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How to use collect_data method in stestr

Best Python code snippet using stestr_python

data_integrity.py

Source:data_integrity.py

1#!/usr/bin/env python32from __future__ import print_function3import re4import os5import sys6import gzip7import argparse8import subprocess9import multiprocessing as mp10from Bio import SeqIO11# For errors / warnings12def eprint(*args, **kwargs):13    print(*args, file=sys.stderr, **kwargs)14def getArgs():15    parser = argparse.ArgumentParser(description="")16    parser.add_argument('-a',dest="manifest",type=str,required=True,help='q2_manifest file')17    parser.add_argument('-e',dest="metadata",type=str,required=True,help='q2_metadata file')18    parser.add_argument('-p',dest="primer",type=int,default=70,help='Percentage of primers supposed to be found in raw reads [%(default)s]')19    parser.add_argument('-c',dest="control",type=str, default='',help='Delimited list of control (comma separated)')20    parser.add_argument('-r',dest="readtype",type=str,default='paired',choices=['paired','single'],help='Sequencing format [%(default)s]')21    parser.add_argument('-t',dest="threads",type=int,default=4,help='Number of threads [%(default)s]')22    arg = parser.parse_args()23    return arg24def collect_check_metadata(metadata_file, data_type):25    collect_data = {}26    # read metadata line by line27    for l in open(metadata_file, 'r'):28        # ignore header29        if not l.startswith('sampleid'):30            sampleid = re.split(r'\t', l.rstrip('\n'))[0]31            collect_data[sampleid] = {}32            collect_data[sampleid]['barcode'] = re.split(r'\t', l.rstrip('\n'))[1]33            if data_type == 'paired':34                collect_data[sampleid]['primerF'] = re.split(r'\t', l.rstrip('\n'))[2]35                collect_data[sampleid]['primerR'] = re.split(r'\t', l.rstrip('\n'))[3]36                collect_data[sampleid]['vars'] = re.split(r'\t', l.rstrip('\n'))[4:]37            else:38                collect_data[sampleid]['primerF'] = re.split(r'\t', l.rstrip('\n'))[2]39                collect_data[sampleid]['vars'] = re.split(r'\t', l.rstrip('\n'))[3:]40            # check that var(s) didn't contains any NA41            for var in collect_data[sampleid]['vars']:42                if var == 'NA' or var == '':43                    eprint('ERROR: '+sampleid+' has NA value(s) in q2_metadata, please remove them before running SAMBA')44                    exit(1)45    # return results46    return collect_data, data_type47def collect_manifest(manifest_file, collect_data, data_type):48    # in order to check that metadata and manifest have the same number of lines49    metadata_size = len(collect_data)50    manifest_size = 051    # read manifest52    for l in open(manifest_file, 'r'):53        # ignore header54        if not l.startswith('sample-id'):55            if data_type == 'paired':56                try:57                    sampleid, R1, R2 = re.split(r'\t', l.rstrip('\n'))58                except ValueError:59                    size = len(re.split(r'\t', l.rstrip('\n')))60                    eprint('ERROR: q2_manifest contains '+str(size)+ 'column(s) instead of 3')61                    exit(1)62                # check that file path are good63                check_fastq_path(R1)64                check_fastq_path(R2)65                # add to collect_data66                try:67                    collect_data[sampleid]['R1'] = R168                    collect_data[sampleid]['R2'] = R269                except KeyError:70                    eprint('ERROR: '+sampleid+' from q2_manifest is absent in q2_metadata')71                    exit(1)72            else:73                try:74                    sampleid, R1 = l.split()75                except ValueError:76                    size = len(re.split(r'\t', l.rstrip('\n')))77                    eprint('ERROR: q2_manifest contains '+str(size)+ 'column(s) instead of 2')78                    exit(1)79                # check that file path are good80                check_fastq_path(R1)81                # add to