collect stats base

src/collect_stats.py

+import click
+import json
+
+from os.path import basename
+
+
+def parse_json_file(path):
+    with open(path) as handle:
+        d = json.load(handle)
+    return d
+
+
+def parse_num_file(path):
+    with open(path) as handle:
+        line = handle.readline()
+    return int(line.strip())
+
+
+def determine_gender(covstat, fthresh):
+    """Determine gender from a covstat json """
+    return None
+
+
+@click.command()
+@click.option("--pre-qc-fastq",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              help="pre-qc json from fastq-count")
+@click.option("--post-qc-fastq",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              help="Post-qc json from fastq-count")
+@click.option("--mapped-num",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              help="Mapped num file")
+@click.option("--mapped-basenum",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              help="Mapped basenum file")
+@click.option("--unique-num",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              help="Unique num file")
+@click.option("--usable-basenum",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              help="Usable basenum")
+@click.option("--female-threshold",
+              type=click.INT,
+              default=0.6,
+              help="Female threshold of X/all cov")
+@click.option("--covstats",
+              type=click.Path(dir_okay=False, exists=True, readable=True),
+              required=True,
+              nargs=-1,
+              help="Covstat json files")
+def main(pre_qc_fastq, post_qc_fastq, mapped_num, mapped_basenum, unique_num,
+         usable_basenum, female_threshold, covstats):
+
+    preqcd = parse_json_file(pre_qc_fastq)
+    posqcd = parse_json_file(post_qc_fastq)
+
+    mpnum = parse_num_file(mapped_num)
+    mpbnum = parse_num_file(mapped_basenum)
+    unum = parse_num_file(unique_num)
+    ubnum = parse_num_file(usable_basenum)
+
+    covl = []
+    for c in covstats:
+        cd = parse_json_file(c)
+        cdd = {
+            "name": basename(c),
+            "gender": determine_gender(cd, female_threshold),
+            "covstats": cd
+        }
+        covl.append(cdd)
+
+    d = {
+        "pre_qc_fastq_count": preqcd,
+        "post_qc_fastq_count": posqcd,
+        "n_mapped_reads": mpnum,
+        "n_mapped_bases": mpbnum,
+        "n_usable_reads": unum,
+        "n_usable_bases": ubnum,
+        "covstats": covl
+    }
+
+    json.dumps(covl)
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