option to provide a fake tuple counts file for analyze_gene_frequenci…

…es.py
phbradley · Dec 6, 2019 · 025902e · 025902e
1 parent 9c47343
commit 025902e
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/analyze_gene_frequencies.py b/analyze_gene_frequencies.py
@@ -14,6 +14,7 @@
     #p.str('args').unspecified_default().multiple().required()
     p.str('clones_file').required()
     p.str('organism').required()
+    p.str('fake_tuple_counts_file')
 
 
 summary_tsvfile = clones_file[:-4] + '_JS_divergence.tsv'
@@ -113,7 +114,11 @@ def get_jsd_normed( P, Q ):
 ## read the background gene-tuple counts
 all_background_tuple_counts = {}
 
-tuplecountsfile = path_to_current_db_files()+'/nextgen_tuple_counts_v2_{}_max10M.log'.format(organism)
+if fake_tuple_counts_file:
+    tuplecountsfile = fake_tuple_counts_file
+    assert exists(fake_tuple_counts_file)
+else:
+    tuplecountsfile = path_to_current_db_files()+'/nextgen_tuple_counts_v2_{}_max10M.log'.format(organism)
 
 if exists( tuplecountsfile ):
     Log('reading {}'.format( tuplecountsfile ))

diff --git a/make_10x_clones_file.py b/make_10x_clones_file.py
@@ -136,7 +136,6 @@ def make_clones_file( organism, outfile, clonotype2tcrs, clonotype2barcodes ):
     outmap = open(bc_mapfile,'w')
     outmap.write('clone_id\tbarcodes\n')
 
-    out = open(tmpfile,'w')
     outfields = 'clone_id subject clone_size va_gene ja_gene vb_gene jb_gene cdr3a cdr3a_nucseq cdr3b cdr3b_nucseq'\
         .split()
     extra_fields = 'alpha_umi beta_umi num_alphas num_betas'.split()