diff GAFA.py @ 0:af9f72ddf7f9 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit 822c798d43a72724eeab174043fdaafcfdac845f-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GAFA.py	Wed Dec 21 07:31:50 2016 -0500
@@ -0,0 +1,120 @@
+from __future__ import print_function
+
+import json
+import optparse
+import sqlite3
+
+version = "0.1.0"
+
+
+def create_tables(conn):
+    cur = conn.cursor()
+    cur.execute('PRAGMA foreign_keys = ON')
+    cur.execute('''CREATE TABLE meta (
+        version VARCHAR)''')
+
+    cur.execute('INSERT INTO meta (version) VALUES (?)',
+                (version, ))
+
+    cur.execute('''CREATE TABLE gene_family (
+        gene_family_id INTEGER PRIMARY KEY,
+        gene_tree VARCHAR NOT NULL)''')
+
+    cur.execute('''CREATE TABLE gene (
+        gene_id VARCHAR PRIMARY KEY NOT NULL,
+        gene_symbol VARCHAR,
+        gene_json VARCHAR NOT NULL)''')
+    cur.execute('CREATE INDEX gene_symbol_index ON gene (gene_symbol)')
+
+    cur.execute('''CREATE TABLE transcript (
+        transcript_id VARCHAR PRIMARY KEY NOT NULL,
+        protein_id VARCHAR UNIQUE,
+        gene_id VARCHAR NOT NULL REFERENCES gene(gene_id))''')
+
+    cur.execute('''CREATE TABLE gene_family_member (
+        gene_family_id INTEGER NOT NULL REFERENCES gene_family(gene_family_id),
+        protein_id VARCHAR KEY NOT NULL REFERENCES transcript(protein_id),
+        alignment VARCHAR NOT NULL,
+        PRIMARY KEY (gene_family_id, protein_id))''')
+    conn.commit()
+
+
+def cigar_to_db(conn, i, fname):
+    cur = conn.cursor()
+    with open(fname) as f:
+        for element in f.readlines():
+            seq_id, cigar = element.rstrip('\n').split('\t')
+            # Trim seq_id by removing everything from the first underscore
+            seq_id = seq_id.split('_', 1)[0]
+
+            cur.execute('SELECT transcript_id, protein_id FROM transcript WHERE transcript_id=? OR protein_id=?',
+                        (seq_id, seq_id))
+            results = cur.fetchall()
+            if len(results) == 0:
+                raise Exception("Sequence id '%s' could not be found among the transcript and protein ids" % seq_id)
+            elif len(results) > 1:
+                raise Exception("Searching sequence id '%s' among the transcript and protein ids returned multiple results" % seq_id)
+            transcript_id, protein_id = results[0]
+            if protein_id is None:
+                print("Skipping transcript '%s' with no protein id" % transcript_id)
+            else:
+                cur.execute('INSERT INTO gene_family_member (gene_family_id, protein_id, alignment) VALUES (?, ?, ?)',
+                            (i, protein_id, cigar))
+                conn.commit()
+
+
+def newicktree_to_db(conn, i, fname):
+    with open(fname) as f:
+        tree = f.read().replace('\n', '')
+
+    cur = conn.cursor()
+    cur.execute('INSERT INTO gene_family (gene_family_id, gene_tree) VALUES (?, ?)',
+                (i, tree))
+    conn.commit()
+
+
+def gene_json_to_db(conn, fname):
+    with open(fname) as f:
+        all_genes_dict = json.load(f)
+
+    cur = conn.cursor()
+    for gene_dict in all_genes_dict.values():
+        gene_id = gene_dict['id']
+        gene_symbol = gene_dict.get('display_name', None)
+        cur.execute("INSERT INTO gene (gene_id, gene_symbol, gene_json) VALUES (?, ?, ?)",
+                    (gene_id, gene_symbol, json.dumps(gene_dict)))
+
+        if "Transcript" in gene_dict:
+            for transcript in gene_dict["Transcript"]:
+                transcript_id = transcript['id']
+                if 'Translation' in transcript and 'id' in transcript['Translation']:
+                    protein_id = transcript["Translation"]["id"]
+                else:
+                    protein_id = None
+                cur.execute("INSERT INTO transcript (transcript_id, protein_id, gene_id) VALUES (?, ?, ?)",
+                            (transcript_id, protein_id, gene_id))
+    conn.commit()
+
+
+def __main__():
+    parser = optparse.OptionParser()
+    parser.add_option('-t', '--tree', action='append', help='Gene tree files')
+    parser.add_option('-c', '--cigar', action='append', help='CIGAR alignments of CDS files in tabular format')
+    parser.add_option('-g', '--gene', help='Gene features file in JSON format')
+    parser.add_option('-o', '--output', help='Path of the output file')
+    options, args = parser.parse_args()
+    if args:
+        raise Exception('Use options to provide inputs')
+
+    conn = sqlite3.connect(options.output)
+    create_tables(conn)
+
+    gene_json_to_db(conn, options.gene)
+
+    for i, (tree, cigar) in enumerate(zip(options.tree, options.cigar), start=1):
+        newicktree_to_db(conn, i, tree)
+        cigar_to_db(conn, i, cigar)
+
+
+if __name__ == '__main__':
+    __main__()