SciCodePile/SciCode-Domain-Code

1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"In Silico","GGFHF/ddRADseqTools","CHANGELOG.md",".md","1482","43","CURRENT VERSION: 0.453 4********************************************************************************5 6Changes of v 0.44 to v 0.45 (February 2018)7 8* Review of parameter values when the mutation function is called in rsitesearch.py.9 10* Processing of verbose and trace options of simcasavaids.py.11 12********************************************************************************13 14Changes of v 0.43 to v 0.44 (January 2018)15 16* Enzymes with ambiguous restriction sites can be used.17 18* Parameters enzyme1 and enzyme2 can be equal in rsiteseach.py (in this case,19  it simulates a digestion with only one enzyme).20 21* simcasavaids.py is a new tool which fixes sequence identifiers of a FASTQ read22  file generated by ddRADseqTools to compatible format with CASAVA.23 24* Several minor improvements.25 26********************************************************************************27 28Changes of v 0.42 to v 0.43 (October 2017)29 30* Parameters enzyme1 and enzyme2 can be an identifier or a restriction site31  sequence, independently of each other.32 33********************************************************************************34 35Changes of v 0.40 to v 0.42 (July 2017)36 37* Fixed a bug in the algorithm to mutate sequences that occurs when there is38  more than one SNP or indel.39 40* Added new options in the programs to control the printing of verbose and41  development info, and the making of statistical graphics.42 43We thank to the professor Alex Buerkle his comments to improve ddRADseqTools.44","Markdown"
45"In Silico","GGFHF/ddRADseqTools","LICENSE.md",".md","35142","675","                    GNU GENERAL PUBLIC LICENSE46                       Version 3, 29 June 200747 48 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>49 Everyone is permitted to copy and distribute verbatim copies50 of this license document, but changing it is not allowed.51 52                            Preamble 53 54  The GNU General Public License is a free, copyleft license for55software and other kinds of works.56 57  The licenses for most software and other practical works are designed58to take away your freedom to share and change the works.  By contrast,59the GNU General Public License is intended to guarantee your freedom to60share and change all versions of a program--to make sure it remains free61software for all its users.  We, the Free Software Foundation, use the62GNU General Public License for most of our software; it applies also to63any other work released this way by its authors.  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It is safest674to attach them to the start of each source file to most effectively675state the exclusion of warranty; and each file should have at least676the ""copyright"" line and a pointer to where the full notice is found.677 678    {one line to give the program's name and a brief idea of what it does.}679    Copyright (C) {year}  {name of author}680 681    This program is free software: you can redistribute it and/or modify682    it under the terms of the GNU General Public License as published by683    the Free Software Foundation, either version 3 of the License, or684    (at your option) any later version.685 686    This program is distributed in the hope that it will be useful,687    but WITHOUT ANY WARRANTY; without even the implied warranty of688    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the689    GNU General Public License for more details.690 691    You should have received a copy of the GNU General Public License692    along with this program.  If not, see <http://www.gnu.org/licenses/>.693 694Also add information on how to contact you by electronic and paper mail.695 696  If the program does terminal interaction, make it output a short697notice like this when it starts in an interactive mode:698 699    {project}  Copyright (C) {year}  {fullname}700    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.701    This is free software, and you are welcome to redistribute it702    under certain conditions; type `show c' for details.703 704The hypothetical commands `show w' and `show c' should show the appropriate705parts of the General Public License.  Of course, your program's commands706might be different; for a GUI interface, you would use an ""about box"".707 708  You should also get your employer (if you work as a programmer) or school,709if any, to sign a ""copyright disclaimer"" for the program, if necessary.710For more information on this, and how to apply and follow the GNU GPL, see711<http://www.gnu.org/licenses/>.712 713  The GNU General Public License does not permit incorporating your program714into proprietary programs.  If your program is a subroutine library, you715may consider it more useful to permit linking proprietary applications with716the library.  If this is what you want to do, use the GNU Lesser General717Public License instead of this License.  But first, please read718<http://www.gnu.org/philosophy/why-not-lgpl.html>.719","Markdown"
