2 // getmimarkspackagecommand.cpp
5 // Created by Sarah Westcott on 3/25/14.
6 // Copyright (c) 2014 Schloss Lab. All rights reserved.
9 #include "getmimarkspackagecommand.h"
13 //**********************************************************************************************************************
14 vector<string> GetMIMarksPackageCommand::setParameters(){
16 //files that have dependancies
17 CommandParameter pgroup("group", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pgroup);
18 CommandParameter pfile("file", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(pfile);
19 CommandParameter poligos("oligos", "InputTypes", "", "", "groupOligos", "none", "none","",false,false); parameters.push_back(poligos);
20 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);
21 CommandParameter prequiredonly("requiredonly", "Boolean", "", "F", "", "", "","",false,false, true); parameters.push_back(prequiredonly);
22 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
23 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
25 vector<string> myArray;
26 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
30 m->errorOut(e, "GetMIMarksPackageCommand", "setParameters");
34 //**********************************************************************************************************************
35 string GetMIMarksPackageCommand::getHelpString(){
37 string helpString = "";
38 helpString += "The get.mimarkspackage command creates a mimarks package form with your groups. The required fields are flagged with * characters. \n";
39 helpString += "Further documentation on the different packages and required formats can be found here, http://www.mothur.org/wiki/MIMarks_Data_Packages.\n";
40 helpString += "The get.mimarkspackage command parameters are: oligos, group, package and requiredonly. oligos or group is required.\n";
41 helpString += "The oligos parameter is used to provide your oligos file so mothur can extract your group names.\n";
42 helpString += "The group parameter is used to provide your group file so mothur can extract your group names.\n";
43 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";
44 helpString += "The requiredonly parameter is used to indicate you only want the required mimarks feilds printed. Default=F.\n";
45 helpString += "The get.mimarkspackage command should be in the following format: get.mimarkspackage(oligos=yourOligosFile, package=yourPackage)\n";
46 helpString += "get.mimarkspackage(oligos=GQY1XT001.oligos, package=human_gut)\n";
50 m->errorOut(e, "GetMIMarksPackageCommand", "getHelpString");
54 //**********************************************************************************************************************
55 string GetMIMarksPackageCommand::getOutputPattern(string type) {
59 if (type == "tsv") { pattern = "[filename],tsv"; }
60 else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
65 m->errorOut(e, "GetMIMarksPackageCommand", "getOutputPattern");
69 //**********************************************************************************************************************
70 GetMIMarksPackageCommand::GetMIMarksPackageCommand(){
72 abort = true; calledHelp = true;
74 vector<string> tempOutNames;
75 outputTypes["tsv"] = tempOutNames;
78 m->errorOut(e, "GetMIMarksPackageCommand", "GetMIMarksPackageCommand");
82 //**********************************************************************************************************************
83 GetMIMarksPackageCommand::GetMIMarksPackageCommand(string option) {
86 abort = false; calledHelp = false;
88 //allow user to run help
89 if(option == "help") { help(); abort = true; calledHelp = true; }
90 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
93 //valid paramters for this command
94 vector<string> myArray = setParameters();
96 OptionParser parser(option);
97 map<string,string> parameters = parser.getParameters();
99 ValidParameters validParameter;
100 map<string,string>::iterator it;
101 //check to make sure all parameters are valid for command
102 for (it = parameters.begin(); it != parameters.end(); it++) {
103 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
106 vector<string> tempOutNames;
107 outputTypes["tsv"] = tempOutNames;
109 //if the user changes the input directory command factory will send this info to us in the output parameter
110 inputDir = validParameter.validFile(parameters, "inputdir", false);
111 if (inputDir == "not found"){ inputDir = ""; }
115 it = parameters.find("oligos");
116 //user has given a template file
117 if(it != parameters.end()){
118 path = m->hasPath(it->second);
119 //if the user has not given a path then, add inputdir. else leave path alone.
120 if (path == "") { parameters["oligos"] = inputDir + it->second; }
123 it = parameters.find("group");
124 //user has given a template file
125 if(it != parameters.end()){
126 path = m->hasPath(it->second);
127 //if the user has not given a path then, add inputdir. else leave path alone.
128 if (path == "") { parameters["group"] = inputDir + it->second; }
131 it = parameters.find("file");
132 //user has given a template file
133 if(it != parameters.end()){
134 path = m->hasPath(it->second);
135 //if the user has not given a path then, add inputdir. else leave path alone.
