//
#include "getmimarkspackagecommand.h"
+#include "groupmap.h"
//**********************************************************************************************************************
vector<string> GetMIMarksPackageCommand::setParameters(){
try {
//files that have dependancies
CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pgroup);
+ CommandParameter pfile("file", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pfile);
CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(poligos);
+ CommandParameter ppackage("package", "Multiple", "air-host_associated-human_associated-human_gut-human_oral-human_skin-human_vaginal-microbial-miscellaneous-plant_associated-sediment-soil-wastewater-water", "miscellaneous", "", "", "","",false,false,true); parameters.push_back(ppackage);
+ CommandParameter prequiredonly("requiredonly", "Boolean", "", "F", "", "", "","",false,false, true); parameters.push_back(prequiredonly);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string GetMIMarksPackageCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.mimarkspackage command creates a mimarks package form with your groups. The required fields are flagged with * characters.\n";
+ helpString += "The get.mimarkspackage command creates a mimarks package form with your groups. The required fields are flagged with * characters. Fields marked with '**' indicated they are in a group where at least one of the fields is required.\n";
helpString += "Further documentation on the different packages and required formats can be found here, http://www.mothur.org/wiki/MIMarks_Data_Packages.\n";
- helpString += "The get.mimarkspackage command parameters are: oligos, group and package. oligos or group is required.\n";
+ helpString += "The get.mimarkspackage command parameters are: oligos, group, package and requiredonly. oligos or group is required.\n";
helpString += "The oligos parameter is used to provide your oligos file so mothur can extract your group names.\n";
helpString += "The group parameter is used to provide your group file so mothur can extract your group names.\n";
- helpString += "The package parameter is used to select the mimarks package you would like to use. Default=???\n";
+ helpString += "The package parameter is used to select the mimarks package you would like to use. The choices are: air, host_associated, human_associated, human_gut, human_oral, human_skin, human_vaginal, microbial, miscellaneous, plant_associated, sediment, soil, wastewater or waterc. Default=miscellaneous.\n";
+ helpString += "The requiredonly parameter is used to indicate you only want the required mimarks feilds printed. Default=F.\n";
helpString += "The get.mimarkspackage command should be in the following format: get.mimarkspackage(oligos=yourOligosFile, package=yourPackage)\n";
- helpString += "get.mimarkspackage(oligos=GQY1XT001.oligos, package=???)\n";
+ helpString += "get.mimarkspackage(oligos=GQY1XT001.oligos, package=human_gut)\n";
return helpString;
}
catch(exception& e) {
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
+
+ it = parameters.find("file");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ }
}
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
+ else { m->setGroupFile(groupfile); inputfile = groupfile; }
+
+ file = validParameter.validFile(parameters, "file", true);
+ if (file == "not open") { file = ""; abort = true; }
+ else if (file == "not found") { file = ""; }
+ else { inputfile = file; }
oligosfile = validParameter.validFile(parameters, "oligos", true);
if (oligosfile == "not found") { oligosfile = ""; }
else if(oligosfile == "not open") { abort = true; }
- else { m->setOligosFile(oligosfile); }
+ else { m->setOligosFile(oligosfile); inputfile = oligosfile; }
- if ((groupfile != "") && (oligosfile != "")) {
- m->mothurOut("[ERROR]: You may not use a group file and an oligos file, only one."); m->mothurOutEndLine(); abort = true;
+ if ((groupfile != "") && (oligosfile != "") && (file != "")) {
+ m->mothurOut("[ERROR]: You may not use a group file, file and an oligos file, only one."); m->mothurOutEndLine(); abort = true;
}
- if ((groupfile == "") && (oligosfile == "")) {
+ if ((groupfile == "") && (oligosfile == "") && (file == "")) {
oligosfile = m->getOligosFile();
- if (oligosfile != "") { m->mothurOut("Using " + oligosfile + " as input file for the oligos parameter."); m->mothurOutEndLine(); }
