Merge pull request #5 from flatironinstitute/with_thresholding

With thresholding
flatironinstitute · Aug 20, 2021 · faf5e47 · faf5e47
2 parents 208fbf3 + 2f0b48f
commit faf5e47
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Showing 2 changed files with 17 additions and 5 deletions.
diff --git a/inferelator_prior/network_from_motifs.py b/inferelator_prior/network_from_motifs.py
@@ -116,13 +116,23 @@ def parse_common_arguments(args):
     _intergenic = args.intergenic if args.intergenic is not None else False
 
     if _species is None:
-        _window = args.window_size if args.window_size is not None else DEFAULT_WINDOW
+        try:
+            _window = args.window_size if args.window_size is not None else DEFAULT_WINDOW
+            _use_tss = args.tss
+        except AttributeError:
+            _window, _use_tss = None, None
+
         _tandem = args.tandem if args.tandem is not None else DEFAULT_TANDEM
-        _use_tss = args.tss
     else:
-        _window = SPECIES_MAP[_species]['window'] if args.window_size is None else args.window_size
+        try:
+            _window = SPECIES_MAP[_species]['window'] if args.window_size is None else args.window_size
+            _use_tss = SPECIES_MAP[_species]['use_tss'] if args.tss else args.tss
+        except AttributeError:
+            _window, _use_tss = None, None
+
         _tandem = SPECIES_MAP[_species]['tandem'] if args.tandem is None else args.tandem
-        _use_tss = SPECIES_MAP[_species]['use_tss'] if args.tss else args.tss
+
+
 
     # Load gene and regulator lists
     _gl = pd.read_csv(args.genes, index_col=None, header=None)[0].tolist() if args.genes is not None else None

diff --git a/inferelator_prior/network_from_motifs_fasta.py b/inferelator_prior/network_from_motifs_fasta.py
@@ -15,14 +15,16 @@ def main():
 
     ap.add_argument("-m", "--motif", dest="motif", help="Motif file", metavar="PATH", required=True)
     ap.add_argument("-f", "--fasta", dest="fasta", help="Promoter FASTA file", metavar="FILE", required=True)
+    #ap.add_argument("--scan-threshold", dest="scan_threshold", default="1e-4", help="Threshold for FIMO")
 
     # Process common arguments into values
     add_common_arguments(ap)
     args = ap.parse_args()
-    out_prefix, _window, _tandem, _use_tss, _gl, _tfl, _minfo = parse_common_arguments(args)
+    out_prefix, _window, _tandem, _use_tss, _gl, _tfl, _minfo, _ = parse_common_arguments(args)
 
     _, _, prior_data = build_motif_prior_from_fasta(args.motif, args.fasta,
                                                     num_cores=args.cores,
+                                                    scanner_thresh=args.scan_thresh,
                                                     motif_ic=args.min_ic,
                                                     tandem=_tandem,
                                                     scanner_type=args.scanner,