--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vsnp_statistics.py	Fri Aug 27 11:45:39 2021 +0000
@@ -0,0 +1,193 @@
+#!/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']
+    prefix = ''
+    try:
+        size = float(size)
+        if size < 0:
+            size = abs(size)
+            prefix = '-'
+    except Exception:
+        return '??? bytes'
+    for ind, word in enumerate(words):
+        step = 1024 ** (ind + 1)
+        if step > size:
+            size = size / float(1024 ** ind)
+            if word == 'bytes':  # No decimals for bytes
+                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
+    with open(idxstats_file, "r") as fh:
+        for i, line in enumerate(fh):
+            line = line.rstrip('\r\n')
+            items = line.split("\t")
+            if i == 0:
+                # NC_002945.4 4349904 213570 4047
+                all_mapped_reads = int(items[2])
+            elif i == 1:
+                # * 0 0 82774
+                unmapped_reads = int(items[3])
+    return all_mapped_reads, unmapped_reads
+
+
+def process_metrics_file(metrics_file):
+    ref_with_coverage = '0%'
+    avg_depth_of_coverage = 0
+    good_snp_count = 0
+    with open(metrics_file, "r") as ifh:
+        for i, line in enumerate(ifh):
+            if i == 0:
+                # Skip comments.
+                continue
+            line = line.rstrip('\r\n')
+            items = line.split("\t")
+            if i == 1:
+                # MarkDuplicates 10.338671 98.74%
+                ref_with_coverage = items[3]
+                avg_depth_of_coverage = items[2]
+            elif i == 2:
+                # VCFfilter 611
+                good_snp_count = items[1]
+    return ref_with_coverage, avg_depth_of_coverage, good_snp_count
+
+
+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)