/Users/tstoeger/apps/anaconda/anaconda3/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
some of the ids being used to subset the data are not present in the metadata for the file being parsed - mismatch_ids: {'LJP009_HT29_24H:A03', 'LJP007_SKL.C_24H:A03', 'LJP008_PC3_24H:G08', 'LJP008_HCC515_24H:G07', 'LJP008_HA1E_24H:G07', 'LJP008_ASC_24H:G10', 'LJP008_NPC.CAS9_24H:A03', 'LJP008_SKL_24H:G08', 'LPROT003_PC3_6H:O11', 'LJP008_A549_24H:G09', 'LJP008_HCC515_24H:G10', 'LJP008_MCF7_24H:G07', 'LJP008_PC3_24H:G11', 'LJP008_HUVEC_24H:G11', 'LJP008_PC3_24H:A03', 'LJP009_A375_24H:A03', 'LJP008_ASC_24H:G11', 'LJP008_A549_24H:G11', 'LJP008_HEPG2_24H:G11', 'LJP008_HT29_24H:G07', 'LPROT003_A549_6H:O12', 'LJP008_HUVEC_24H:G07', 'LJP008_HUVEC_24H:G10', 'LJP008_HME1_24H:G12', 'LJP007_A375_24H:A03', 'LJP008_SKL.C_24H:G09', 'LJP008_NPC.CAS9_24H:G09', 'LJP007_HEPG2_24H:A03', 'LJP007_CD34_24H:A03', 'LPROT003_NPC_6H:P11', 'LJP008_HT29_24H:G12', 'LPROT001_A375_6H:P11', 'LJP008_HUVEC_24H:G12', 'LJP008_PC3_24H:G07', 'LJP008_ASC.C_24H:G11', 'LJP008_NEU_24H:G11', 'LJP008_SKL_24H:G10', 'LPROT003_A375_6H:P08', 'LPROT002_MCF7_6H:P12', 'LJP008_NEU_24H:G08', 'LJP008_HCC515_24H:G09', 'LJP008_ASC_24H:G08', 'LJP008_HME1_24H:A03', 'LJP008_NEU_24H:G09', 'LPROT001_PC3_6H:P10', 'LJP008_HEPG2_24H:G08', 'LJP008_HCC515_24H:A03', 'LJP009_SKL.C_24H:A03', 'LPROT003_A549_6H:O08', 'LJP009_HCC515_24H:A03', 'LJP008_ASC.C_24H:G10', 'LJP008_SKL.C_24H:G08', 'LJP008_CD34_24H:G12', 'LJP007_MCF7_24H:A03', 'LJP008_NPC_24H:G08', 'LJP008_SKL.C_24H:A03', 'LJP008_HEPG2_24H:G09', 'LJP008_HT29_24H:A03', 'LJP008_HA1E_24H:A03', 'LJP008_NPC_24H:G12', 'LJP008_A375_24H:G11', 'LJP009_CD34_24H:A03', 'LJP007_HME1_24H:A03', 'LJP009_MCF7_24H:A03', 'LJP008_A549_24H:G07', 'LJP008_NEU_24H:G12', 'LJP007_HT29_24H:A03', 'LJP008_HUVEC_24H:G08', 'LJP008_HUVEC_24H:A03', 'LJP008_A375_24H:G08', 'LJP008_HT29_24H:G10', 'LJP008_NPC.CAS9_24H:G11', 'LJP008_A375_24H:G09', 'LJP008_NEU_24H:G07', 'LJP008_SKL.C_24H:G10', 'LJP008_NEU_24H:A03', 'LJP009_NPC.CAS9_24H:A03', 'LPROT002_A549_6H:O09', 'LJP008_CD34_24H:G11', 'LJP008_NPC.CAS9_24H:G12', 'LJP009_ASC_24H:A03', 'LJP008_ASC_24H:G09', 'LJP008_HA1E_24H:G08', 'LJP008_SKL_24H:G07', 'LPROT001_MCF7_6H:O11', 'LJP008_A375_24H:A03', 