X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getmimarkspackagecommand.cpp;h=2f37405a509125f25d77d7baf3363ca0cb030e4c;hp=43138e1cefd75544e9cd699985fad484fc21a862;hb=f7184748e1519090deecfb6dd9fda118ffba2b53;hpb=cac38e9e251998fa0b825d00189534534948d226 diff --git a/getmimarkspackagecommand.cpp b/getmimarkspackagecommand.cpp index 43138e1..2f37405 100644 --- a/getmimarkspackagecommand.cpp +++ b/getmimarkspackagecommand.cpp @@ -7,13 +7,17 @@ // #include "getmimarkspackagecommand.h" +#include "groupmap.h" //********************************************************************************************************************** vector 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); @@ -30,14 +34,15 @@ vector GetMIMarksPackageCommand::setParameters(){ 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) { @@ -121,42 +126,57 @@ GetMIMarksPackageCommand::GetMIMarksPackageCommand(string option) { //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); } } @@ -172,10 +192,131 @@ int GetMIMarksPackageCommand::execute(){ 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 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(); @@ -185,7 +326,296 @@ int GetMIMarksPackageCommand::execute(){ } 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 primerNameVector, barcodeNameVector; + set uniquePrimers; + set 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> oligo; + + if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); } + + for(int i=0;igobble(inOligos); + + inOligos >> roligo; + + for(int i=0;i> 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 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::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } } + + for (set::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 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 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); } }