
return -1; return -1;
} }
return 0; return 1;
} }
@ -698,6 +701,7 @@ int obi_ecopcr(const char* i_dms_name,
obiint_t taxid; obiint_t taxid;
char* sequence; char* sequence;
int printed;
SeqPtr apatseq=NULL; SeqPtr apatseq=NULL;
int32_t o1Hits; int32_t o1Hits;
@ -1072,7 +1076,7 @@ int obi_ecopcr(const char* i_dms_name,
(!max_len || (length <= max_len))) (!max_len || (length <= max_len)))
{ {
// Print the found amplicon // Print the found amplicon
if (print_seq(i_view, o_view, printed = print_seq(i_view, o_view,
i_idx, o_idx, i_idx, o_idx,
taxonomy, taxonomy,
sequence, sequence,
@ -1098,11 +1102,13 @@ int obi_ecopcr(const char* i_dms_name,
o_strand_column, o_strand_column,
o_primer1_column, o_primer2_column, o_primer1_column, o_primer2_column,
o_error1_column, o_error2_column, o_error1_column, o_error2_column,
o_temp1_column, o_temp2_column) < 0) o_temp1_column, o_temp2_column);
if (printed < 0)
{ {
obidebug(1, "\nError writing the ecopcr result"); obidebug(1, "\nError writing the ecopcr result");
return -1; return -1;
} }
else if (printed > 0)
o_idx++; o_idx++;
} }
} }
@ -1160,7 +1166,7 @@ int obi_ecopcr(const char* i_dms_name,
(!max_len || (length <= max_len))) (!max_len || (length <= max_len)))
{ {
// Print the found amplicon // Print the found amplicon
if (print_seq(i_view, o_view, printed = print_seq(i_view, o_view,
i_idx, o_idx, i_idx, o_idx,
taxonomy, taxonomy,
sequence, sequence,
@ -1186,11 +1192,13 @@ int obi_ecopcr(const char* i_dms_name,
o_strand_column, o_strand_column,
o_primer1_column, o_primer2_column, o_primer1_column, o_primer2_column,
o_error1_column, o_error2_column, o_error1_column, o_error2_column,
o_temp1_column, o_temp2_column) < 0) o_temp1_column, o_temp2_column);
if (printed < 0)
{ {
obidebug(1, "\nError writing the ecopcr result"); obidebug(1, "\nError writing the ecopcr result");
return -1; return -1;
} }
else if (printed > 0)
o_idx++; o_idx++;
} }
} }