'LJP008_CD34_24H:G07', 'LJP008_NPC.TAK_24H:G08', 'LPROT001_MCF7_6H:O07', 'LJP008_ASC_24H:A03', 'LJP008_PC3_24H:G10', 'LPROT001_A375_6H:P07', 'LPROT003_A375_6H:P10', 'LJP009_ASC.C_24H:A03', 'LPROT002_NPC.TAK_6H:O10', 'LJP009_SKL_24H:A03', 'LJP008_HT29_24H:G08', 'LJP008_PC3_24H:G09', 'LJP008_HCC515_24H:G08', 'LJP008_HME1_24H:G07', 'LJP008_SKL.C_24H:G07', 'LJP008_ASC.C_24H:G07', 'LJP008_ASC.C_24H:G09', 'LJP008_A375_24H:G12', 'LPROT003_NPC_6H:P09', 'LJP008_HT29_24H:G09', 'LPROT001_MCF7_6H:O09', 'LJP009_HA1E_24H:A03', 'LPROT003_PC3_6H:O07', 'LJP008_CD34_24H:A03', 'LJP007_A549_24H:A03', 'LJP008_HA1E_24H:G11', 'LJP007_HUES3_24H:A03', 'LPROT002_A375_6H:P07', 'LJP008_CD34_24H:G08', 'LJP008_MCF7_24H:G11', 'LJP008_A549_24H:G08', 'LJP009_HEPG2_24H:A03', 'LPROT001_PC3_6H:P08', 'LPROT003_NPC_6H:P07', 'LJP008_HME1_24H:G10', 'LJP007_SKL_24H:A03', 'LJP008_HA1E_24H:G10', 'LJP008_PC3_24H:G12', 'LJP008_SKL_24H:G09', 'LPROT001_PC3_6H:P12', 'LJP008_ASC_24H:G07', 'LPROT002_A375_6H:P11', 'LPROT003_A375_6H:P12', 'LJP008_NPC.TAK_24H:G11', 'LJP009_HUVEC_24H:A03', 'LJP009_HME1_24H:A03', 'LJP008_HCC515_24H:G12', 'LJP007_MNEU.E_24H:A03', 'LJP008_SKL_24H:G12', 'LJP008_A375_24H:G10', 'LJP009_NPC_24H:A03', 'LJP008_CD34_24H:G09', 'LJP008_HME1_24H:G09', 'LJP008_NEU_24H:G10', 'LJP008_MCF7_24H:G10', 'LJP008_A549_24H:A03', 'LJP008_HEPG2_24H:A03', 'LJP008_HME1_24H:G08', 'LJP008_NPC_24H:G07', 'LJP008_NPC.CAS9_24H:G08', 'LPROT002_MCF7_6H:P08', 'LJP008_NPC_24H:G09', 'LPROT001_A375_6H:P09', 'LJP008_ASC.C_24H:G08', 'LJP009_PC3_24H:A03', 'LJP008_HT29_24H:G11', 'LJP008_MCF7_24H:A03', 'LJP007_ASC_24H:A03', 'LJP008_NPC.CAS9_24H:G07', 'LPROT002_A549_6H:O07', 'LJP009_NPC.TAK_24H:A03', 'LJP007_NPC.TAK_24H:A03', 'LJP008_HEPG2_24H:G12', 'LJP008_NPC.CAS9_24H:G10', 'LPROT002_NPC.TAK_6H:O12', 'LJP008_NPC.TAK_24H:G10', 'LJP008_SKL_24H:A03', 'LJP008_SKL.C_24H:G11', 'LPROT001_NPC.TAK_6H:O10', 'LJP008_HCC515_24H:G11', 'LJP008_SKL.C_24H:G12', 'LJP008_ASC.C_24H:G12', 'LJP008_NPC_24H:A03', 'LJP007_NPC_24H:A03', 'LJP008_NPC.TAK_24H:G12', 'LPROT002_A549_6H:O11', 'LJP008_NPC.TAK_24H:A03', 'LJP008_HME1_24H:G11', 'LJP007_ASC.C_24H:A03', 'LJP008_MCF7_24H:G08', 'LJP007_HA1E_24H:A03', 'LJP008_MCF7_24H:G09', 'LJP008_ASC.C_24H:A03', 