+ if (oligosfile != "") { inputfile = oligosfile; m->mothurOut("Using " + oligosfile + " as input file for the oligos parameter."); m->mothurOutEndLine(); }
else {
groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ if (groupfile != "") { inputfile = groupfile; m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("[ERROR]: You must provide groupfile or oligos file for the get.mimarkspackage command."); m->mothurOutEndLine(); abort = true;
+ m->mothurOut("[ERROR]: You must provide file, groupfile or oligos file for the get.mimarkspackage command."); m->mothurOutEndLine(); abort = true;
}
}
}
- package = validParameter.validFile(parameters, "package", false); if (package == "not found") { package = "package"; }
- //if (!checkCasesPackage(package)) { abort = true; } //error message in function
+ package = validParameter.validFile(parameters, "package", false); if (package == "not found") { package = "miscellaneous"; }
- //turn _ to spaces mothur's work around
- for (int i = 0; i < package.length(); i++) { if (package[i] == '_') { package[i] = ' '; } }
-
-
+ if ((package == "air") || (package == "host_associated") || (package == "human_associated") || (package == "human_gut") || (package == "human_oral") || (package == "human_skin") || (package == "human_vaginal") || (package == "microbial") || (package == "miscellaneous") || (package == "plant_associated") || (package == "sediment") || (package == "soil") || (package == "wastewater") || (package == "water")) {}
+ else {
+ m->mothurOut("[ERROR]: " + package + " is not a valid package selection. Choices are: air, host_associated, human_associated, human_gut, human_oral, human_skin, human_vaginal, microbial, miscellaneous, plant_associated, sediment, soil, wastewater or water. Aborting.\n."); abort = true;
+ }
+
+ string temp;
+ temp = validParameter.validFile(parameters, "requiredonly", false); if(temp == "not found"){ temp = "F"; }
+ requiredonly = m->isTrue(temp);
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
-
+ if (oligosfile != "") { readOligos(); }
+ else if (file != "") { readFile(); }
+ else { GroupMap groupmap(groupfile); groupmap.readMap(); Groups = groupmap.getNamesOfGroups(); }
+ if (outputDir == "") { outputDir += m->hasPath(inputfile); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+ string outputFileName = getOutputFileName("tsv", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["tsv"].push_back(outputFileName);
+
+ out << "#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages." << endl;
+ out << "#Please fill all the required fields indicated with '*'" << endl;
+ out << "#Fields marked with '**' indicated they are in a group where at least one of the fields is required." << endl;
+ out << "#Unknown or inapplicable fields can be assigned NA value." << endl;
+ out << "#You may add extra custom fields to this template. Make sure all the fields are separated by tabs." << endl;
+ out << "#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs." << endl;
+ out << "#You can edit this template using Microsoft Excel or any other editor. But while saving the file please make sure to save them as 'TAB-DELIMITED' TEXT FILE." << endl;
+
+ if (package == "air") {
+ out << "#Environmental:MIMARKS.specimen.air.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *altitude" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *altitude barometric_press carb_dioxide carb_monoxide chem_administration elev humidity methane misc_param organism_count oxygen oxy_stat_samp perturbation pollutants resp_part_matter samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp solar_irradiance temp ventilation_rate ventilation_type volatile_org_comp wind_direction wind_speed" << endl;
+ }
+ }else if (package == "host_associated") {
+ out << "#Environmental:MIMARKS.specimen.host-associated.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host **clone **isolate **strain" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods **clone **isolate **strain rel_to_oxygen samp_collect_device samp_mat_process *host age altitude blood_press_diast blood_press_syst body_habitat body_product tissue chem_administration depth diet disease_stat dry_mass elev family_relationship genotype gravidity height_or_length host_body_temp host_color host_growth_cond host_shape host_subject_id host_taxid infra_specific_name infra_specific_rank last_meal life_stage misc_param organism_count oxy_stat_samp perturbation phenotype samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp sex substrate temp tot_mass" << endl;
