diff --git a/README.rst b/README.rst index 06b473b1..16f16735 100644 --- a/README.rst +++ b/README.rst @@ -5,7 +5,7 @@ +-------------------------------------+---------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------+ | | .. image:: https://travis-ci.org/3DGenomes/TADbit.png?branch=master | .. image:: https://coveralls.io/repos/github/3DGenomes/tadbit/badge.svg?branch=master :target: https://coveralls.io/github/3DGenomes/tadbit?branch=master | -| Current version: 0.1_alpha.689 | :target: https://travis-ci.org/3DGenomes/TADbit | :target: https://coveralls.io/github/3DGenomes/tadbit?branch=master | +| Current version: 0.1_alpha.690 | :target: https://travis-ci.org/3DGenomes/TADbit | :target: https://coveralls.io/github/3DGenomes/tadbit?branch=master | | | | | +-------------------------------------+---------------------------------------------------------------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/_pytadbit/_version.py b/_pytadbit/_version.py index 1935a161..17de5ecd 100644 --- a/_pytadbit/_version.py +++ b/_pytadbit/_version.py @@ -1 +1 @@ -__version__ = "0.1_alpha.689" \ No newline at end of file +__version__ = "0.1_alpha.690" \ No newline at end of file diff --git a/_pytadbit/tools/tadbit_normalize.py b/_pytadbit/tools/tadbit_normalize.py index fedf8043..e6dcb004 100644 --- a/_pytadbit/tools/tadbit_normalize.py +++ b/_pytadbit/tools/tadbit_normalize.py @@ -167,6 +167,7 @@ def run(opts): save_to_db (opts, cis_trans_N_D, cis_trans_N_d, cis_trans_n_D, cis_trans_n_d, a2, bad_columns_file, bias_file, inter_vs_gcoord, mreads, + len(hic_data.bads.keys()), len(hic_data), intra_dir_nrm_fig, intra_dir_nrm_txt, inter_dir_nrm_fig, inter_dir_nrm_txt, genom_map_nrm_fig, genom_map_nrm_txt, @@ -177,6 +178,7 @@ def run(opts): def save_to_db(opts, cis_trans_N_D, cis_trans_N_d, cis_trans_n_D, cis_trans_n_d, a2, bad_columns_file, bias_file, inter_vs_gcoord, mreads, + nbad_columns, ncolumns, intra_dir_nrm_fig, intra_dir_nrm_txt, inter_dir_nrm_fig, inter_dir_nrm_txt, genom_map_nrm_fig, genom_map_nrm_txt, @@ -195,6 +197,8 @@ def save_to_db(opts, cis_trans_N_D, cis_trans_N_d, cis_trans_n_D, cis_trans_n_d, (Id integer primary key, JOBid int, Input int, + N_columns int, + N_filtered int, CisTrans_nrm_all real, CisTrans_nrm_out real, CisTrans_raw_all real, @@ -251,10 +255,10 @@ def save_to_db(opts, cis_trans_N_D, cis_trans_N_d, cis_trans_n_D, cis_trans_n_d, cur.execute(""" insert into NORMALIZE_OUTPUTs - (Id , JOBid, Input, CisTrans_nrm_all, CisTrans_nrm_out, CisTrans_raw_all, CisTrans_raw_out, Slope_700kb_10Mb, Resolution, Factor) + (Id , JOBid, Input, N_columns, N_filtered, CisTrans_nrm_all, CisTrans_nrm_out, CisTrans_raw_all, CisTrans_raw_out, Slope_700kb_10Mb, Resolution, Factor) values - (NULL, %d, %d, %f, %f, %f, %f, %f, %d, %f) - """ % (jobid, input_bed, cis_trans_N_D, cis_trans_N_d, cis_trans_n_D, cis_trans_n_d, a2, opts.reso, opts.factor)) + (NULL, %d, %d, %d, %d, %f, %f, %f, %f, %f, %d, %f) + """ % (jobid, input_bed, ncolumns, nbad_columns, cis_trans_N_D, cis_trans_N_d, cis_trans_n_D, cis_trans_n_d, a2, opts.reso, opts.factor)) print_db(cur, 'MAPPED_INPUTs') print_db(cur, 'PATHs') print_db(cur, 'MAPPED_OUTPUTs')