'LJP008_SKL_24H:G11', 'LJP008_A549_24H:G12', 'LPROT003_PC3_6H:O09', 'LJP007_HUVEC_24H:A03', 'LJP008_NPC_24H:G11', 'LPROT003_A549_6H:O10', 'LJP008_NPC.TAK_24H:G09', 'LJP008_HUVEC_24H:G09', 'LPROT001_NPC.TAK_6H:O08', 'LJP007_NEU_24H:A03', 'LJP008_NPC_24H:G10', 'LJP008_HA1E_24H:G09', 'LJP008_HEPG2_24H:G07', 'LJP008_A375_24H:G07', 'LJP008_MCF7_24H:G12', 'LJP008_NPC.TAK_24H:G07', 'LJP008_HEPG2_24H:G10', 'LPROT001_NPC.TAK_6H:O12', 'LJP007_JURKAT_24H:A03', 'LJP009_A549_24H:A03', 'LJP007_PC3_24H:A03', 'LPROT002_A375_6H:P09', 'LPROT002_NPC.TAK_6H:O08', 'LJP007_NPC.CAS9_24H:A03', 'LPROT002_MCF7_6H:P10', 'LJP008_HA1E_24H:G12', 'LJP009_NEU_24H:A03', 'LJP008_CD34_24H:G10', 'LJP007_HCC515_24H:A03', 'LJP008_ASC_24H:G12', 'LJP008_A549_24H:G10'}
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
<ipython-input-3-f03c31e62771> in <module>()
2 vorinostat_only_gctoo = parse(
3 "GSE70138_Broad_LINCS_Level5_COMPZ_n118050x12328.gctx", # updated file name
----> 4 cid=vorinostat_ids)
~/apps/anaconda/anaconda3/lib/python3.6/site-packages/cmapPy/pandasGEXpress/parse.py in parse(file_path, convert_neg_666, rid, cid, ridx, cidx, row_meta_only, col_meta_only, make_multiindex)
60 elif file_path.endswith(".gctx"):
61 curr = parse_gctx.parse(file_path, convert_neg_666, rid, cid, ridx, cidx, row_meta_only, col_meta_only,
---> 62 make_multiindex)
63 else:
64 err_msg = "File to parse must be .gct or .gctx!"
~/apps/anaconda/anaconda3/lib/python3.6/site-packages/cmapPy/pandasGEXpress/parse_gctx.py in parse(gctx_file_path, convert_neg_666, rid, cid, ridx, cidx, row_meta_only, col_meta_only, make_multiindex)
101
102 # validate optional input ids & get indexes to subset by
--> 103 (sorted_ridx, sorted_cidx) = check_and_order_id_inputs(rid, ridx, cid, cidx, row_meta, col_meta)
104
105 data_dset = gctx_file[data_node]
~/apps/anaconda/anaconda3/lib/python3.6/site-packages/cmapPy/pandasGEXpress/parse_gctx.py in check_and_order_id_inputs(rid, ridx, cid, cidx, row_meta_df, col_meta_df)
140 ordered_ridx = get_ordered_idx(row_type, row_ids, row_meta_df)
141
--> 142 col_ids = check_and_convert_ids(col_type, col_ids, col_meta_df)
143 ordered_cidx = get_ordered_idx(col_type, col_ids, col_meta_df)
144 return (ordered_ridx, ordered_cidx)