720"In Silico","GGFHF/ddRADseqTools","Package/seqlocation.py",".py","9429","257","#!/usr/bin/env python3721# -*- coding: utf-8 -*-722 723#-------------------------------------------------------------------------------724 725'''This software has been developed by:726 727       GI Genética, Fisiología e Historia Forestal728       Dpto. Sistemas y Recursos Naturales729       ETSI Montes, Forestal y del Medio Natural730       Universidad Politécnica de Madrid731       https://github.com/ggfhf/732 733   Licence: GNU General Public Licence Version 3734'''735 736#-------------------------------------------------------------------------------737 738'''This source contains the program of the ddRADseqTools software package that739   locates a sequence into the genome.740'''741#-------------------------------------------------------------------------------742 743import gzip744import re745import sys746 747from genlib import *748 749#-------------------------------------------------------------------------------750 751def main(argv):752    '''Main line of the program.'''753 754    # build the options dictionary755    options_dict = build_options()756 757    # it has been requested the help or to build a new config file758    for param in argv:759        # show the help and exit OK760        if param.startswith('--help'):761            print_help(options_dict)762            sys.exit(0)763        # build the config file and exit OK764        elif param.startswith('--config'):765            build_config(options_dict)766            sys.exit(0)767 768    # get the config file769    config_file = get_config_file(__file__)770 771    # get options from the config file and the input parameters772    options_dict = get_options(options_dict, config_file, argv)773 774    # locate sequence775    locate_seq(options_dict)776 777#-------------------------------------------------------------------------------778 779def locate_seq(options_dict):780    '''Locate a sequence into the genome.'''781 782    genfile = options_dict['genfile']['value']783    seq = options_dict['seq']['value']784    verbose = options_dict['verbose']['value']785    trace = options_dict['trace']['value']786 787    # set the verbose and trace status788    if verbose.upper() == 'YES':789        Message.set_verbose_status(True)790    else:791        Message.set_verbose_status(False)792    if trace.upper() == 'YES':793        Message.set_trace_status(True)794    else:795        Message.set_trace_status(False)796 797    # ...798    Message.print('info', 'seq to be locate: {0}'.format(seq))799    Message.print('info', 'reverse compl.  : {0}'.format(get_reverse_complementary_sequence(seq)))800 801    # open the genome file802    try:803        if genfile.endswith('.gz'):804            genfile_id = gzip.open(genfile, mode='rt', encoding='iso-8859-1')805        else:806            genfile_id = open(genfile, mode='r', encoding='iso-8859-1')807    except:808        raise ProgramError('F002', genfile)809 810    # set the pattern of the head records (>locus_info)811    pattern = r'^>(.*)$'812 813    # initialize the found site count814    found_site_count = 0815 816    # read the first record817    record = genfile_id.readline()818 819    # while there are records820    while record != '':821 822        # process the head record 823        if record.startswith('>'):824 825            # extract the data 826            mo = re.search(pattern, record)827            locus_info = mo.group(1)828 829            # initialize the locus sequence of Watson strand830            watson_locus_seq = ''831 832            # read the next record833            record = genfile_id.readline()834 835        else:836 837            # control the FASTA format838            raise ProgramError('F003', genfile, 'FASTA')839 840        # while there are records and they are sequence841        while record != '' and not record.startswith('>'):842 843            # concatenate the record to the locus sequence of Watson strand844            watson_locus_seq += record.strip().upper()845 846            # read the next record847            record = genfile_id.readline()848 849        # find the first location in Watson locus sequence850        start = watson_locus_seq.find(seq.upper())851 852        # while the sequence is found in the Watson strand853        while start >= 0:854 855            # print the location data856            Message.print('info', 'Locus info: {0} | strand: + | start position: {1} | end position: {2}'.format(locus_info, (start + 1), (start + len(seq))))857 858            # add 1 to found site count859            found_site_count += 1860 861            # find the next location862            start = watson_locus_seq.find(seq.upper(), (start + len(seq)))863 864        # get the sequence of the Crick strand865        crick_locus_seq = get_reverse_complementary_sequence(watson_locus_seq)866 867        # find the first location in Crick locus sequence868        start = crick_locus_seq.find(seq.upper())869 870        # while the sequence is the Crick strand871        while start >= 0:872 873            # print the loation data874            Message.print('info', 'Locus info: {0} | strand: - | start position: {1} | end position: {2}'.format(locus_info, (len(crick_locus_seq) - start), (len(crick_locus_seq) - start - len(seq) + 1)))875 876            # add 1 to found site count877            found_site_count += 1878 879            # find the next location880            start = crick_locus_seq.find(seq.upper(), (start + len(seq)))881 882    # close genfile883    genfile_id.close()884 885    # show the found site count886    if found_site_count == 0:887        Message.print('info', 'The sequence is not found')888    else:889        Message.print('info', 'The sequence is found in {0} sites'.format(found_site_count))890 891#-------------------------------------------------------------------------------892 893def build_options():894    '''Build a dictionary with the program options.'''895 896    # get all options dictionary897    all_options_dict = get_all_options_dict()898 899    # define the options dictionary900    options_dict = {901        'genfile': all_options_dict['genfile'],902        'seq': all_options_dict['seq'],903        'verbose': all_options_dict['verbose'],904        'trace': all_options_dict['trace']905    }906 907    # return the options dictionary908    return options_dict909 910#-------------------------------------------------------------------------------911 912def print_help(options_dict):913    '''Print the program help.'''914 915    # get general data916    project_name = get_project_name()917    project_version = get_project_version()918    program_file = get_file_name(__file__)919    config_file = get_config_file(__file__)920 921    # print the helpplot_graphic(intervals)922    Message.print('info', '')923    Message.print('info', '{0} version {1}'.format(project_name, project_version))924    Message.print('info', '')925    Message.print('info', '{0} locates a sequence into the genome.'.format(program_file))926    Message.print('info', '')927    Message.print('info', 'Usage: {0} --help'.format(program_file))928    Message.print('info', '')929    Message.print('info', '       Show the help of {0}.'.format(program_file))930    Message.print('info', '')931    Message.print('info', '   or: {0} --config'.format(program_file))932    Message.print('info', '')933    Message.print('info', '       Create the config file {0} with the default value of the options.'.format(config_file))934    Message.print('info', '       The default value of the options can be modified.'.format(config_file))935    Message.print('info', '')936    Message.print('info', '   or: {0} [--option=<value> [--option=<value>, ...]]'.format(program_file))937    Message.print('info', '')938    Message.print('info', '       The options values are read from the config file {0}, but they can be modified'.format(config_file))939    Message.print('info', '       in command line. The options are:')940    Message.print('info', '')941    Message.print('info', '       {0:9}   {1}'.format('option', 'value'))942    Message.print('info', '       {0:9}   {1}'.format('=' * 9, '=' * 44))943    Message.print('info', '       {0:9}   {1}'.format('--genfile', options_dict['genfile']['comment']))944    Message.print('info', '       {0:9}   {1}'.format('--seq', options_dict['seq']['comment']))945    Message.print('info', '       {0:9}   {1}'.format('--verbose', options_dict['verbose']['comment']))946    Message.print('info', '       {0:9}   {1}'.format('--trace', options_dict['trace']['comment']))947 948#-------------------------------------------------------------------------------949 950def build_config(options_dict):951    '''Build the file with the options by default.'''952 953    # get the config file954    config_file = get_config_file(__file__)955 956    # create the config file and write the default options957    try:958        with open(config_file, mode='w', encoding='iso-8859-1') as config_file_id:959            config_file_id.write('{0:33} # {1}\n'.format('genfile' + '=' + options_dict['genfile']['default'], options_dict['genfile']['comment']))960            config_file_id.write('{0:33} # {1}\n'.format('seq' + '=' + options_dict['seq']['default'], options_dict['seq']['comment']))961            config_file_id.write('{0:33} # {1}\n'.format('verbose' + '=' + options_dict['verbose']['default'], options_dict['verbose']['comment']))962            config_file_id.write('{0:33} # {1}\n'.format('trace' + '=' + options_dict['trace']['default'], options_dict['trace']['comment']))963    except:964        raise ProgramError('F001', config_file)965 966    # show OK message 967    Message.print('info', 'The configuration file {0} is created.'