+ }
+ }else if (package == "human_associated") {
+ out << "#Environmental:MIMARKS.specimen.human-associated.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *host hiv_stat ihmc_ethnicity ihmc_medication_code age amniotic_fluid_color foetal_health_stat gestation_state maternal_health_stat blood_blood_disord body_product tissue body_mass_index chem_administration diet disease_stat drug_usage family_relationship genotype height host_body_temp host_subject_id last_meal nose_throat_disord pulmonary_disord diet_last_six_month medic_hist_perform misc_param occupation organism_count oxy_stat_samp perturbation phenotype pet_farm_animal pulse samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp sex smoker study_complt_stat temp tot_mass travel_out_six_month twin_sibling urine_collect_meth kidney_disord urogenit_tract_disor weight_loss_3_month" << endl;
+ }
+ }else if (package == "human_gut") {
+ out << "#Environmental:MIMARKS.specimen.human-gut.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *host ihmc_ethnicity ihmc_medication_code age body_product tissue body_mass_index chem_administration diet disease_stat family_relationship gastrointest_disord genotype height host_body_temp host_subject_id last_meal liver_disord medic_hist_perform misc_param occupation organism_count oxy_stat_samp perturbation phenotype pulse samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp sex special_diet temp tot_mass" << endl;
+ }
+ }else if (package == "human_oral") {
+ out << "#Environmental:MIMARKS.specimen.human-oral.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *host ihmc_ethnicity ihmc_medication_code age body_product tissue body_mass_index chem_administration diet disease_stat family_relationship genotype height host_body_temp host_subject_id last_meal medic_hist_perform misc_param nose_mouth_teeth_throat_disord occupation organism_count oxy_stat_samp perturbation phenotype pulse samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp sex temp time_last_toothbrush tot_mass" << endl;
+ }
+ }else if (package == "human_skin") {
+ out << "#Environmental:MIMARKS.specimen.human-skin.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *host ihmc_ethnicity ihmc_medication_code age body_product tissue body_mass_index chem_administration dermatology_disord diet disease_stat dominant_hand family_relationship genotype height host_body_temp host_subject_id last_meal medic_hist_perform misc_param occupation organism_count oxy_stat_samp perturbation phenotype pulse samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp sex temp time_since_last_wash tot_mass" << endl;
+ }
+ }else if (package == "human_vaginal") {
+ out << "#Environmental:MIMARKS.specimen.human-vaginal.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *host hrt ihmc_ethnicity ihmc_medication_code age birth_control body_product tissue body_mass_index chem_administration diet disease_stat douche family_relationship genotype gynecologic_disord height host_body_temp host_subject_id hysterectomy last_meal medic_hist_perform menarche menopause misc_param occupation organism_count oxy_stat_samp perturbation phenotype pregnancy pulse samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp sex sexual_act temp tot_mass urogenit_disord" << endl;
+ }
+ }else if (package == "microbial") {
+ out << "#Environmental:MIMARKS.specimen.microbial.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth *elev" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *depth *elev alkalinity alkyl_diethers altitude aminopept_act ammonium bacteria_carb_prod biomass bishomohopanol bromide calcium carb_nitro_ratio chem_administration chloride chlorophyll diether_lipids diss_carb_dioxide diss_hydrogen diss_inorg_carb diss_org_carb diss_org_nitro diss_oxygen glucosidase_act magnesium mean_frict_vel mean_peak_frict_vel methane misc_param n_alkanes nitrate nitrite nitro org_carb org_matter org_nitro organism_count oxy_stat_samp ph part_org_carb perturbation petroleum_hydrocarb phaeopigments phosphate phosplipid_fatt_acid potassium pressure redox_potential salinity samp_size samp_store_dur samp_store_loc samp_store_temp silicate sodium sulfate sulfide temp tot_carb tot_nitro tot_org_carb turbidity water_content" << endl;
+ }
+ }else if (package == "miscellaneous") {