~/apps/anaconda/anaconda3/lib/python3.6/site-packages/cmapPy/pandasGEXpress/parse_gctx.py in check_and_convert_ids(id_type, id_list, meta_df)
173 if id_type == "id":
174 id_list = convert_ids_to_meta_type(id_list, meta_df)
--> 175 check_id_validity(id_list, meta_df)
176 else:
177 check_idx_validity(id_list, meta_df)
~/apps/anaconda/anaconda3/lib/python3.6/site-packages/cmapPy/pandasGEXpress/parse_gctx.py in check_id_validity(id_list, meta_df)
189 mismatch_ids)
190 logger.error(msg)
--> 191 raise Exception("parse_gctx check_id_validity " + msg)
192
193
Exception: parse_gctx check_id_validity some of the ids being used to subset the data are not present in the metadata for the file being parsed - mismatch_ids: {'LJP009_HT29_24H:A03', 'LJP007_SKL.C_24H:A03', 'LJP008_PC3_24H:G08', 'LJP008_HCC515_24H:G07', 'LJP008_HA1E_24H:G07', 'LJP008_ASC_24H:G10', 'LJP008_NPC.CAS9_24H:A03', 'LJP008_SKL_24H:G08', 'LPROT003_PC3_6H:O11', 'LJP008_A549_24H:G09', 'LJP008_HCC515_24H:G10', 'LJP008_MCF7_24H:G07', 'LJP008_PC3_24H:G11', 'LJP008_HUVEC_24H:G11', 'LJP008_PC3_24H:A03', 'LJP009_A375_24H:A03', 'LJP008_ASC_24H:G11', 'LJP008_A549_24H:G11', 'LJP008_HEPG2_24H:G11', 'LJP008_HT29_24H:G07', 'LPROT003_A549_6H:O12', 'LJP008_HUVEC_24H:G07', 'LJP008_HUVEC_24H:G10', 'LJP008_HME1_24H:G12', 'LJP007_A375_24H:A03', 'LJP008_SKL.C_24H:G09', 'LJP008_NPC.CAS9_24H:G09', 'LJP007_HEPG2_24H:A03', 'LJP007_CD34_24H:A03', 'LPROT003_NPC_6H:P11', 'LJP008_HT29_24H:G12', 'LPROT001_A375_6H:P11', 'LJP008_HUVEC_24H:G12', 'LJP008_PC3_24H:G07', 'LJP008_ASC.C_24H:G11', 'LJP008_NEU_24H:G11', 'LJP008_SKL_24H:G10', 'LPROT003_A375_6H:P08', 'LPROT002_MCF7_6H:P12', 'LJP008_NEU_24H:G08', 'LJP008_HCC515_24H:G09', 'LJP008_ASC_24H:G08', 'LJP008_HME1_24H:A03', 'LJP008_NEU_24H:G09', 'LPROT001_PC3_6H:P10', 'LJP008_HEPG2_24H:G08', 'LJP008_HCC515_24H:A03', 'LJP009_SKL.C_24H:A03', 'LPROT003_A549_6H:O08', 'LJP009_HCC515_24H:A03', 'LJP008_ASC.C_24H:G10', 'LJP008_SKL.C_24H:G08', 'LJP008_CD34_24H:G12', 'LJP007_MCF7_24H:A03', 'LJP008_NPC_24H:G08', 'LJP008_SKL.C_24H:A03', 'LJP008_HEPG2_24H:G09', 'LJP008_HT29_24H:A03', 'LJP008_HA1E_24H:A03', 'LJP008_NPC_24H:G12', 'LJP008_A375_24H:G11', 'LJP009_CD34_24H:A03', 'LJP007_HME1_24H:A03', 'LJP009_MCF7_24H:A03', 