.format(get_file_name(config_file)))968 969#-------------------------------------------------------------------------------970 971if __name__ == '__main__':972    main(sys.argv[1:])973    sys.exit(0)974 975#-------------------------------------------------------------------------------976","Python"
977"In Silico","GGFHF/ddRADseqTools","Package/pcrdupremoval.py",".py","36786","914","#!/usr/bin/env python3978# -*- coding: utf-8 -*-979 980#-------------------------------------------------------------------------------981 982'''This software has been developed by:983 984       GI Genética, Fisiología e Historia Forestal985       Dpto. Sistemas y Recursos Naturales986       ETSI Montes, Forestal y del Medio Natural987       Universidad Politécnica de Madrid988       https://github.com/ggfhf/989 990   Licence: GNU General Public Licence Version 3991'''992 993#-------------------------------------------------------------------------------994 995'''This source contains the program of the ddRADseqTools software package that996   quantifies the PCR duplicates and removes them from a file(s) in FASTQ/FASTA997   format with sequences of a double digest RADseq.998'''999#-------------------------------------------------------------------------------1000 1001import os.path1002import re1003import subprocess1004import sys1005 1006from genlib import *1007 1008#-------------------------------------------------------------------------------1009 1010def main(argv):1011    '''Main line of the program.'''1012 1013    # build the options dictionary1014    options_dict = build_options()1015 1016    # it has been requested the help or to build a new config file1017    for param in argv:1018        # show the help and exit OK1019        if param.startswith('--help'):1020            print_help(options_dict)1021            sys.exit(0)1022        # build the config file and exit OK1023        elif param.startswith('--config'):1024            build_config(options_dict)1025            sys.exit(0)1026 1027    # get the config file1028    config_file = get_config_file(__file__)1029 1030    # get options from the config file and the input parameters1031    options_dict = get_options(options_dict, config_file, argv)1032 1033    # process PCR duplicates of a double digest RADseq1034    process_pcr_duplicates(options_dict)1035 1036#-------------------------------------------------------------------------------1037 1038def process_pcr_duplicates(options_dict):1039    '''Process PCR duplicates of a double digest RADseq.'''1040 1041    format = options_dict['format']['value']1042    readtype = options_dict['readtype']['value']1043    readsfile1 = options_dict['readsfile1']['value']1044    readsfile2 = options_dict['readsfile2']['value']1045    clearfile = options_dict['clearfile']['value']1046    dupstfile = options_dict['dupstfile']['value']1047    plot = options_dict['plot']['value']1048    verbose = options_dict['verbose']['value']1049    trace = options_dict['trace']['value']1050 1051    # set the verbose and trace status1052    if verbose.upper() == 'YES':1053        Message.set_verbose_status(True)1054    else:1055        Message.set_verbose_status(False)1056    if trace.upper() == 'YES':1057        Message.set_trace_status(True)1058    else:1059        Message.set_trace_status(False)1060 1061    # initialize the statistics1062    stats_dict = {}1063 1064    # asign the temporal file name with records unified by read1065    unified_reads_file = readsfile1 + '.unified'1066 1067    # build temporal file unifing records by read1068    unify_records(format, readtype, readsfile1, readsfile2, unified_reads_file)1069 1070    # asign the temporal file name with sorted records unified by read1071    sorted_reads_file = unified_reads_file + '.sorted'1072 1073    # sort the temporal file with records unified by read1074    sort_records(unified_reads_file, sorted_reads_file)1075 1076    # delete temporal file with records unified by read1077    os.remove(unified_reads_file)1078    Message.print('info', 'The temporal file {0} is deleted.'