cdhit-utility.c++

#include<stdlib.h>
#include<iostream>
#include"cdhit-common.h"

using namespace std;

// information
char cd_hit_ver[]  = "\t\t====== CD-HIT version " CDHIT_VERSION " (built on " __DATE__ ") ======";
char cd_hit_ref1[] = "\"CD-HIT: a fast program for clustering and comparing large sets of protein or nucleotide sequences\", Weizhong Li & Adam Godzik. Bioinformatics, (2006) 22:1658-1659";
char cd_hit_ref2[] = "\"CD-HIT: accelerated for clustering the next generation sequencing data\", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152";
char cd_hit_ref3[] = "\"Beifang Niu, Limin Fu, Shulei Sun and Weizhong Li. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics (2010) 11:187";
//

char contacts[] =
  "   Questions, bugs, contact Weizhong Li at liwz@sdsc.edu\n"
  "   For updated versions and information, please visit: http://cd-hit.org\n"
  "                                                    or https://github.com/weizhongli/cdhit\n\n"
  "   cd-hit web server is also available from http://cd-hit.org\n\n"
  "   If you find cd-hit useful, please kindly cite:\n\n";

char txt_option_i[] = "\tinput filename in fasta format, required, can be in .gz format\n";
char txt_option_j[] = 
"\tinput filename in fasta/fastq format for R2 reads if input are paired end (PE) files\n \
\t -i R1.fq -j R2.fq -o output_R1 -op output_R2 or\n \
\t -i R1.fa -j R2.fa -o output_R1 -op output_R2 \n";
char txt_option_i_2d[] = "\tinput filename for db1 in fasta format, required, can be in .gz format\n";
char txt_option_i2[] = "\tinput filename for db2 in fasta format, required, can be in .gz format\n";
char txt_option_j2[] = 
"\tinput filename in fasta/fastq format for R2 reads if input are paired end (PE) files\n \
\t -i db1-R1.fq -j db1-R2.fq -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2 or\n \
\t -i db1-R1.fa -j db1-R2.fa -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2 \n";
char txt_option_o[] = "\toutput filename, required\n";
char txt_option_op[] = "\toutput filename for R2 reads if input are paired end (PE) files\n";
char txt_option_c[] = 
"\tsequence identity threshold, default 0.9\n \
\tthis is the default cd-hit's \"global sequence identity\" calculated as:\n \
\tnumber of identical amino acids or bases in alignment\n \
\tdivided by the full length of the shorter sequence\n";
char txt_option_G[] = 
"\tuse global sequence identity, default 1\n \
\tif set to 0, then use local sequence identity, calculated as :\n \
\tnumber of identical amino acids or bases in alignment\n \
\tdivided by the length of the alignment\n \
\tNOTE!!! don't use -G 0 unless you use alignment coverage controls\n \
\tsee options -aL, -AL, -aS, -AS\n";
char txt_option_g[] =
"\t1 or 0, default 0\n \
\tby cd-hit's default algorithm, a sequence is clustered to the first \n \
\tcluster that meet the threshold (fast cluster). If set to 1, the program\n \
\twill cluster it into the most similar cluster that meet the threshold\n \
\t(accurate but slow mode)\n \
\tbut either 1 or 0 won't change the representatives of final clusters\n";
char txt_option_b[] = "\tband_width of alignment, default 20\n";
char txt_option_M[] = "\tmemory limit (in MB) for the program, default 800; 0 for unlimitted;\n";
char txt_option_n[] = "\tword_length, default 5, see user's guide for choosing it\n";
char txt_option_n_est[] = "\tword_length, default 10, see user's guide for choosing it\n";
char txt_option_l[] = "\tlength of throw_away_sequences, default 10\n";
char txt_option_t[] = "\ttolerance for redundance, default 2\n";
char txt_option_T[] = "\tnumber of threads, default 1; with 0, all CPUs will be used\n";
char txt_option_d[] =
"\tlength of description in .clstr file, default 20\n \
\tif set to 0, it takes the fasta defline and stops at first space\n";
char txt_option_s[] =
"\tlength difference cutoff, default 0.0\n \
\tif set to 0.9, the shorter sequences need to be\n \
