Initial commit

.gitignore

+.idea

miniannotator.py

+#!/usr/bin/env python3
+
+import os
+import pysam
+import sys
+import yaml
+import subprocess
+from collections import OrderedDict
+
+PRG_PATH = os.path.dirname(os.path.realpath(__file__))
+
+
+class Miniannotator:
+
+    def __init__(self, reference, assembly, map=None):
+        self.conf = self._load_config()
+        self.reference = reference
+        self.assembly = assembly
+        self.map = map
+
+    @staticmethod
+    def _load_config():
+        """
+        Load config file to a dictionary
+
+        :return: config dictionary
+        :rtype: dict
+        """
+        with open(os.path.join(PRG_PATH, "miniannotator.yml"), "r") as cfg_f:
+            conf = yaml.safe_load(cfg_f)
+        return conf
+
+    def launch_minimap(self, map_f="map.bam"):
+        """
+        Launch mapping with minimap2. Compress output SAM as BAM
+
+        :param map_f: output bam file path
+        :type map_f: str
+        :return: 0 if succeed, else error return code
+        :rtype: int
+        """
+        print("Mapping assembly to reference genome...", flush=True)
+        minimap = [self.conf["minimap2"], "-ax", "splice", "-t", str(self.conf["threads"]), self.reference,
+                   self.assembly]
+        samtools_sort = [self.conf["samtools"], "sort"]
+        samtools_bam = [self.conf["samtools"], "view", "-b", "-o", map_file]
+        p1 = subprocess.Popen(minimap, stdout=subprocess.PIPE)
+        p2 = subprocess.Popen(samtools_sort, stdin=p1.stdout, stdout=subprocess.PIPE)
+        p1.stdout.close()
+        p3 = subprocess.Popen(samtools_bam, stdin=p2.stdout, stdout=subprocess.PIPE)
+        p2.stdout.close()
+        output = p3.communicate()[0]
+        p3.wait()
+        rcode = p3.returncode
+        self.map = map_f
+        return rcode
+
+    def search_genes(self):
+        """
+        Parse BAM file to search genes and exons positions
+        Query match position on the reference defines gene position
+        Splice reads define exons: introns are the "N" in the cigarline
+        Save also DEL/INS events in genes
+
+        :return:
+        """
+        genes = OrderedDict()
+        exons = OrderedDict()
+        indels = OrderedDict()
+
+        align = pysam.AlignmentFile(self.map)
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Annotate genome and fix reference genome")
+    parser.add_argument("-r", "--reference", help="Reference fasta file", required=True)
+    parser.add_argument("-a", "--assembly", help="De novo assembly fasta file", required=True)
+    parser.add_argument("-m", "--map", help="BAM map file build with minimap2 (if not given, will be computed now)",
+                        required=False)
+    parser.add_argument("-o", "--output-dir", help="Output folder path", required=False, default=".")
+
+    args = parser.parse_args()
+
+    if not os.path.exists(args.output_dir):
+        os.makedirs(args.output_dir)
+    elif not os.path.isdir(args.output_dir):
+        print("Error: output folder %s exists but is not a folder" % args.output_dir, file=sys.stderr)
+
+    annotator = Miniannotator(args.reference, args.assembly)
+
+    # Map:
+    if args.map is None:
+        map_file = os.path.join(args.output_dir, "map.bam")
+        annotator.launch_minimap(map_file)
+    else:
+        print("Using map from %s..." % args.map)
+        map_file = args.map

miniannotator.yml

+minimap2: minimap2
+samtools: samtools
+threads: 4
\ No newline at end of file