diff --git a/analyze_gene_frequencies.py b/analyze_gene_frequencies.py index d38ba41..e8051d0 100644 --- 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 index ea4ed7e..3afc014 100644 --- 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()