collect_data82                try:83                    collect_data[sampleid]['R1'] = R184                except KeyError:85                    eprint('ERROR: '+sampleid+' from q2_manifest is absent in q2_metadata')86                    exit(1)87            # increase line counter88            manifest_size += 189    # check that manifest have the same size as metadata90    if manifest_size != metadata_size:91        eprint('ERROR: q2_manifest and q2_metadata did not have the same number of lines')92        exit(1)93    # return update dict94    return collect_data95def check_fastq(collect_data, sample, data_type):96    out = {}97    print("\tanalyse sample: "+sample)98    barcode = collect_data[sample]['barcode']99    # by default, single-end100    reads = ['R1']101    # in case of paired, add R2 analysis102    if data_type == 'paired':103        reads.append('R2')104    # check fastq105    for r in reads:106        R=collect_data[sample][r]107        if r == 'R1':108            primer=collect_data[sample]['primerF']109        else:110            primer=collect_data[sample]['primerR']111        instrument, index, reads_count, primer = read_fastq(R, primer)112        collect_data[sample]['reads_count_'+r] = reads_count113        collect_data[sample]['instrument_'+r] = instrument114        collect_data[sample]['nb_instrument_'+r] = len(instrument)115        collect_data[sample]['index_'+r] = index116        collect_data[sample]['primer_'+r] = primer117        collect_data[sample]['perc_primer_'+r] = round(primer * 100 / reads_count, 2)118        collect_data[sample]['nb_barcode_'+r] = len(index)119        collect_data[sample]['barcode_seq_'+r] = 'FALSE'120        # chech that barcode are the same as in metadata121        if len(index) == 1:122            if index[0] == barcode:123                collect_data[sample]['barcode_seq_'+r]  = 'TRUE'124    # return updated dict125    out[sample] = collect_data[sample]126    return out127def read_fastq(fastq, primer):128    primer = re.sub(r"([RYSWKMBDHVNI])", r".", primer)129    reads_count = 0130    primers_count = 0131    instrument = []132    index = []133    with gzip.open(fastq, "rt") as handle:134            for record in SeqIO.parse(handle, "fastq"):135                # check instrument name136                h_1, h_2 = record.description.split()137                instrument_name = h_1.split(':')[0]138                if not instrument_name in instrument:139                    instrument.append(instrument_name)140                # check index141                sequence_index = h_2.split(':')[3]142                if not sequence_index in index:143                    index.append(sequence_index)144                # check primers145                if re.search(primer, str(record.seq)):146                    primers_count += 1147                # increase read count148                reads_count += 1149    return instrument, index, reads_count, primers_count150def check_fastq_path(path):151    if not os.path.isfile(path):152        eprint('ERROR: ' + path + ' from q2_manifest not exit. Wrong path?')153        exit(1)154def write_report(collect_data, data_type):155    # open output file for writting156    report = open('data_integrity.txt', 'w')157    # header158    header_S = ['SampleID', 'Reads_R1', 'Barcode', 'Uniq_in_R1', 'Same_as_ref_R1', 'Uniq_sequencer_R1', 'PrimerF_in_R1', 'Perc_primerF_R1']159    header_P = ['SampleID', 'Reads_R1', 'Reads_R2', 'Barcode', 'Uniq_in_R1', 'Same_as_ref_R1', 'Uniq_in_R2', 'Same_as_ref_R2', 'Uniq_sequencer_R1', 'Uniq_sequencer_R2', 'PrimerF_in_R1', 'Perc_primerF_R1', 'PrimerR_in_R2', 'Perc_primerR_R2']160    if data_type == 'paired':161        report.write('\t'.join(header_P)+'\n')162    else:163        report.write('\t'.join(header_S)+'\n')164    for sample, val in collect_data.items():165        if data_type == 'paired':166            report.write(sample+'\t'+'{reads_count_R1}\t{reads_count_R2}\t{barcode}\t{nb_barcode_R1}\t{barcode_seq_R1}\t{nb_barcode_R2}\t{barcode_seq_R2}\t{nb_instrument_R1}\t{nb_instrument_R2}\t{primer_R1}\t{perc_primer_R1}\t{primer_R2}\t{perc_primer_R2}\n'.format(**val))167        