\tat least 90% length of the representative of the cluster\n";
char txt_option_S[] =
"\tlength difference cutoff in amino acid, default 999999\n \
\tif set to 60, the length difference between the shorter sequences\n \
\tand the representative of the cluster can not be bigger than 60\n";
char txt_option_s2[] =
"\tlength difference cutoff for db1, default 1.0\n \
\tby default, seqs in db1 >= seqs in db2 in a same cluster\n \
\tif set to 0.9, seqs in db1 may just >= 90% seqs in db2\n";
char txt_option_S2[] =
"\tlength difference cutoff, default 0\n \
\tby default, seqs in db1 >= seqs in db2 in a same cluster\n \
\tif set to 60, seqs in db2 may 60aa longer than seqs in db1\n";
char txt_option_aL[] = 
"\talignment coverage for the longer sequence, default 0.0\n \
\tif set to 0.9, the alignment must covers 90% of the sequence\n";
char txt_option_AL[] = 
"\talignment coverage control for the longer sequence, default 99999999\n \
\tif set to 60, and the length of the sequence is 400,\n \
\tthen the alignment must be >= 340 (400-60) residues\n";
char txt_option_aS[] = 
"\talignment coverage for the shorter sequence, default 0.0\n \
\tif set to 0.9, the alignment must covers 90% of the sequence\n";
char txt_option_AS[] = 
"\talignment coverage control for the shorter sequence, default 99999999\n \
\tif set to 60, and the length of the sequence is 400,\n \
\tthen the alignment must be >= 340 (400-60) residues\n";
char txt_option_A[] = 
"\tminimal alignment coverage control for the both sequences, default 0\n \
\talignment must cover >= this value for both sequences \n"; 
char txt_option_B[] =
"\t1 or 0, default 0, by default, sequences are stored in RAM\n \
\tif set to 1, sequence are stored on hard drive\n \
\t!! No longer supported !!\n";
char txt_option_P[] =
"\tinput paired end (PE) reads, default 0, single file\n \
\tif set to 1, please use -i R1 -j R2 to input both PE files\n";
char txt_option_cx[] =
"\tlength to keep after trimming the tail of sequence, default 0, not trimming\n \
\tif set to 50, the program only uses the first 50 letters of input sequence\n";
char txt_option_cy[] =
"\tlength to keep after trimming the tail of R2 sequence, default 0, not trimming\n \
\tif set to 50, the program only uses the first 50 letters of input R2 sequence\n \
\te.g. -cx 100 -cy 80 for paired end reads\n";
char txt_option_ap[] =
"\talignment position constrains,  default 0, no constrain\n \
\tif set to 1, the program will force sequences to align at beginings\n \
\twhen set to 1, the program only does +/+ alignment\n";
char txt_option_uL[] = 
"\tmaximum unmatched percentage for the longer sequence, default 1.0\n \
\tif set to 0.1, the unmatched region (excluding leading and tailing gaps)\n \
\tmust not be more than 10% of the sequence\n";
char txt_option_uS[] = 
"\tmaximum unmatched percentage for the shorter sequence, default 1.0\n \
\tif set to 0.1, the unmatched region (excluding leading and tailing gaps)\n \
\tmust not be more than 10% of the sequence\n";
char txt_option_U[] = 
"\tmaximum unmatched length, default 99999999\n \
\tif set to 10, the unmatched region (excluding leading and tailing gaps)\n \
\tmust not be more than 10 bases\n";
char txt_option_p[] =
"\t1 or 0, default 0\n \tif set to 1, print alignment overlap in .clstr file\n";
char txt_option_r[] =
"\t1 or 0, default 1, by default do both +/+ & +/- alignments\n \
\tif set to 0, only +/+ strand alignment\n";
char txt_option_bak[] =
"\twrite backup cluster file (1 or 0, default 0)\n";
char txt_option_sc[] =
"\tsort clusters by size (number of sequences), default 0, output clusters by decreasing length\n \
\tif set to 1, output clusters by decreasing size\n";
char txt_option_sf[] =
"\tsort fasta/fastq by cluster size (number of sequences), default 0, no sorting\n \
\tif set to 1, output sequences by decreasing cluster size\n \
\tthis can be very slow if the input is in .gz format\n";

