comparison vsnp_statistics.py @ 7:6dc6dd4666e3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"

6:9ddeef840a07

#!/usr/bin/env python

import argparse
import csv
import gzip
import os
from functools import partial

import numpy
import pandas
from Bio import SeqIO


def nice_size(size):
    # Returns a readably formatted string with the size
    words = ['bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB']

                return "%s%d bytes" % (prefix, size)
            return "%s%.1f %s" % (prefix, size, word)
    return '??? bytes'


def output_statistics(fastq_files, idxstats_files, metrics_files, output_file, gzipped, dbkey):
    # Produce an Excel spreadsheet that
    # contains a row for each sample.
    columns = ['Reference', 'File Size', 'Mean Read Length', 'Mean Read Quality', 'Reads Passing Q30',
               'Total Reads', 'All Mapped Reads', 'Unmapped Reads', 'Unmapped Reads Percentage of Total',
               'Reference with Coverage', 'Average Depth of Coverage', 'Good SNP Count']
    data_frames = []
    for i, fastq_file in enumerate(fastq_files):
        idxstats_file = idxstats_files[i]
        metrics_file = metrics_files[i]
        file_name_base = os.path.basename(fastq_file)
        # Read fastq_file into a data frame.
        _open = partial(gzip.open, mode='rt') if gzipped else open
        with _open(fastq_file) as fh:
            identifiers = []
            seqs = []
            letter_annotations = []
            for seq_record in SeqIO.parse(fh, "fastq"):
                identifiers.append(seq_record.id)
                seqs.append(seq_record.seq)
                letter_annotations.append(seq_record.letter_annotations["phred_quality"])
        # Convert lists to Pandas series.
        s1 = pandas.Series(identifiers, name='id')
        s2 = pandas.Series(seqs, name='seq')
        # Gather Series into a data frame.
        fastq_df = pandas.DataFrame(dict(id=s1, seq=s2)).set_index(['id'])
        total_reads = int(len(fastq_df.index) / 4)
        current_sample_df = pandas.DataFrame(index=[file_name_base], columns=columns)
        # Reference
        current_sample_df.at[file_name_base, 'Reference'] = dbkey
        # File Size
        current_sample_df.at[file_name_base, 'File Size'] = nice_size(os.path.getsize(fastq_file))
        # Mean Read Length
        sampling_size = 10000
        if sampling_size > total_reads:
            sampling_size = total_reads
        fastq_df = fastq_df.iloc[3::4].sample(sampling_size)
        dict_mean = {}
        list_length = []
        i = 0
        for id, seq, in fastq_df.iterrows():
            dict_mean[id] = numpy.mean(letter_annotations[i])
            list_length.append(len(seq.array[0]))
            i += 1
        current_sample_df.at[file_name_base, 'Mean Read Length'] = '%.1f' % numpy.mean(list_length)
        # Mean Read Quality
        df_mean = pandas.DataFrame.from_dict(dict_mean, orient='index', columns=['ave'])
        current_sample_df.at[file_name_base, 'Mean Read Quality'] = '%.1f' % df_mean['ave'].mean()
        # Reads Passing Q30
        reads_gt_q30 = len(df_mean[df_mean['ave'] >= 30])
        reads_passing_q30 = '{:10.2f}'.format(reads_gt_q30 / sampling_size)
        current_sample_df.at[file_name_base, 'Reads Passing Q30'] = reads_passing_q30
        # Total Reads
        current_sample_df.at[file_name_base, 'Total Reads'] = total_reads
        # All Mapped Reads
        all_mapped_reads, unmapped_reads = process_idxstats_file(idxstats_file)
        current_sample_df.at[file_name_base, 'All Mapped Reads'] = all_mapped_reads
        # Unmapped Reads
        current_sample_df.at[file_name_base, 'Unmapped Reads'] = unmapped_reads
        # Unmapped Reads Percentage of Total
        if unmapped_reads > 0:
            unmapped_reads_percentage = '{:10.2f}'.format(unmapped_reads / total_reads)
        else:
            unmapped_reads_percentage = 0
        current_sample_df.at[file_name_base, 'Unmapped Reads Percentage of Total'] = unmapped_reads_percentage
        # Reference with Coverage
        ref_with_coverage, avg_depth_of_coverage, good_snp_count = process_metrics_file(metrics_file)
        current_sample_df.at[file_name_base, 'Reference with Coverage'] = ref_with_coverage
        # Average Depth of Coverage
        current_sample_df.at[file_name_base, 'Average Depth of Coverage'] = avg_depth_of_coverage
        # Good SNP Count
        current_sample_df.at[file_name_base, 'Good SNP Count'] = good_snp_count
        data_frames.append(current_sample_df)
    output_df = pandas.concat(data_frames)
    output_df.to_csv(output_file, sep='\t', quoting=csv.QUOTE_NONE, escapechar='\\')


def process_idxstats_file(idxstats_file):
    all_mapped_reads = 0
    unmapped_reads = 0

parser = argparse.ArgumentParser()