140 groupfile = validParameter.validFile(parameters, "group", true);
141 if (groupfile == "not open") { groupfile = ""; abort = true; }
142 else if (groupfile == "not found") { groupfile = ""; }
143 else { m->setGroupFile(groupfile); inputfile = groupfile; }
145 file = validParameter.validFile(parameters, "file", true);
146 if (file == "not open") { file = ""; abort = true; }
147 else if (file == "not found") { file = ""; }
148 else { inputfile = file; }
150 oligosfile = validParameter.validFile(parameters, "oligos", true);
151 if (oligosfile == "not found") { oligosfile = ""; }
152 else if(oligosfile == "not open") { abort = true; }
153 else { m->setOligosFile(oligosfile); inputfile = oligosfile; }
155 if ((groupfile != "") && (oligosfile != "") && (file != "")) {
156 m->mothurOut("[ERROR]: You may not use a group file, file and an oligos file, only one."); m->mothurOutEndLine(); abort = true;
159 if ((groupfile == "") && (oligosfile == "") && (file == "")) {
160 oligosfile = m->getOligosFile();
161 if (oligosfile != "") { inputfile = oligosfile; m->mothurOut("Using " + oligosfile + " as input file for the oligos parameter."); m->mothurOutEndLine(); }
163 groupfile = m->getGroupFile();
164 if (groupfile != "") { inputfile = groupfile; m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
166 m->mothurOut("[ERROR]: You must provide file, groupfile or oligos file for the get.mimarkspackage command."); m->mothurOutEndLine(); abort = true;
171 package = validParameter.validFile(parameters, "package", false); if (package == "not found") { package = "miscellaneous"; }
173 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")) {}
175 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;
179 temp = validParameter.validFile(parameters, "requiredonly", false); if(temp == "not found"){ temp = "F"; }
180 requiredonly = m->isTrue(temp);
184 catch(exception& e) {
185 m->errorOut(e, "GetMIMarksPackageCommand", "GetMIMarksPackageCommand");
189 //**********************************************************************************************************************
191 int GetMIMarksPackageCommand::execute(){
194 if (abort == true) { if (calledHelp) { return 0; } return 2; }
196 if (oligosfile != "") { Oligos oligos(oligosfile); Groups = oligos.getGroupNames(); }
197 else if (file != "") { readFile(); }
198 else { GroupMap groupmap(groupfile); groupmap.readMap(); Groups = groupmap.getNamesOfGroups(); }
200 if (outputDir == "") { outputDir += m->hasPath(inputfile); }
201 map<string, string> variables;
202 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
203 string outputFileName = getOutputFileName("tsv", variables);
206 m->openOutputFile(outputFileName, out);
207 outputNames.push_back(outputFileName); outputTypes["tsv"].push_back(outputFileName);
209 out << "#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages." << endl;
210 out << "#Please fill all the required fields indicated with '*'" << endl;
211 out << "#Unknown or inapplicable fields can be assigned NA value." << endl;
212 out << "#You may add extra custom fields to this template. Make sure all the fields are separated by tabs." << endl;
213 out << "#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs." << endl;
214 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;
216 if (package == "air") {
217 out << "#Environmental:MIMARKS.specimen.air.3.0" << endl;
219 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *altitude" << endl;
221 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;
223 }else if (package == "host_associated") {
224 out << "#Environmental:MIMARKS.specimen.host-associated.3.0" << endl;
226 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host " << endl;
228 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 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;
230 }else if (package == "human_associated") {
231 out << "#Environmental:MIMARKS.specimen.human-associated.3.0" << endl;
233 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
235 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;
237 }else if (package == "human_gut") {
238 out << "#Environmental:MIMARKS.specimen.human-gut.3.0" << endl;
240 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
242 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;
244 }else if (package == "human_oral") {
245 out << "#Environmental:MIMARKS.specimen.human-oral.3.0" << endl;
247 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
249 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;
251 }else if (package == "human_skin") {
252 out << "#Environmental:MIMARKS.specimen.human-skin.3.0" << endl;
254 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
256 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;
258 }else if (package == "human_vaginal") {
259 out << "#Environmental:MIMARKS.specimen.human-vaginal.3.0" << endl;
261 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
263 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;
265 }else if (package == "microbial") {
266 out << "#Environmental:MIMARKS.specimen.microbial.3.0" << endl;
268 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth *elev" << endl;
270 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;
272 }else if (package == "miscellaneous") {
273 out << "#Environmental:MIMARKS.specimen.miscellaneous.3.0" << endl;
275 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *title *seq_methods *lat_lon" << endl;
277 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;
279 }else if (package == "plant_associated") {
280 out << "#Environmental:MIMARKS.specimen.plant-associated.3.0" << endl;
