Update PosgreSQL urls.

codes3d/codes3d.py

@@ -438,14 +438,17 @@ def map_non_spatial_eqtls(
             'pval', 'b', 'b_se', 
             'snp_chrom', 'snp_locus', 'maf',
             'gene_chrom', 'gene_start', 'gene_end']
-    eqtl_df = eqtl_df[cols].drop_duplicates()
+    eqtl_df = eqtl_df[cols].dropna().drop_duplicates()
     eqtl_project = tissues['project'].iloc[0]
     if not args.no_afc:
         afc_start_time = time.time()
         eqtl_df['sid'] = eqtl_df['variant_id']
         eqtl_df['sid_chr'] = eqtl_df['snp_chrom']
         eqtl_df['sid_pos'] = eqtl_df['snp_locus']
         eqtl_df['pid'] = eqtl_df['gencode_id']
+        fp = os.path.join(args.output_dir, 'eqtls.txt') 
+        eqtl_df.to_csv(fp, sep='\t', index=False)
+        print(eqtl_df)
         eqtl_df = calc_afc(
             eqtl_df,
             genotypes_fp,

data_preparation/digest_genome.py

@@ -106,9 +106,9 @@ def build_fragment_index(fragment_fp, output_db):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(
         description=(
-            'Digest a genome with a restriction enzyme. ',
-            'Creates a BED file where the fourth column denotes the restriction',
-            ' fragment number of the fragment specified'))
+            """Digest a genome with a restriction enzyme, and create
+            a BED file where the fourth column denotes the restriction 
+            fragment number of the fragment specified"""))
     parser.add_argument(
         "-g", "--genome",
         help="Genome in genbank or fasta format.")
@@ -117,21 +117,20 @@ def build_fragment_index(fragment_fp, output_db):
         help="Is the genome linear? (default: False)")
     parser.add_argument(
         "-e", "--enzyme", nargs='+',
-        help=("The restriction enzyme with which to fragment the genome, ",
-              "for example, `-e MspI`"))
+        help="""The restriction enzyme with which to digest the fragment 
+        for example, `-e MspI`""")
     parser.add_argument(
         "-o", "--output_dir",
-        help=("Output directory for fragment BED and database files. ",
-              "(default: the directory of input genome.)"))
+        help="""Output directory for fragment BED and database 
+        (default: the directory of input genome.""")
     parser.add_argument(
         "-b", "--do_not_index", action="store_true",
-        help=("Suppress building of fragment index from resultant ",
-              "fragmented genome."))
+        help="""Suppress building of fragment index from the fragmented genome.""")
     parser.add_argument(
         "-d", "--output_db",
-        help=("Output file path for fragment BED file and database ",
-              "(default: the name of the input file, with the extension ",
-              "\".db\"/\".bed\", respectively.)"))
+        help="""Output file path for fragment BED file and database
+        (default: the name of the input file, with the extension,
+        "\".db\"/\".bed\", respectively.)""")
     parser.add_argument(
         "-z", "--list_enzymes",
         help="List the available enzymes for digestion.", action="store_true")

data_preparation/init_eqtl_meta.py

@@ -9,8 +9,8 @@
 Create PostgreSQL table of list of eQTL projects. 
 Requires a meta_eqtls.txt
 """
-eqtl_fp = os.path.join(os.path.dirname(__file__), '../lib/meta_eqtls.txt')
+eqtl_fp = os.path.join(os.path.dirname(__file__), '../lib/meta_info/meta_eqtls.txt')
 eqtls = pd.read_csv(eqtl_fp, sep='\t')
 db = create_engine(
-    'postgres://codes3d:[email protected]/codes3d_commons', echo=False)
+    'postgresql://codes3d:[email protected]/codes3d_commons', echo=False)
 eqtls.to_sql('meta_eqtls', con=db, if_exists='replace', index=False)

data_preparation/init_gene_variant_db.py

@@ -82,20 +82,20 @@ def build_gene_table(
     parser = argparse.ArgumentParser(
         description='Build database tables gene and variant fragments')
     parser.add_argument(
-        '-v', '--variants',
+        "-v", "--variants",
         help='The filepath to the variant lookup file')
     parser.add_argument(
-        '-g', '--genes',
-        help=('The filepath to a sorted gene reference file containing ',
-              'id, chrom, start, end, name, and gencode_id columns.',
-              'Note that the id indicates the sorting (chrom, start) ',
-              'order of the file starting at 1.'))
+        "-g", "--genes",
+        help="""The filepath to a sorted gene reference file containing
+        id, chrom, start, end, name, and gencode_id columns.
+        Note that the id indicates the sorting (chrom, start) 
+        order of the file starting at 1.""")
     parser.add_argument(
         "-t", "--table",
-        help='Name of table e.g. variant_lookup_mboi.')
+        help="Name of table e.g. variant_lookup_mboi.")
     parser.add_argument(
         "-u", "--db-url", required=True,
-        help='URL of database e.g posgresql://user:password@hostname/database')
+        help="URL of database e.g posgresql://user:password@hostname/database")
     parser.add_argument(
         "-c", "--config",
         default=os.path.join(os.path.dirname(__file__),

data_preparation/init_hic_meta.py

@@ -29,5 +29,5 @@
     ).drop_duplicates()
 
     db = create_engine(
-        'postgres://codes3d:[email protected]/codes3d_commons', echo=False)
+        'postgresql://codes3d:[email protected]/codes3d_commons', echo=False)
     libraries.drop_duplicates().to_sql('meta_hic', con=db, if_exists='replace')

environment.yaml

@@ -9,12 +9,12 @@ dependencies:
     - numpy=1.19.1
     - pandas=1.0.5
     - pandas-plink #=2.0.4
-    - psycopg2 #=2.8.5
+    - psycopg2 =2.8.5
     - pybedtools #=0.8.1
     - requests #=2.24.0
     - scikits-bootstrap #=1.0.1
-    - SQLAlchemy #=1.3.18
-    - SQLAlchemy-Utils #=0.36.8
+    - SQLAlchemy =1.3.18
+    - SQLAlchemy-Utils =0.36.8
     - statsmodels #=0.11.1
     - pytorch #=1.9.0
     - tqdm #=4.48.0