char txt_option_mask[] = "\tmasking letters (e.g. -mask NX, to mask out both 'N' and 'X')\n";
char txt_option_match[] = "\tmatching score, default 2 (1 for T-U and N-N)\n";
char txt_option_match2[] = "\tmatching score, default 2\n";
char txt_option_mismatch[] = "\tmismatching score, default -2\n";
char txt_option_mismatch2[] = "\tmismatching score, default -1\n";
char txt_option_gap[] = "\tgap opening score, default -6\n";
char txt_option_gap2[] = "\tgap opening score, default -3\n";
char txt_option_gap_ext[] = "\tgap extension score, default -1\n";

int print_usage (char *arg) {
  cout << cd_hit_ver << "\n\n" ;
  cout << "Usage: "<< arg << " [Options] \n\nOptions\n\n";
  cout << "   -i" << txt_option_i;
  cout << "   -o" << txt_option_o;
  cout << "   -c" << txt_option_c;
  cout << "   -G" << txt_option_G;
  cout << "   -b" << txt_option_b;
  cout << "   -M" << txt_option_M;
  cout << "   -T" << txt_option_T;
  cout << "   -n" << txt_option_n;
  cout << "   -l" << txt_option_l;
  cout << "   -t" << txt_option_t;
  cout << "   -d" << txt_option_d;
  cout << "   -s" << txt_option_s;
  cout << "   -S" << txt_option_S;
  cout << "   -aL" << txt_option_aL;
  cout << "   -AL" << txt_option_AL;
  cout << "   -aS" << txt_option_aS;
  cout << "   -AS" << txt_option_AS;
  cout << "   -A" << txt_option_A;
  cout << "   -uL" << txt_option_uL;
  cout << "   -uS" << txt_option_uS;
  cout << "   -U" << txt_option_U;
  cout << "   -B" << txt_option_B;
  cout << "   -p" << txt_option_p;
  cout << "   -g" << txt_option_g;
  cout << "   -sc"<< txt_option_sc;
  cout << "   -sf"<< txt_option_sf;
  cout << "   -bak" << txt_option_bak;
  cout << "   -h\tprint this help\n\n";
  cout << contacts;
  cout << "   " << cd_hit_ref1 << "\n";
  cout << "   " << cd_hit_ref2 << "\n\n\n";
  exit(1);
} // END print_usage



int print_usage_2d (char *arg) {
  cout << cd_hit_ver << "\n\n" ;
  cout << "Usage: "<< arg << " [Options] \n\nOptions\n\n";
  cout << "   -i" << txt_option_i_2d;
  cout << "   -i2"<< txt_option_i2;
  cout << "   -o" << txt_option_o;
  cout << "   -c" << txt_option_c;
  cout << "   -G" << txt_option_G;
  cout << "   -b" << txt_option_b;
  cout << "   -M" << txt_option_M;
  cout << "   -T" << txt_option_T;
  cout << "   -n" << txt_option_n;
  cout << "   -l" << txt_option_l;
  cout << "   -t" << txt_option_t;
  cout << "   -d" << txt_option_d;
  cout << "   -s" << txt_option_s;
  cout << "   -S" << txt_option_S;
  cout << "   -s2" << txt_option_s2;
  cout << "   -S2" << txt_option_S2;
  cout << "   -aL" << txt_option_aL;
  cout << "   -AL" << txt_option_AL;
  cout << "   -aS" << txt_option_aS;
  cout << "   -AS" << txt_option_AS;
  cout << "   -A" << txt_option_A;
  cout << "   -uL" << txt_option_uL;
  cout << "   -uS" << txt_option_uS;
  cout << "   -U" << txt_option_U;
  cout << "   -B" << txt_option_B;
  cout << "   -p" << txt_option_p;
  cout << "   -g" << txt_option_g;
  cout << "   -bak" << txt_option_bak;
  cout << "   -h\tprint this help\n\n";
  cout << "   Questions, bugs, contact Weizhong Li at liwz@sdsc.edu\n\n";
  cout << "   If you find cd-hit useful, please kindly cite:\n\n";
  cout << "   " << cd_hit_ref1 << "\n";
  cout << "   " << cd_hit_ref2 << "\n\n\n";
  exit(1);
} // END print_usage_2d