parser.add_argument('--dbkey', action='store', dest='dbkey', help='Reference dbkey')
parser.add_argument('--gzipped', action='store_true', dest='gzipped', required=False, default=False, help='Input files are gzipped')
parser.add_argument('--input_idxstats_dir', action='store', dest='input_idxstats_dir', required=False, default=None, help='Samtools idxstats input directory')
parser.add_argument('--input_metrics_dir', action='store', dest='input_metrics_dir', required=False, default=None, help='vSNP add zero coverage metrics input directory')
parser.add_argument('--input_reads_dir', action='store', dest='input_reads_dir', required=False, default=None, help='Samples input directory')
parser.add_argument('--list_paired', action='store_true', dest='list_paired', required=False, default=False, help='Input samples is a list of paired reads')
parser.add_argument('--output', action='store', dest='output', help='Output Excel statistics file')
parser.add_argument('--read1', action='store', dest='read1', help='Required: single read')
parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
parser.add_argument('--samtools_idxstats', action='store', dest='samtools_idxstats', help='Output of samtools_idxstats')
parser.add_argument('--vsnp_azc', action='store', dest='vsnp_azc', help='Output of vsnp_add_zero_coverage')

args = parser.parse_args()

fastq_files = []
idxstats_files = []
metrics_files = []
# Accumulate inputs.
if args.read1 is not None:
    # The inputs are not dataset collections, so
    # read1, read2 (possibly) and vsnp_azc will also
    # not be None.
    fastq_files.append(args.read1)
    idxstats_files.append(args.samtools_idxstats)
    metrics_files.append(args.vsnp_azc)
    if args.read2 is not None:
        fastq_files.append(args.read2)
        idxstats_files.append(args.samtools_idxstats)
        metrics_files.append(args.vsnp_azc)
else:
    for file_name in sorted(os.listdir(args.input_reads_dir)):
        fastq_files.append(os.path.join(args.input_reads_dir, file_name))
    for file_name in sorted(os.listdir(args.input_idxstats_dir)):
        idxstats_files.append(os.path.join(args.input_idxstats_dir, file_name))
        if args.list_paired:
            # Add the idxstats file for reverse.
            idxstats_files.append(os.path.join(args.input_idxstats_dir, file_name))
    for file_name in sorted(os.listdir(args.input_metrics_dir)):
        metrics_files.append(os.path.join(args.input_metrics_dir, file_name))
        if args.list_paired:
            # Add the metrics file for reverse.
            metrics_files.append(os.path.join(args.input_metrics_dir, file_name))
output_statistics(fastq_files, idxstats_files, metrics_files, args.output, args.gzipped, args.dbkey)

7:6dc6dd4666e3

#!/usr/bin/env python

import argparse
import gzip
import os
from functools import partial

import numpy
import pandas
from Bio import SeqIO


class Statistics:

    def __init__(self, reference, fastq_file, file_size, total_reads, mean_read_length, mean_read_quality, reads_passing_q30):
        self.reference = reference
        self.fastq_file = fastq_file
        self.file_size = file_size
        self.total_reads = total_reads
        self.mean_read_length = mean_read_length
        self.mean_read_quality = mean_read_quality
        self.reads_passing_q30 = reads_passing_q30


def nice_size(size):
    # Returns a readably formatted string with the size
    words = ['bytes', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB']

                return "%s%d bytes" % (prefix, size)
            return "%s%.1f %s" % (prefix, size, word)
    return '??? bytes'


def get_statistics(dbkey, fastq_file, gzipped):
    sampling_size = 10000
    # Read fastq_file into a data fram to
    # get the phred quality scores.
    _open = partial(gzip.open, mode='rt') if gzipped else open
    with _open(fastq_file) as fh:
        identifiers = []
        seqs = []
        letter_annotations = []
        for seq_record in SeqIO.parse(fh, "fastq"):
            identifiers.append(seq_record.id)
            seqs.append(seq_record.seq)
            letter_annotations.append(seq_record.letter_annotations["phred_quality"])
    # Convert lists to Pandas series.
    s1 = pandas.Series(identifiers, name='id')
    s2 = pandas.Series(seqs, name='seq')
    # Gather Series into a data frame.
    fastq_df = pandas.DataFrame(dict(id=s1, seq=s2)).set_index(['id'])
    # Starting at row 3, keep every 4 row
    # random sample specified number of rows.
    file_size = nice_size(os.path.getsize(fastq_file))
    total_reads = len(seqs)
    # Mean Read Length
    if sampling_size > total_reads:
        sampling_size = total_reads
    try:
        fastq_df = fastq_df.iloc[3::4].sample(sampling_size)
    except ValueError:
        fastq_df = fastq_df.iloc[3::4].sample(sampling_size, replace=True)
    dict_mean = {}
    list_length = []
    i = 0
    for id, seq, in fastq_df.iterrows():
        dict_mean[id] = numpy.mean(letter_annotations[i])
        list_length.append(len(seq.array[0]))
        i += 1
    mean_read_length = '%.1f' % numpy.mean(list_length)
    # Mean Read Quality
    df_mean = pandas.DataFrame.from_dict(dict_mean, orient='index', columns=['ave'])
    mean_read_quality = '%.1f' % df_mean['ave'].mean()
    # Reads Passing Q30
    reads_gt_q30 = len(df_mean[df_mean['ave'] >= 30])
    reads_passing_q30 = '{:10.2f}'.format(reads_gt_q30 / sampling_size)
    stats = Statistics(dbkey, os.path.basename(fastq_file), file_size, total_reads, mean_read_length,
                       mean_read_quality, reads_passing_q30)
    return stats


