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Extract based on regex match on the defline #13

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4510073
wrong implicit conversion not allowed in recent compilers
May 2, 2017
aaf83a6
Merge https://github.com/tomoakin/klab
May 2, 2017
9157ff1
search on deflines with regex, using c++11 regex
May 2, 2017
0a12053
explanation for extract --regex
May 2, 2017
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46 changes: 27 additions & 19 deletions src/fatt.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
#include <cstdlib>
#include <algorithm>
#include <numeric>
#include <regex>
#include <getopt.h>
#include <unistd.h>
#include <sys/types.h>
Expand Down Expand Up @@ -220,7 +221,7 @@ class FileLineBufferWithAutoExpansion
line_count = 0;
off_count = 0;
fileName = file_name;
return ist;
return true;
}
void close() {
ist.close();
Expand Down Expand Up @@ -1116,6 +1117,22 @@ void do_index(int argc, char** argv)
}
}

static bool check_read_conditions(long long param_start, const char* head_inf, set <string> readNamesToTake, regex re, bool flag_reverse_condition, long long number_of_sequences, long long param_end)
{
bool current_read_has_been_taken;
if(param_start == -1) {
string read_name = get_read_name_from_header(head_inf);
if(!readNamesToTake.empty()) {
current_read_has_been_taken = (readNamesToTake.count(read_name) != 0) ^ flag_reverse_condition;
} else {
current_read_has_been_taken = regex_search(head_inf, re) ^ flag_reverse_condition;
}
} else {
current_read_has_been_taken = param_start + 1 <= number_of_sequences && number_of_sequences <= param_end;
}
return current_read_has_been_taken;
}

void do_extract(int argc, char** argv)
{
bool flag_reverse_condition = false;
Expand All @@ -1132,6 +1149,7 @@ void do_extract(int argc, char** argv)
{"reverse", no_argument , 0, 'r'},
{"force", no_argument , 0, 'F'},
{"seq", required_argument, 0, 's'},
{"regex", required_argument, 0, 'x'}, //x is chosen because r and e was used for other options
{"file", required_argument, 0, 'f'},
{"stdin", no_argument, 0, 'c'},
{"unique", no_argument, 0, 'u'},
Expand All @@ -1144,6 +1162,7 @@ void do_extract(int argc, char** argv)
};

set<string> readNamesToTake;
std::regex re;
vector<string> fileInputs;

while(true) {
Expand All @@ -1163,6 +1182,9 @@ void do_extract(int argc, char** argv)
case 's':
readNamesToTake.insert(optarg);
break;
case 'x':
re = std::regex(optarg);
break;
case 'f':
fileInputs.push_back(optarg);
break;
Expand Down Expand Up @@ -1362,24 +1384,14 @@ void do_extract(int argc, char** argv)
if(f.getline()) {
number_of_sequences++;
size_t number_of_nucleotides_in_read = 0;
if(param_start == -1) {
current_read_has_been_taken = (readNamesToTake.count(get_read_name_from_header(f.b)) != 0) ^ flag_reverse_condition;
} else {
current_read_has_been_taken = param_start + 1 <= number_of_sequences && number_of_sequences <= param_end;
// NOTE: the latter condition never hold, if I properly implemented.
}
current_read_has_been_taken = check_read_conditions(param_start, f.b, readNamesToTake, re, flag_reverse_condition, number_of_sequences, param_end);
if(current_read_has_been_taken) cout << f.b << endl;
if(flag_output_unique) readNamesToTake.insert(get_read_name_from_header(f.b));
if(!f.looksLikeFASTQHeader()) {
while(f.getline()) {
if(f.looksLikeFASTAHeader()) {
number_of_sequences++;
if(param_start == -1) {
current_read_has_been_taken = (readNamesToTake.count(get_read_name_from_header(f.b)) != 0) ^ flag_reverse_condition;
} else {
current_read_has_been_taken = param_start + 1 <= number_of_sequences && number_of_sequences <= param_end;
// NOTE: the latter condition never hold, if I properly implemented.
}
current_read_has_been_taken = check_read_conditions(param_start, f.b, readNamesToTake, re, flag_reverse_condition, number_of_sequences, param_end);
if(current_read_has_been_taken) cout << f.b << endl;
if(flag_output_unique) readNamesToTake.insert(get_read_name_from_header(f.b));
number_of_nucleotides_in_read = 0;
Expand All @@ -1404,12 +1416,7 @@ void do_extract(int argc, char** argv)
if(!f.getline()) break;
f.registerHeaderLine();
++number_of_sequences;
if(param_start == -1) {
current_read_has_been_taken = (readNamesToTake.count(get_read_name_from_header(f.b)) != 0) ^ flag_reverse_condition;
} else {
current_read_has_been_taken = param_start + 1 <= number_of_sequences && number_of_sequences <= param_end;
// NOTE: the latter condition never hold, if I properly implemented.
}
current_read_has_been_taken = check_read_conditions(param_start, f.b, readNamesToTake, re, flag_reverse_condition, number_of_sequences, param_end);
if(param_end < number_of_sequences) // NOTE: param_end is 0-origin, number_of_sequences is 1-origin.
break;
if(current_read_has_been_taken) cout << f.b << endl;
Expand Down Expand Up @@ -3029,6 +3036,7 @@ void show_help(const char* subcommand)
cerr << "Usage: fatt extract [options...] <FAST(A|Q) files>\n\n";
cerr << "--unique\tOutput only unique reads. Reads with the same read name are removed.\n";
cerr << "--seq\tSpecify the name of the read to be retrieved. You can specify this option as many times as you wish.\n";
cerr << "--regex\tSpecify a regular expression. The deflines (i.e. read name AND description) are searched for a match. \n";
cerr << "--file\tSpecify a file in which you listed the read names. One line, one read.\n";
cerr << "--stdin\tRead the list of read names from stdin. It may be useful when you combine with *NIX pipe.\n";
cerr << "--reverse\tReverse the extracting condition. It is like -v option of grep.\n";
Expand Down
2 changes: 1 addition & 1 deletion wscript
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ def configure(conf):
conf.check_perl_version((5,6,0))
conf.check_perl_ext_devel()
conf.check_python_version((2,4,2))
conf.env.append_unique('CXXFLAGS', ['-O2', '-DVERSION_STRING=' + VERSION])
conf.env.append_unique('CXXFLAGS', ['-std=c++11', '-O2', '-DVERSION_STRING=' + VERSION])
conf.env.INCLUDES += '.'
conf.env.LIB += ['pthread', 'dl']

Expand Down