+ out << "#Environmental:MIMARKS.specimen.miscellaneous.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *title *seq_methods *lat_lon" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process alkalinity altitude ammonium biomass bromide calcium chem_administration chloride chlorophyll current density depth diether_lipids diss_carb_dioxide diss_hydrogen diss_inorg_carb diss_org_nitro diss_oxygen elev misc_param nitrate nitrite nitro org_carb org_matter org_nitro organism_count oxy_stat_samp ph perturbation phosphate phosplipid_fatt_acid potassium pressure salinity samp_size samp_store_dur samp_store_loc samp_store_temp silicate sodium sulfate sulfide temp" << endl;
+ }
+ }else if (package == "plant_associated") {
+ out << "#Environmental:MIMARKS.specimen.plant-associated.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *host age air_temp_regm altitude antibiotic_regm body_product chem_administration chem_mutagen climate_environment depth disease_stat dry_mass elev fertilizer_regm fungicide_regm gaseous_environment genotype gravity growth_hormone_regm growth_med height_or_length herbicide_regm host_taxid humidity_regm infra_specific_name infra_specific_rank life_stage mechanical_damage mineral_nutr_regm misc_param non_mineral_nutr_regm organism_count oxy_stat_samp ph_regm perturbation pesticide_regm phenotype tissue plant_product radiation_regm rainfall_regm salt_regm samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp season_environment standing_water_regm temp tiss_cult_growth_med tot_mass water_temp_regm watering_regm wet_mass" << endl;
+ }
+ }else if (package == "sediment") {
+ out << "#Environmental:MIMARKS.specimen.sediment.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth *elev" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *depth *elev alkalinity alkyl_diethers aminopept_act ammonium bacteria_carb_prod biomass bishomohopanol bromide calcium carb_nitro_ratio chem_administration chloride chlorophyll density diether_lipids diss_carb_dioxide diss_hydrogen diss_inorg_carb diss_org_carb diss_org_nitro diss_oxygen glucosidase_act magnesium mean_frict_vel mean_peak_frict_vel methane misc_param n_alkanes nitrate nitrite nitro org_carb org_matter org_nitro organism_count oxy_stat_samp ph particle_class part_org_carb perturbation petroleum_hydrocarb phaeopigments phosphate phosplipid_fatt_acid porosity potassium pressure redox_potential salinity samp_size samp_store_dur samp_store_loc samp_store_temp sediment_type silicate sodium sulfate sulfide temp tidal_stage tot_carb tot_nitro tot_org_carb turbidity water_content" << endl;
+ }
+ }else if (package == "soil") {
+ out << "#Environmental:MIMARKS.specimen.soil.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth *elev" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *depth *elev altitude sieving cur_land_use cur_vegetation_meth cur_vegetation drainage_class al_sat al_sat_meth heavy_metals_meth heavy_metals salinity_meth extreme_salinity fao_class agrochem_addition crop_rotation extreme_event fire flooding previous_land_use_meth previous_land_use tillage horizon_meth horizon link_class_info link_climate_info link_addit_analys annual_season_precpt annual_season_temp microbial_biomass_meth microbial_biomass misc_param other ph_meth ph pool_dna_extracts profile_position samp_size samp_weight_dna_ext slope_aspect slope_gradient soil_type_meth soil_type local_class_meth local_class store_cond texture_meth texture tot_n_meth tot_n tot_org_c_meth tot_org_carb water_content_soil_meth water_content_soil" << endl;
+ }
+ }else if (package == "wastewater") {
+ out << "#Environmental:MIMARKS.specimen.wastewater.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process alkalinity biochem_oxygen_dem chem_administration chem_oxygen_dem depth efficiency_percent emulsions gaseous_substances indust_eff_percent inorg_particles misc_param nitrate org_particles organism_count oxy_stat_samp ph perturbation phosphate pre_treatment primary_treatment reactor_type samp_size samp_salinity samp_store_dur samp_store_loc samp_store_temp secondary_treatment sewage_type sludge_retent_time sodium soluble_inorg_mat soluble_org_mat suspend_solids temp tertiary_treatment tot_nitro tot_phosphate wastewater_type" << endl;
+ }
+ }else if (package == "water") {
+ out << "#Environmental:MIMARKS.specimen.water.3.0" << endl;
+ if (requiredonly) {
+ out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth" << endl;
+ }else {