else:168            report.write(sample+'\t'+'{reads_count_R1}\t{barcode}\t{nb_barcode_R1}\t{barcode_seq_R1}\t{nb_instrument_R1}\t{primer_R1}\t{perc_primer_R1}\n'.format(**val))169def integrity_validation(collect_data_out,control_list, data_type, primer_threshold):170    # collect control(s)171    controls = [str(control) for control in control_list.split(',')]172    # let's check the integrity173    for sample_id, val in collect_data_out.items():174        if data_type == 'paired':175            # 1 - check reads count R1 vs R2176            if val['reads_count_R1'] != val['reads_count_R2']:177                eprint('ERROR: different number of reads between R1 and R2 for ' + sample_id)178                exit(1)179            # 2 - check single sequencing instrument in reads180            if val['nb_instrument_R1'] != 1 or val['nb_instrument_R2'] != 1:181                eprint('ERROR: multiple sequencing machines detected in ' + sample_id)182                exit(1)183            # 3 - check primer percentage found, except for control(s)184            if not sample_id in controls:185                if val['perc_primer_R1'] < primer_threshold or val['perc_primer_R2'] < primer_threshold:186                    eprint('ERROR: ' + sample_id + " did not reach the minimum threshold for primer percentage [" + str(primer_threshold) +"%]")187                    exit(1)188        else:189            # 1 - check single sequencing instrument in reads190            if val['nb_instrument_R1'] != 1:191                eprint('ERROR: multiple sequencing machines detected in ' + sample_id)192                exit(1)193            # 2 - check primer percentage found, except for control(s)194            if not sample_id in controls:195                if val['perc_primer_R1'] < primer_threshold:196                    eprint('ERROR: ' + sample_id + " did not reach the minimum threshold for primer percentage [" + str(primer_threshold) + "%]")197                    exit(1)198def sort_process(input_file, output_file):199    cmd_sort = '(head -n 1 {in_file} && tail -n +2 {in_file} | sort) > {out_file}'.format(in_file=input_file, out_file=output_file)200    p = subprocess.Popen(cmd_sort, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)201    stdout, stderr = p.communicate()202    if p.returncode != 0:203        eprint('ERROR: sort metadata/manifest failed')204        raise Exception(stderr)205        exit(1)206def main(args):207    # 1 - Collect metadata infos and check variable names208    print("Step 1 - parse and collect data from q2_metadata")209    collect_data, data_type = collect_check_metadata(args.metadata, args.readtype)210    # 2 - Collect reads location from manifest211    print("Step 2 - parse and collect data from q2_manifest")212    collect_data = collect_manifest(args.manifest, collect_data, data_type)213    # 3 - Check fastq integrity214    print("Step 3 - collect fastq integrity")215    pool = mp.Pool(args.threads)216    collect_data_para = pool.starmap(check_fastq, [(collect_data, sample,data_type) for sample in collect_data.keys()])217    pool.close()218    # Clean all this mess219    collect_data_out = {}220    for result in collect_data_para:221        for sample, vals in result.items():222            collect_data_out[sample] = vals223    # 4 - Report fastq intergrity before validation224    # Allow exploration by user for a better understanding225    print("Step 4 - write integrity report")226    write_report(collect_data_out, data_type)227    # 5 - Validate manifest, metadata and fastq228    print("Step 5 - validation of data")229    integrity_validation(collect_data_out, args.control, data_type, args.primer)230    # 6 - Sort manifest and metadata231    print("Step 6 - Sort manifest and metadata by sample id")232    print("\tsort manifest...")233    output_file_manifest = args.manifest + ".sort"234    sort_process(args.manifest, output_file_manifest)235    print("\tsort metadata...")236    output_file_metadata = args.metadata + ".sort"237    sort_process(args.metadata, output_file_metadata)238if __name__ == '__main__':239    args = getArgs()...

