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Various display improvements

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This commit is contained in:
Celine Mercier
2019-09-03 21:46:39 +02:00
parent d491480af2
commit f296517716
6 changed files with 16 additions and 8 deletions
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7
python/obitools3/commands/grep.pyx
View File

@ -34,10 +34,11 @@ def addOptions(parser):
metavar="<PREDICATE>",
default=None,
type=str,
help="Python boolean expression to be evaluated in the "
help="Warning: use bytes for character strings (b'text' instead of 'text'). "
"Python boolean expression to be evaluated in the "
"sequence/line context. The attribute name can be "
"used in the expression as a variable name."
"An extra variable named 'sequence' or 'line' refers"
"used in the expression as a variable name. "
"An extra variable named 'sequence' or 'line' refers "
"to the sequence or line object itself. "
"Several -p options can be used on the same "
"commande line.")

1
python/obitools3/commands/import.pyx
View File

@ -289,6 +289,7 @@ def run(config):
if pb is not None:
pb(i, force=True)
print("", file=sys.stderr)
logger("info", "Imported %d entries", i)
# Save command config in View and DMS comments
command_line = " ".join(sys.argv[1:])

5
python/obitools3/commands/uniq.pyx
View File

@ -374,7 +374,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
if MERGED_COLUMN in o_view:
o_merged_col = o_view[MERGED_COLUMN]
print("\n") # TODO because in the middle of progress bar. Better solution?
pb(len(view), force=True)
print("")
logger("info", "Second browsing through the input")
# Initialize the progress bar
pb = ProgressBar(len(uniques), seconde=5)
@ -487,7 +488,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
o_view.delete_column(QUALITY_COLUMN)
if taxonomy is not None:
print("\n") # TODO because in the middle of progress bar. Better solution?
print("") # TODO because in the middle of progress bar. Better solution?
logger("info", "Merging taxonomy classification")
merge_taxonomy_classification(o_view, taxonomy)

2
src/build_reference_db.c
View File

@ -849,7 +849,7 @@ int build_reference_db(const char* dms_name,
free(matrix_view_name);
free(matrix_with_lca_view_name);
fprintf(stderr,"\rDone : 100 %% ");
fprintf(stderr,"\rDone : 100 %% \n");
return 0;
}

7
src/obi_ecopcr.c
View File

@ -424,7 +424,12 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
tm = (tm1 < tm2) ? tm1:tm2;
//tm = (tm1 < tm2) ? tm1:tm2;
if isnan(tm1)
tm1 = OBIFloat_NA;
if isnan(tm2)
tm2 = OBIFloat_NA;
// Get the taxon structure
main_taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);

2
src/obi_ecotag.c
View File

@ -655,7 +655,7 @@ int obi_ecotag(const char* dms_name,
obi_close_dms(ref_dms, false);
obi_close_dms(taxo_dms, false);
fprintf(stderr,"\rDone : 100 %% ");
fprintf(stderr,"\rDone : 100 %% \n");
return 0;
}