int print_usage_est (char *arg) {
  cout << cd_hit_ver << "\n\n" ;
  cout << "Usage: "<< arg << " [Options] \n\nOptions\n\n";
  cout << "   -i" << txt_option_i;
  cout << "   -j" << txt_option_j;
  cout << "   -o" << txt_option_o;
  cout << "   -op" << txt_option_op;
  cout << "   -c" << txt_option_c;
  cout << "   -G" << txt_option_G;
  cout << "   -b" << txt_option_b;
  cout << "   -M" << txt_option_M;
  cout << "   -T" << txt_option_T;
  cout << "   -n" << txt_option_n_est;
  cout << "   -l" << txt_option_l;
  cout << "   -d" << txt_option_d;
  cout << "   -s" << txt_option_s;
  cout << "   -S" << txt_option_S;
  cout << "   -aL" << txt_option_aL;
  cout << "   -AL" << txt_option_AL;
  cout << "   -aS" << txt_option_aS;
  cout << "   -AS" << txt_option_AS;
  cout << "   -A" << txt_option_A;
  cout << "   -uL" << txt_option_uL;
  cout << "   -uS" << txt_option_uS;
  cout << "   -U" << txt_option_U;
  cout << "   -B" << txt_option_B;
  cout << "   -P" << txt_option_P;
  cout << "   -cx"<< txt_option_cx;
  cout << "   -cy"<< txt_option_cy;
  cout << "   -ap"<< txt_option_ap;
  cout << "   -p" << txt_option_p;
  cout << "   -g" << txt_option_g;
  cout << "   -r" << txt_option_r;
  cout << "   -mask" << txt_option_mask;
  cout << "   -match" << txt_option_match;
  cout << "   -mismatch" << txt_option_mismatch;
  cout << "   -gap" << txt_option_gap;
  cout << "   -gap-ext" << txt_option_gap_ext;
  cout << "   -bak" << txt_option_bak;
  cout << "   -sc"<< txt_option_sc;
  cout << "   -sf"<< txt_option_sf;
  cout << "   -h\tprint this help\n\n";
  cout << contacts;
  cout << "   " << cd_hit_ref1 << "\n";
  cout << "   " << cd_hit_ref2 << "\n\n\n";
  exit(1);
} // END print_usage_est