main_buttons.py

Source:main_buttons.py

...85    Args:86        window (QMainWindow): Ventana principal87    """88    window.btn_header.clicked.connect(89        lambda: collect_data(window, "Header"),90    )91    window.btn_free.clicked.connect(92        lambda: collect_data(window, "Free"),93    )94    window.btn_comment.clicked.connect(95        lambda: collect_data(window, "Comment"),96    )97    window.btn_subroutine.clicked.connect(98        lambda: collect_data(window, "Subroutine")99    )100    window.btn_collect.clicked.connect(101        lambda: collect_data(window, "Collect"),102    )103    window.btn_end.clicked.connect(104        lambda: collect_data(window, "End"),105    )106    window.btn_tool_call.clicked.connect(107        lambda: collect_data(window, "Tool_call"),108    )109    window.btn_tool_close.clicked.connect(110        lambda: collect_data(window, "Tool_close"),111    )112    window.btn_spindle.clicked.connect(113        lambda: collect_data(window, "Spindle"),114    )115    window.btn_spindle_index.clicked.connect(116        lambda: collect_data(window, "Spindle_index"),117    )118    window.btn_misc.clicked.connect(119        lambda: collect_data(window, "Misc"),120    )121    window.btn_turn_ini.clicked.connect(122        lambda: collect_data(window, "Turn_ini"),123    )124    window.btn_lineal_turn.clicked.connect(125        lambda: collect_data(window, "Lineal_turn"),126    )127    window.btn_radial_turn.clicked.connect(128        lambda: collect_data(window, "Radial_turn"),129    )130    window.btn_thread.clicked.connect(131        lambda: collect_data(window, "Thread"),132    )133    window.btn_cutoff.clicked.connect(134        lambda: collect_data(window, "Cutoff"),135    )136    window.btn_mill_ini.clicked.connect(137        lambda: collect_data(window, "Mill_ini"),138    )139    window.btn_mill_end.clicked.connect(140        lambda: collect_data(window, "Mill_end"),141    )142    window.btn_lineal_mill.clicked.connect(143        lambda: collect_data(window, "Lineal_mill"),144    )145    window.btn_radial_mill.clicked.connect(146        lambda: collect_data(window, "Radial_mill"),147    )148    window.btn_drill_ini.clicked.connect(149        lambda: collect_data(window, "Drill_ini"),150    )151    window.btn_drill_end.clicked.connect(152        lambda: collect_data(window, "Drill_end"),153    )154    window.btn_center.clicked.connect(155        lambda: collect_data(window, "Center_drill"),156    )157    window.btn_drill.clicked.connect(158        lambda: collect_data(window, "Drill"),159    )160    window.btn_csink.clicked.connect(161        lambda: collect_data(window, "Csink"),162    )163    window.btn_tapping.clicked.connect(164        lambda: collect_data(window, "Tapping"),165    )166    window.btn_rough_turn_cycle.clicked.connect(167        lambda: collect_data(window, "Rough_turn_cycle"),168    )169    window.btn_rough_turn_cycle_end.clicked.connect(170        lambda: collect_data(window, "Rough_turn_cycle_end"),171    )172    window.btn_flat_mill.clicked.connect(173        lambda: collect_data(window, "Flat_mill"),174    )175    window.btn_face_mill.clicked.connect(176        lambda: collect_data(window, "Face_mill"),...

collect_main.py

Source:collect_main.py

1import os23os.system("python ./collect_data/collect_data.py 0.1 1")4os.system("python ./collect_data/collect_data.py 0.5 2")5os.system("python ./collect_data/collect_data.py 1.0 3")6os.system("python ./collect_data/collect_data.py 2.0 4")
...

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