def accrue_statistics(dbkey, read1, read2, gzipped):
    read1_stats = get_statistics(dbkey, read1, gzipped)
    if read2 is None:
        read2_stats = None
    else:
        read2_stats = get_statistics(dbkey, read2, gzipped)
    return read1_stats, read2_stats


def output_statistics(read1_stats, read2_stats, idxstats_file, metrics_file, output_file):
    paired_reads = read2_stats is not None
    if paired_reads:
        columns = ['Read1 FASTQ', 'File Size', 'Reads', 'Mean Read Length', 'Mean Read Quality',
                   'Reads Passing Q30', 'Read2 FASTQ', 'File Size', 'Reads', 'Mean Read Length', 'Mean Read Quality',
                   'Reads Passing Q30', 'Total Reads', 'All Mapped Reads', 'Unmapped Reads',
                   'Unmapped Reads Percentage of Total', 'Reference with Coverage', 'Average Depth of Coverage',
                   'Good SNP Count', 'Reference']
    else:
        columns = ['FASTQ', 'File Size', 'Mean Read Length', 'Mean Read Quality', 'Reads Passing Q30',
                   'Total Reads', 'All Mapped Reads', 'Unmapped Reads', 'Unmapped Reads Percentage of Total',
                   'Reference with Coverage', 'Average Depth of Coverage', 'Good SNP Count', 'Reference']
    with open(output_file, "w") as outfh:
        # Make sure the header starts with a # so
        # MultiQC can properly handle the output.
        outfh.write("%s\n" % "\t".join(columns))
        line_items = []
        # Get the current stats and associated files.
        # Get and output the statistics.
        line_items.append(read1_stats.fastq_file)
        line_items.append(read1_stats.file_size)
        if paired_reads:
            line_items.append(read1_stats.total_reads)
        line_items.append(read1_stats.mean_read_length)
        line_items.append(read1_stats.mean_read_quality)
        line_items.append(read1_stats.reads_passing_q30)
        if paired_reads:
            line_items.append(read2_stats.fastq_file)
            line_items.append(read2_stats.file_size)
            line_items.append(read2_stats.total_reads)
            line_items.append(read2_stats.mean_read_length)
            line_items.append(read2_stats.mean_read_quality)
            line_items.append(read2_stats.reads_passing_q30)
        # Total Reads
        if paired_reads:
            total_reads = read1_stats.total_reads + read2_stats.total_reads
        else:
            total_reads = read1_stats.total_reads
        line_items.append(total_reads)
        # All Mapped Reads
        all_mapped_reads, unmapped_reads = process_idxstats_file(idxstats_file)
        line_items.append(all_mapped_reads)
        line_items.append(unmapped_reads)
        # Unmapped Reads Percentage of Total
        if unmapped_reads > 0:
            unmapped_reads_percentage = '{:10.2f}'.format(unmapped_reads / total_reads)
        else:
            unmapped_reads_percentage = 0
        line_items.append(unmapped_reads_percentage)
        # Reference with Coverage
        ref_with_coverage, avg_depth_of_coverage, good_snp_count = process_metrics_file(metrics_file)
        line_items.append(ref_with_coverage)
        line_items.append(avg_depth_of_coverage)
        line_items.append(good_snp_count)
        line_items.append(read1_stats.reference)
        outfh.write('%s\n' % '\t'.join(str(x) for x in line_items))


def process_idxstats_file(idxstats_file):
    all_mapped_reads = 0
    unmapped_reads = 0

parser = argparse.ArgumentParser()

parser.add_argument('--dbkey', action='store', dest='dbkey', help='Reference dbkey')
parser.add_argument('--gzipped', action='store_true', dest='gzipped', required=False, default=False, help='Input files are gzipped')
parser.add_argument('--output', action='store', dest='output', help='Output Excel statistics file')
parser.add_argument('--read1', action='store', dest='read1', help='Required: single read')
parser.add_argument('--read2', action='store', dest='read2', required=False, default=None, help='Optional: paired read')
parser.add_argument('--samtools_idxstats', action='store', dest='samtools_idxstats', help='Output of samtools_idxstats')
parser.add_argument('--vsnp_azc_metrics', action='store', dest='vsnp_azc_metrics', help='Output of vsnp_add_zero_coverage')

args = parser.parse_args()

stats_list = []
idxstats_files = []
metrics_files = []
# Accumulate inputs.
read1_stats, read2_stats = accrue_statistics(args.dbkey, args.read1, args.read2, args.gzipped)
output_statistics(read1_stats, read2_stats, args.samtools_idxstats, args.vsnp_azc_metrics, args.output)