282 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *host" << endl;
284 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;
286 }else if (package == "sediment") {
287 out << "#Environmental:MIMARKS.specimen.sediment.3.0" << endl;
289 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth *elev" << endl;
291 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;
293 }else if (package == "soil") {
294 out << "#Environmental:MIMARKS.specimen.soil.3.0" << endl;
296 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth *elev" << endl;
298 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;
300 }else if (package == "wastewater") {
301 out << "#Environmental:MIMARKS.specimen.wastewater.3.0" << endl;
303 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods" << endl;
305 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;
307 }else if (package == "water") {
308 out << "#Environmental:MIMARKS.specimen.water.3.0" << endl;
310 out << "*sample_name *organism *collection_date *biome *feature *material *geo_loc_name *lat_lon *title *seq_methods *depth" << endl;
312 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;
316 for (int i = 0; i < Groups.size(); i++) { out << Groups[i] << '\t' << endl; }
320 //output files created by command
321 m->mothurOutEndLine();
322 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
323 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
324 m->mothurOutEndLine();
328 catch(exception& e) {
329 m->errorOut(e, "GetMIMarksPackageCommand", "execute");
333 //***************************************************************************************************************
335 // going to have to rework this to allow for other options --
345 fastqfile1 oligosfile1
346 fastqfile2 oligosfile2
351 fastqfile fastqfile group
352 fastqfile fastqfile group
353 fastqfile fastqfile group
358 int GetMIMarksPackageCommand::readFile(){
364 m->openInputFile(file, in);
368 if (m->control_pressed) { return 0; }
370 string line = m->getline(in); m->gobble(in);
371 vector<string> pieces = m->splitWhiteSpace(line);
374 string thisFileName1, thisFileName2; thisFileName1 = ""; thisFileName2 = "";
375 if (pieces.size() == 2) {
376 thisFileName1 = pieces[0];
377 thisFileName2 = pieces[1];
378 }else if (pieces.size() == 3) {
379 thisFileName1 = pieces[1];
380 thisFileName2 = pieces[2];
381 string group = pieces[0];
383 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;
386 if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", thisFileName1 = " + thisFileName1 + ", thisFileName2 = " + thisFileName2 + ".\n"); }
388 if (inputDir != "") {
389 string path = m->hasPath(thisFileName2);
390 if (path == "") { thisFileName2 = inputDir + thisFileName2; }
392 path = m->hasPath(thisFileName1);
393 if (path == "") { thisFileName1 = inputDir + thisFileName1; }
396 //check to make sure both are able to be opened
398 int openForward = m->openInputFile(thisFileName1, in2, "noerror");
400 //if you can't open it, try default location
401 if (openForward == 1) {
402 if (m->getDefaultPath() != "") { //default path is set
403 string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName1);
404 m->mothurOut("Unable to open " + thisFileName1 + ". Trying default " + tryPath); m->mothurOutEndLine();
406 openForward = m->openInputFile(tryPath, in3, "noerror");
408 thisFileName1 = tryPath;
412 //if you can't open it, try output location
413 if (openForward == 1) {
414 if (m->getOutputDir() != "") { //default path is set
415 string tryPath = m->getOutputDir() + m->getSimpleName(thisFileName1);
416 m->mothurOut("Unable to open " + thisFileName1 + ". Trying output directory " + tryPath); m->mothurOutEndLine();
418 openForward = m->openInputFile(tryPath, in4, "noerror");
419 thisFileName1 = tryPath;
424 if (openForward == 1) { //can't find it
425 m->mothurOut("[WARNING]: can't find " + thisFileName1 + ", ignoring.\n");
426 }else{ in2.close(); }
431 openReverse = m->openInputFile(thisFileName2, in3, "noerror");
433 //if you can't open it, try default location
434 if (openReverse == 1) {
435 if (m->getDefaultPath() != "") { //default path is set
436 string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName2);
437 m->mothurOut("Unable to open " + thisFileName2 + ". Trying default " + tryPath); m->mothurOutEndLine();
439 openReverse = m->openInputFile(tryPath, in3, "noerror");
441 thisFileName2 = tryPath;
445 //if you can't open it, try output location
446 if (openReverse == 1) {
447 if (m->getOutputDir() != "") { //default path is set
448 string tryPath = m->getOutputDir() + m->getSimpleName(thisFileName2);
449 m->mothurOut("Unable to open " + thisFileName2 + ". Trying output directory " + tryPath); m->mothurOutEndLine();
451 openReverse = m->openInputFile(tryPath, in4, "noerror");
452 thisFileName2 = tryPath;
457 if (openReverse == 1) { //can't find it
458 m->mothurOut("[WARNING]: can't find " + thisFileName2 + ", ignoring pair.\n");
459 }else{ in3.close(); }
462 if ((pieces.size() == 2) && (openForward != 1) && (openReverse != 1)) { //good pair and sff or fastq and oligos
463 oligosfile = thisFileName2;
464 if (m->debug) { m->mothurOut("[DEBUG]: about to read oligos\n"); }
465 oligos.read(oligosfile);
466 }else if((pieces.size() == 3) && (openForward != 1) && (openReverse != 1)) { //good pair and paired read
467 Groups.push_back(group);
472 Groups = oligos.getGroupNames();
478 catch(exception& e) {
479 m->errorOut(e, "GetMIMarksPackageCommand", "readFile");
483 //**********************************************************************************************************************