static int GenomeAlignmentFromCmd(string[] args)
{
string keyFilePath = args[0];
string rCmapFilePath = args[1];
string outputDirPath = args[2];
int projectId = int.Parse(args[3]);
float lengthFilter = float.Parse(args[4]) * 1000;
float confidenceFilter = float.Parse(args[5]);
float alignedLenPercentFilter = float.Parse(args[6]);
string queryLocation = args[7];
bool saveChannel1 = int.Parse(args[8]) == 1 ? true : false;
bool saveChannel2 = int.Parse(args[9]) == 1 ? true : false;
int readKeyChroms = CMAPParser.ReadKeyFile(keyFilePath);
Tuple <List <int>, List <Tuple <int, int, int> > > locations = UserInputParser.getLocations(queryLocation, null);
List <int> chromIdsFilter = locations.Item1;
List <Tuple <int, int, int> > chromStartEndFilter = locations.Item2;
CMAPParser.rCmapPositions = CMAPParser.ParseCmap(rCmapFilePath, 1);
List <Molecule> selectedMolecules = DatabaseManager.SelectMoleculesForGenomeAlignment(projectId, lengthFilter, confidenceFilter, alignedLenPercentFilter, null, chromIdsFilter,
chromStartEndFilter);
foreach (Molecule molecule in selectedMolecules)
{
CMAPParser.FitMoleculeToRef(molecule, saveChannel1, saveChannel2, outputDirPath);
}
return(0);
}
private void filterMolecules_Click(object sender, EventArgs e)
{
alignmentFilter = aligned_filter_ckbx.Checked ? 1 : 0;
lengthFilter = String.IsNullOrEmpty(min_len_txtbx.Text) ? 0 : float.Parse(min_len_txtbx.Text) * 1000;
confidenceFilter = String.IsNullOrEmpty(min_conf_txtbx.Text) ? 0 : float.Parse(min_conf_txtbx.Text);
alignedLenPercentFilter = String.IsNullOrEmpty(min_aligned_len_txtbx.Text) ? 0 : float.Parse(min_aligned_len_txtbx.Text);
molIdsFilterArray = null;
chromIdsFilter = null;
chromStartEndFilter = null;
if (!String.IsNullOrEmpty(mols_ids_txtbx.Text) && !String.IsNullOrEmpty(mol_ids_file_path_txtbx.Text))
{
MessageBox.Show("For molecule IDs filter either input into the text box, or upload a file, but not both", "Error parsing filter options");
return;
}
if (!String.IsNullOrEmpty(mols_ids_txtbx.Text) || !String.IsNullOrEmpty(mol_ids_file_path_txtbx.Text))
{
molIdsFilterArray = UserInputParser.getMolIds(mols_ids_txtbx.Text, mol_ids_file_path_txtbx.Text);
if (molIdsFilterArray == null)
{
MessageBox.Show("Can't open molecule IDs file", "Error parsing filter options");
return;
}
}
if (!String.IsNullOrEmpty(mol_locations_txtbx.Text) && !String.IsNullOrEmpty(mol_locations_file_path_txtbx.Text))
{
MessageBox.Show("For molecule locations filter either input into the text box, or upload a file, but not both", "Error parsing filter options");
return;
}
if (!String.IsNullOrEmpty(mol_locations_txtbx.Text) || !String.IsNullOrEmpty(mol_locations_file_path_txtbx.Text))
{
if (String.IsNullOrEmpty(key_file_path_txtbx.Text))
{
MessageBox.Show("For molecule locations filter you must supply a key file", "Error parsing filter options");
return;
}
else //file and lines are present, parse the input
{
int readKeyChroms = CMAPParser.ReadKeyFile(key_file_path_txtbx.Text); //reading the key file to translate chromosome names to IDs, becaues chromosomes are saved as IDs in DB
if (readKeyChroms == -1)
{
MessageBox.Show("Can't open specified key file", "Error opening file");
return;
}
else
{
//get the locations from user input
Tuple <List <int>, List <Tuple <int, int, int> > > locations = UserInputParser.getLocations(mol_locations_txtbx.Text, mol_locations_file_path_txtbx.Text);
chromIdsFilter = locations.Item1;
chromStartEndFilter = locations.Item2;
}
}
}
}
private void get_output_button_Click(object sender, EventArgs e)
{
Stopwatch stopwatch = new Stopwatch();
string rCmapPath = r_cmap_file_path_txtbx.Text;
string keyFilePath = key_file_path_txtbx2.Text;
string outputDir = output_dir_txtbx.Text;
if (String.IsNullOrEmpty(rCmapPath) || String.IsNullOrEmpty(keyFilePath))
{
MessageBox.Show("r_cmap and key file required for analysis", "Missing file");
return;
}
if (String.IsNullOrEmpty(outputDir))
{
MessageBox.Show("Missing output directory path", "Missing path");
return;
}
stopwatch.Start();
CMAPParser.rCmapPositions = CMAPParser.ParseCmap(rCmapPath, 1);
if (CMAPParser.rCmapPositions == null)
{
MessageBox.Show("Unable to open file: " + rCmapPath, "Problem accessing file");
return;
}
int chroms = CMAPParser.ReadKeyFile(keyFilePath);
if (chroms < 0)
{
MessageBox.Show("Unable to open file: " + keyFilePath, "Problem accessing file");
return;
}
List <Molecule> selectedMolecules = DatabaseManager.SelectMoleculesForGenomeAlignment(projectID, lengthFilter, confidenceFilter, alignedLenPercentFilter, molIdsFilterArray, chromIdsFilter,
chromStartEndFilter);
foreach (Molecule molecule in selectedMolecules)
{
CMAPParser.FitMoleculeToRef(molecule, save_ch1_checkbx.Checked, save_ch2_checkbx.Checked, outputDir);
}
MessageBox.Show(stopwatch.Elapsed.ToString());
}
