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Input can now be stdin

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This commit is contained in:
Celine Mercier
2016-02-22 15:56:46 +01:00
parent 9ed2385fd6
commit fcb9dbcf86
3 changed files with 7 additions and 10 deletions
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13
sumaclust.c
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@ -23,7 +23,7 @@
#include "mtcompare_sumaclust.h" #include "mtcompare_sumaclust.h"
#include "sumaclust.h" #include "sumaclust.h"
#define VERSION "1.0.10" #define VERSION "1.0.20"
/* ----------------------------------------------- */ /* ----------------------------------------------- */
@ -73,9 +73,10 @@ static void PrintHelp()
PP " -f : Output in FASTA format is deactivated.\n"); PP " -f : Output in FASTA format is deactivated.\n");
PP "\n"); PP "\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 "------------------------------------------------------------\n");
PP " http://metabarcoding.org/sumatra\n"); PP " http://metabarcoding.org/sumaclust\n");
PP "------------------------------------------------------------\n\n"); PP "------------------------------------------------------------\n\n");
} }
@ -794,7 +795,6 @@ int main(int argc, char** argv)
BOOL reverse = FALSE; BOOL reverse = FALSE;
BOOL onlyATGC = TRUE; BOOL onlyATGC = TRUE;
int reference = ALILEN; int reference = ALILEN;
int ndb = 0;
int nproc = 1; int nproc = 1;
BOOL printBIOM = FALSE; BOOL printBIOM = FALSE;
BOOL printOTUtable = FALSE; BOOL printOTUtable = FALSE;
@ -941,10 +941,6 @@ int main(int argc, char** argv)
} }
} }
ndb = argc - optind;
if (ndb != 1)
errflag++;
if (errflag) if (errflag)
ExitUsage(errflag); ExitUsage(errflag);
@ -965,6 +961,7 @@ int main(int argc, char** argv)
fprintf(stderr,"Reading dataset..."); fprintf(stderr,"Reading dataset...");
db = seq_readAllSeq2(argv[optind], TRUE, onlyATGC); db = seq_readAllSeq2(argv[optind], TRUE, onlyATGC);
fprintf(stderr,"\n%d sequences\n",db.count); fprintf(stderr,"\n%d sequences\n",db.count);
if (db.count == 0) if (db.count == 0)

4
sumaclust_user_manual.md
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@ -46,12 +46,12 @@ Sumaclust clusters sequences using the same clustering algorithm as UCLUST and C
#### Input #### Input
Input file must be in FASTA format. The input can be either the standard input (stdin), or a file in FASTA format.
#### Usage #### 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. Argument: the sequence dataset to cluster.

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sumaclust_user_manual.pdf
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