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OBITools
sumaclust
Commits
fcb9dbcf
Commit
fcb9dbcf
authored
Feb 22, 2016
by
Celine Mercier
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Input can now be stdin
parent
9ed2385f
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3 changed files
with
7 additions
and
10 deletions
+7
-10
sumaclust.c
sumaclust.c
+5
-8
sumaclust_user_manual.md
sumaclust_user_manual.md
+2
-2
sumaclust_user_manual.pdf
sumaclust_user_manual.pdf
+0
-0
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sumaclust.c
View file @
fcb9dbcf
...
...
@@ -23,7 +23,7 @@
#include "mtcompare_sumaclust.h"
#include "sumaclust.h"
#define VERSION "1.0.
1
0"
#define VERSION "1.0.
2
0"
/* ----------------------------------------------- */
...
...
@@ -73,9 +73,10 @@ static void PrintHelp()
PP
" -f : Output in FASTA format is deactivated.
\n
"
);
PP
"
\n
"
);
PP
"------------------------------------------------------------
\n
"
);
PP
" Argument : the nucleotide dataset to cluster
\n
"
);
PP
" Argument : the nucleotide dataset to cluster (or nothing
\n
"
);
PP
" if the standard input should be used).
\n
"
);
PP
"------------------------------------------------------------
\n
"
);
PP
" http://metabarcoding.org/suma
tra
\n
"
);
PP
" http://metabarcoding.org/suma
clust
\n
"
);
PP
"------------------------------------------------------------
\n\n
"
);
}
...
...
@@ -794,7 +795,6 @@ int main(int argc, char** argv)
BOOL
reverse
=
FALSE
;
BOOL
onlyATGC
=
TRUE
;
int
reference
=
ALILEN
;
int
ndb
=
0
;
int
nproc
=
1
;
BOOL
printBIOM
=
FALSE
;
BOOL
printOTUtable
=
FALSE
;
...
...
@@ -941,10 +941,6 @@ int main(int argc, char** argv)
}
}
ndb
=
argc
-
optind
;
if
(
ndb
!=
1
)
errflag
++
;
if
(
errflag
)
ExitUsage
(
errflag
);
...
...
@@ -965,6 +961,7 @@ int main(int argc, char** argv)
fprintf
(
stderr
,
"Reading dataset..."
);
db
=
seq_readAllSeq2
(
argv
[
optind
],
TRUE
,
onlyATGC
);
fprintf
(
stderr
,
"
\n
%d sequences
\n
"
,
db
.
count
);
if
(
db
.
count
==
0
)
...
...
sumaclust_user_manual.md
View file @
fcb9dbcf
...
...
@@ -46,12 +46,12 @@ Sumaclust clusters sequences using the same clustering algorithm as UCLUST and C
#### Input
Input file must b
e in FASTA format.
The input can be either the standard input (stdin), or a fil
e in FASTA format.
#### Usage
```
sumaclust [-l|L|a|n|r|d|e|o|g|f] [-t threshold_value] [-s sorting_key] [-R maximum_ratio] [-p number_of_threads] [-B file_name_for_BIOM-formatted_output] [-O file_name_for_OTU_table-formatted_output] [-F file_name_for_FASTA-formatted_output]
dataset
sumaclust [-l|L|a|n|r|d|e|o|g|f] [-t threshold_value] [-s sorting_key] [-R maximum_ratio] [-p number_of_threads] [-B file_name_for_BIOM-formatted_output] [-O file_name_for_OTU_table-formatted_output] [-F file_name_for_FASTA-formatted_output]
[dataset]
```
Argument: the sequence dataset to cluster.
...
...
sumaclust_user_manual.pdf
View file @
fcb9dbcf
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