+ out << "*sample_name description bioproject_id sample_title *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods rel_to_oxygen samp_collect_device samp_mat_process *depth alkalinity alkyl_diethers aminopept_act ammonium atmospheric_data bacteria_carb_prod biomass bishomohopanol bromide calcium carb_nitro_ratio chem_administration chloride chlorophyll current density diether_lipids diss_carb_dioxide diss_hydrogen diss_inorg_carb diss_inorg_nitro diss_inorg_phosp diss_org_carb diss_org_nitro diss_oxygen elev glucosidase_act light_intensity magnesium mean_frict_vel mean_peak_frict_vel misc_param n_alkanes nitrate nitrite nitro org_carb org_matter org_nitro organism_count oxy_stat_samp ph part_org_carb part_org_nitro perturbation petroleum_hydrocarb phaeopigments phosphate phosplipid_fatt_acid photon_flux potassium pressure primary_prod redox_potential salinity samp_size samp_store_dur samp_store_loc samp_store_temp silicate sodium soluble_react_phosp sulfate sulfide suspend_part_matter temp tidal_stage tot_depth_water_col tot_diss_nitro tot_inorg_nitro tot_nitro tot_part_carb tot_phosp" << endl;
+ }
+ }
+
+ for (int i = 0; i < Groups.size(); i++) { out << Groups[i] << '\t' << endl; }
+
+ out.close();
+
//output files created by command
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
catch(exception& e) {
- m->errorOut(e, "GetMIMarksPackageCommand", "GetMIMarksPackageCommand");
+ m->errorOut(e, "GetMIMarksPackageCommand", "execute");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int GetMIMarksPackageCommand::readOligos(){
+ try {
+ ifstream inOligos;
+ m->openInputFile(oligosfile, inOligos);
+
+ string type, oligo, roligo, group;
+ vector<string> primerNameVector, barcodeNameVector;
+ set<string> uniquePrimers;
+ set<string> uniqueBarcodes;
+
+ while(!inOligos.eof()){
+
+ inOligos >> type;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
+
+ if(type[0] == '#'){
+ while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ m->gobble(inOligos);
+ }
+ else{
+ m->gobble(inOligos);
+ //make type case insensitive
+ for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
+
+ inOligos >> oligo;
+
+ if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
+
+ for(int i=0;i<oligo.length();i++){
+ oligo[i] = toupper(oligo[i]);
+ if(oligo[i] == 'U') { oligo[i] = 'T'; }
+ }
+
+ if(type == "FORWARD"){
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ primerNameVector.push_back(group);
+ }
+ else if (type == "PRIMER"){
+ m->gobble(inOligos);
+
+ inOligos >> roligo;
+
+ for(int i=0;i<roligo.length();i++){
+ roligo[i] = toupper(roligo[i]);
+ if(roligo[i] == 'U') { roligo[i] = 'T'; }
+ }
+
+ group = "";
+
+ // get rest of line in case there is a primer name
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { group += c; }
+ }
+
+ primerNameVector.push_back(group);
+ }else if(type == "BARCODE"){
+ inOligos >> group;
+
+ //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
+ //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
+
+ string temp = "";
+ while (!inOligos.eof()) {
+ char c = inOligos.get();
+ if (c == 10 || c == 13 || c == -1){ break; }
+ else if (c == 32 || c == 9){;} //space or tab
+ else { temp += c; }
+ }
+
+ //then this is illumina data with 4 columns
+ if (temp != "") {
+
+ string reverseBarcode = group; //reverseOligo(group); //reverse barcode
+ group = temp;
+
+ barcodeNameVector.push_back(group);
+ }else {
+ barcodeNameVector.push_back(group);
+ }
+ }
+ }
+ m->gobble(inOligos);
+ }
+ inOligos.close();
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ primerNameVector.push_back("");
+ }
+
+ set<string> uniqueNames;
+ for(int i = 0; i < barcodeNameVector.size(); i++){
+ for(int j = 0; j < primerNameVector.size(); j++){
+
+ string primerName = primerNameVector[j];
+ string barcodeName = barcodeNameVector[i];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { }
+ else {
+ string comboGroupName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[i];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[j];
+ }
+ else{
+ comboGroupName = barcodeNameVector[i] + "." + primerNameVector[j];
+ }
+ }
+ uniqueNames.insert(comboGroupName);
+ }
+ }
+ }
+
+
+
+ if (m->debug) { int count = 0; for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } }
+
+ for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { Groups.push_back(*it); }
+
+ return true;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "readOligos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+// going to have to rework this to allow for other options --
+/*
+ file option 1
+
+ sfffile1 oligosfile1
+ sfffile2 oligosfile2
+ ...