.format(get_file_name(unified_reads_file)))1079 1080    # asign the purged temporal file(s) name1081    purged_reads_file = sorted_reads_file + '.purged'1082 1083    # quantify and remove the PCR duplicates1084    stats_dict = purge_records(format, readtype, sorted_reads_file, purged_reads_file)1085 1086    # delete temporal file with sorted records unified by read1087    os.remove(sorted_reads_file)1088    Message.print('info', 'The temporal file {0} is deleted.'.format(get_file_name(sorted_reads_file)))1089 1090    # assign the output file(s) name1091    extention = '.fastq' if format == 'FASTQ' else '.fasta'1092    if readtype == 'SE':1093        clearfile1 = clearfile + extention1094        clearfile2 = None1095    elif readtype == 'PE':1096        clearfile1 = clearfile + '-1' + extention1097        clearfile2 = clearfile + '-2' + extention1098 1099    # restore the original file(s) format1100    restore_format(format, readtype, purged_reads_file, clearfile1, clearfile2)1101 1102    # delete temporal file without PCR duplicates1103    os.remove(purged_reads_file)1104    Message.print('info', 'The temporal file {0} is deleted.'.format(get_file_name(purged_reads_file)))1105 1106    # write the PCR duplicates statistics1107    write_pcrdup_stats(dupstfile, stats_dict)1108 1109    # plot the PCR duplicates graphics1110    if plot.upper() == 'YES':1111        plot_pcrdup_graphics(dupstfile, stats_dict)1112 1113    # plot the graphic of the individuals without data per locus1114    if plot.upper() == 'YES':1115        plot_individuals_withoutdata_graphic(dupstfile, stats_dict)1116 1117    # plot the graphic of the loci without data per individual1118    if plot.upper() == 'YES':1119        plot_loci_withoutdata_graphic(dupstfile, stats_dict)1120 1121#-------------------------------------------------------------------------------1122 1123def unify_records(format, readtype, readsfile1, readsfile2, unified_reads_file):1124    '''Build file(s) unifing records by read.'''1125 1126    # open the reads file(s)1127    try:1128        readsfile1_id = open(readsfile1, mode='r', encoding='iso-8859-1')1129    except:1130        raise ProgramError('F002', readsfile1)1131    if readtype == 'PE':1132        try:1133            readsfile2_id = open(readsfile2, mode='r', encoding='iso-8859-1')1134        except:1135            raise ProgramError('F002', readsfile2)1136 1137    # open the file unifing records by read1138    try:1139        unified_reads_file_id = open(unified_reads_file, mode='w', encoding='iso-8859-1')1140    except:1141        raise ProgramError('F002', unified_reads_file)1142 1143    # initialize the count of reads1144    reads_count = 01145 1146    # if the format is FASTA1147    if format == 'FASTA':1148 1149        # set the pattern of the head records (>read_info)1150        pattern = r'^>(.*)$'1151 1152        # if readtype is SE1153        if readtype == 'SE':1154 1155            # read the first record of readsfile(s)1156            record1 = readsfile1_id.readline()1157 1158            # while there are records in readsfile11159            while record1 != '':1160 1161                # process the head record 1162                if record1.startswith('>'):1163 1164                    # extract the data 1165                    mo = re.search(pattern, record1)1166                    info1 = mo.group(1).strip()1167 1168                    # initialize the sequence1169                    seq1 = ''1170 1171                    # read the next record of readsfile11172                    record1 = readsfile1_id.readline()1173 1174                else:1175 1176                    # control the FASTA format1177                    raise ProgramError('F003', readsfile1, 'FASTA')1178 1179                # while there are records in readsfile1 and they are sequence1180                while record1 != '' and not record1.startswith('>'):1181 1182                    # add the record to the sequence1183                    seq1 += record1.strip()1184 1185                    # read the next record of readsfile11186                    record1 = readsfile1_id.readline()1187 1188                #  write record in unifile1189                unified_reads_file_id.write('{0}|||{1}\n'.format(seq1, info1))1190 1191                # notify the reads have been processed1192                reads_count += 11193                Message.print('verbose', '\rProcessed reads: {0:9d}'.format(reads_count))1194 1195        # if the readtype is PE1196        elif readtype == 'PE':1197 1198            # read the first record of readsfile1 and readfile21199            record1 = readsfile1_id.readline()1200            record2 = readsfile2_id.readline()

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