int print_usage_est_2d (char *arg) {
  cout << cd_hit_ver << "\n\n" ;
  cout << "Usage: "<< arg << " [Options] \n\nOptions\n\n";
  cout << "   -i" << txt_option_i_2d;
  cout << "   -i2"<< txt_option_i2;
  cout << "   -j, -j2"<< txt_option_j2;
  cout << "   -o" << txt_option_o;
  cout << "   -op" << txt_option_op;
  cout << "   -c" << txt_option_c;
  cout << "   -G" << txt_option_G;
  cout << "   -b" << txt_option_b;
  cout << "   -M" << txt_option_M;
  cout << "   -T" << txt_option_T;
  cout << "   -n" << txt_option_n_est;
  cout << "   -l" << txt_option_l;
  cout << "   -d" << txt_option_d;
  cout << "   -s" << txt_option_s;
  cout << "   -S" << txt_option_S;
  cout << "   -s2" << txt_option_s2;
  cout << "   -S2" << txt_option_S2;
  cout << "   -aL" << txt_option_aL;
  cout << "   -AL" << txt_option_AL;
  cout << "   -aS" << txt_option_aS;
  cout << "   -AS" << txt_option_AS;
  cout << "   -A" << txt_option_A;
  cout << "   -uL" << txt_option_uL;
  cout << "   -uS" << txt_option_uS;
  cout << "   -U" << txt_option_U;
  cout << "   -B" << txt_option_B;
  cout << "   -P" << txt_option_P;
  cout << "   -cx"<< txt_option_cx;
  cout << "   -cy"<< txt_option_cy;
  cout << "   -p" << txt_option_p;
  cout << "   -g" << txt_option_g;
  cout << "   -r" << txt_option_r;
  cout << "   -mask" << txt_option_mask;
  cout << "   -match" << txt_option_match;
  cout << "   -mismatch" << txt_option_mismatch;
  cout << "   -gap" << txt_option_gap;
  cout << "   -gap-ext" << txt_option_gap_ext;
  cout << "   -bak" << txt_option_bak;
  cout << "   -h\tprint this help\n\n";
  cout << contacts;
  cout << "   " << cd_hit_ref1 << "\n";
  cout << "   " << cd_hit_ref2 << "\n\n\n";
  exit(1);
} // END print_usage_est_2d


int print_usage_div (char *arg) {
  cout << cd_hit_ver << "\n\n" ;
  cout << "Usage: "<< arg << " [Options] \n\nOptions\n\n";
  cout << "Options " << endl << endl;
  cout << "   -i in_dbname, required" << endl;
  cout << "   -o out_dbname, required" << endl;
  cout << "   -div number of divide, required " << endl;
//  cout << "   -dbmax max size of your db\n\n\n";
  exit(1);
} // END print_usage_div

char mytxt_option_c[] =
"\tsequence identity threshold, default 0.98\n \
\tthis is a \"global sequence identity\" calculated as :\n \
\tnumber of identical amino acids or bases in alignment\n \
\tdivided by the full length of the shorter sequence + gaps\n";
char mytxt_option_b[] = "\tband_width of alignment, default 10\n";
char mytxt_option_n_est[] = "\tword_length, default 10, see user's guide for choosing it\n";
char mytxt_option_D[] = "\tmax size per indel, default 1\n";
int print_usage_454 (char *arg)
{
  cout << cd_hit_ver << "\n\n" ;
  cout << "Usage: "<< arg << " [Options] \n\nOptions\n\n";
  cout << "   -i" << txt_option_i;
  cout << "   -o" << txt_option_o;
  cout << "   -c" << mytxt_option_c;
  cout << "   -b" << mytxt_option_b;
  cout << "   -M" << txt_option_M;
  cout << "   -T" << txt_option_T;
  cout << "   -n" << mytxt_option_n_est;
  cout << "   -aL" << txt_option_aL;
  cout << "   -AL" << txt_option_AL;
  cout << "   -aS" << txt_option_aS;
  cout << "   -AS" << txt_option_AS;
  cout << "   -B" << txt_option_B;
  cout << "   -g" << txt_option_g;
  cout << "   -D" << mytxt_option_D;
  cout << "   -match" << txt_option_match2;
  cout << "   -mismatch" << txt_option_mismatch2;
  cout << "   -gap" << txt_option_gap2;
  cout << "   -gap-ext" << txt_option_gap_ext;
  cout << "   -bak" << txt_option_bak;
  cout << "   -h\tprint this help\n\n";
  cout << "   Questions, bugs, contact Weizhong Li at liwz@sdsc.edu\n\n";
  cout << "   If you find cd-hit useful, please kindly cite:\n\n";
  cout << "   " << cd_hit_ref1 << "\n";
  cout << "   " << cd_hit_ref2 << "\n";
  cout << "   " << cd_hit_ref3 << "\n\n\n";
  exit(1);
}

float current_time()
{
	return ((float)clock())/CLOCKS_PER_SEC;
}