+
+ file option 2
+
+ fastqfile1 oligosfile1
+ fastqfile2 oligosfile2
+ ...
+
+ file option 3
+
+ fastqfile fastqfile group
+ fastqfile fastqfile group
+ fastqfile fastqfile group
+ ...
+
+ */
+
+int GetMIMarksPackageCommand::readFile(){
+ try {
+ //vector<string> theseFiles;
+ inputfile = file;
+
+ ifstream in;
+ m->openInputFile(file, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { return 0; }
+
+ string line = m->getline(in); m->gobble(in);
+ vector<string> pieces = m->splitWhiteSpace(line);
+
+ string group = "";
+ string thisFileName1, thisFileName2; thisFileName1 = ""; thisFileName2 = "";
+ if (pieces.size() == 2) {
+ thisFileName1 = pieces[0];
+ thisFileName2 = pieces[1];
+ }else if (pieces.size() == 3) {
+ thisFileName1 = pieces[1];
+ thisFileName2 = pieces[2];
+ string group = pieces[0];
+ }else {
+ m->mothurOut("[ERROR]: file lines can be 2 or 3 columns. The 2 column files are sff file then oligos or fastqfile then oligos. You may have multiple lines in the file. The 3 column files are for paired read libraries. The format is groupName, forwardFastqFile reverseFastqFile. \n"); m->control_pressed = true;
+ }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", thisFileName1 = " + thisFileName1 + ", thisFileName2 = " + thisFileName2 + ".\n"); }
+
+ //check to make sure both are able to be opened
+ ifstream in2;
+ int openForward = m->openInputFile(thisFileName1, in2, "noerror");
+
+ //if you can't open it, try default location
+ if (openForward == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName1);
+ m->mothurOut("Unable to open " + thisFileName1 + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in3;
+ openForward = m->openInputFile(tryPath, in3, "noerror");
+ in3.close();
+ thisFileName1 = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (openForward == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(thisFileName1);
+ m->mothurOut("Unable to open " + thisFileName1 + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openForward = m->openInputFile(tryPath, in4, "noerror");
+ thisFileName1 = tryPath;
+ in4.close();
+ }
+ }
+
+ if (openForward == 1) { //can't find it
+ m->mothurOut("[WARNING]: can't find " + thisFileName1 + ", ignoring.\n");
+ }else{ in2.close(); }
+
+ int openReverse = 1;
+
+ ifstream in3;
+ openReverse = m->openInputFile(thisFileName2, in3, "noerror");
+
+ //if you can't open it, try default location
+ if (openReverse == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName2);
+ m->mothurOut("Unable to open " + thisFileName2 + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in3;
+ openReverse = m->openInputFile(tryPath, in3, "noerror");
+ in3.close();
+ thisFileName2 = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (openReverse == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(thisFileName2);
+ m->mothurOut("Unable to open " + thisFileName2 + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in4;
+ openReverse = m->openInputFile(tryPath, in4, "noerror");
+ thisFileName2 = tryPath;
+ in4.close();
+ }
+ }
+
+ if (openReverse == 1) { //can't find it
+ m->mothurOut("[WARNING]: can't find " + thisFileName2 + ", ignoring pair.\n");
+ }else{ in3.close(); }
+
+
+ if ((pieces.size() == 2) && (openForward != 1) && (openReverse != 1)) { //good pair and sff or fastq and oligos
+ oligosfile = thisFileName2;
+ if (m->debug) { m->mothurOut("[DEBUG]: about to read oligos\n"); }
+ readOligos();
+ }else if((pieces.size() == 3) && (openForward != 1) && (openReverse != 1)) { //good pair and paired read
+ Groups.push_back(group);
+ }
+ }
+ in.close();
+
+ inputfile = file;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMIMarksPackageCommand", "readFile");
exit(1);
}
}
projects / mothur.git / blobdiff