Skip to content

Change createdb.cpp so that it takes in ".txt" file containing paths of different fasta files #879

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Change createdb.cpp so that it takes in ".txt" file containing paths of different fasta files #879

Changes from 2 commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
df80f07
Change createdb.cpp so that it takes in ".txt" file containing paths …
elpis51613 Aug 25, 2024
1073ec9
Merge remote-tracking branch 'refs/remotes/origin/master'
elpis51613 Aug 25, 2024
3617ea7
Change filepath format from txt to tsv. Also add explanations of its …
elpis51613 Aug 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 22 additions & 0 deletions src/util/createdb.cpp
100644 → 100755
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,28 @@ int createdb(int argc, const char **argv, const Command& command) {
std::vector<std::string> filenames(par.filenames);
std::string dataFile = filenames.back();
filenames.pop_back();
if (Util::endsWith(".txt", filenames[0])) {
Copy link
Member

@milot-mirdita milot-mirdita Aug 26, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please use .tsv.

Also please adjust MMseqsBase.cpp to explain that users can pass in a tsv

Copy link
Author

@elpis51613 elpis51613 Aug 26, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

In the createdb module only, or in all search/cluster modules as well?

if (filenames.size() > 1) {
Debug(Debug::ERROR) << "Only one txt file can be given\n";
EXIT(EXIT_FAILURE);
}
std::string tsv = filenames.back();
filenames.pop_back();

FILE* file = FileUtil::openFileOrDie(tsv.c_str(), "r", true);
char* line = NULL;
size_t len = 0;
ssize_t read;
while ((read = getline(&line, &len, file)) != -1) {
if (line[read - 1] == '\n') {
line[read - 1] = '\0';
read--;
}
filenames.push_back(line);
}
free(line);
fclose(file);
}

for (size_t i = 0; i < filenames.size(); i++) {
if (FileUtil::directoryExists(filenames[i].c_str()) == true) {
Expand Down