'LJP008_A549_24H:G07', 'LJP008_NEU_24H:G12', 'LJP007_HT29_24H:A03', 'LJP008_HUVEC_24H:G08', 'LJP008_HUVEC_24H:A03', 'LJP008_A375_24H:G08', 'LJP008_HT29_24H:G10', 'LJP008_NPC.CAS9_24H:G11', 'LJP008_A375_24H:G09', 'LJP008_NEU_24H:G07', 'LJP008_SKL.C_24H:G10', 'LJP008_NEU_24H:A03', 'LJP009_NPC.CAS9_24H:A03', 'LPROT002_A549_6H:O09', 'LJP008_CD34_24H:G11', 'LJP008_NPC.CAS9_24H:G12', 'LJP009_ASC_24H:A03', 'LJP008_ASC_24H:G09', 'LJP008_HA1E_24H:G08', 'LJP008_SKL_24H:G07', 'LPROT001_MCF7_6H:O11', 'LJP008_A375_24H:A03', 'LJP008_CD34_24H:G07', 'LJP008_NPC.TAK_24H:G08', 'LPROT001_MCF7_6H:O07', 'LJP008_ASC_24H:A03', 'LJP008_PC3_24H:G10', 'LPROT001_A375_6H:P07', 'LPROT003_A375_6H:P10', 'LJP009_ASC.C_24H:A03', 'LPROT002_NPC.TAK_6H:O10', 'LJP009_SKL_24H:A03', 'LJP008_HT29_24H:G08', 'LJP008_PC3_24H:G09', 'LJP008_HCC515_24H:G08', 'LJP008_HME1_24H:G07', 'LJP008_SKL.C_24H:G07', 'LJP008_ASC.C_24H:G07', 'LJP008_ASC.C_24H:G09', 'LJP008_A375_24H:G12', 'LPROT003_NPC_6H:P09', 'LJP008_HT29_24H:G09', 'LPROT001_MCF7_6H:O09', 'LJP009_HA1E_24H:A03', 'LPROT003_PC3_6H:O07', 'LJP008_CD34_24H:A03', 'LJP007_A549_24H:A03', 'LJP008_HA1E_24H:G11', 'LJP007_HUES3_24H:A03', 'LPROT002_A375_6H:P07', 'LJP008_CD34_24H:G08', 'LJP008_MCF7_24H:G11', 'LJP008_A549_24H:G08', 'LJP009_HEPG2_24H:A03', 'LPROT001_PC3_6H:P08', 'LPROT003_NPC_6H:P07', 'LJP008_HME1_24H:G10', 'LJP007_SKL_24H:A03', 'LJP008_HA1E_24H:G10', 'LJP008_PC3_24H:G12', 'LJP008_SKL_24H:G09', 'LPROT001_PC3_6H:P12', 'LJP008_ASC_24H:G07', 'LPROT002_A375_6H:P11', 'LPROT003_A375_6H:P12', 'LJP008_NPC.TAK_24H:G11', 'LJP009_HUVEC_24H:A03', 'LJP009_HME1_24H:A03', 'LJP008_HCC515_24H:G12', 'LJP007_MNEU.E_24H:A03', 'LJP008_SKL_24H:G12', 'LJP008_A375_24H:G10', 'LJP009_NPC_24H:A03', 'LJP008_CD34_24H:G09', 'LJP008_HME1_24H:G09', 'LJP008_NEU_24H:G10', 'LJP008_MCF7_24H:G10', 'LJP008_A549_24H:A03', 'LJP008_HEPG2_24H:A03', 'LJP008_HME1_24H:G08', 'LJP008_NPC_24H:G07', 'LJP008_NPC.CAS9_24H:G08', 'LPROT002_MCF7_6H:P08', 'LJP008_NPC_24H:G09', 'LPROT001_A375_6H:P09', 'LJP008_ASC.C_24H:G08', 'LJP009_PC3_24H:A03', 'LJP008_HT29_24H:G11', 'LJP008_MCF7_24H:A03', 'LJP007_ASC_24H:A03', 'LJP008_NPC.CAS9_24H:G07', 'LPROT002_A549_6H:O07', 'LJP009_NPC.TAK_24H:A03', 'LJP007_NPC.TAK_24H:A03', 'LJP008_HEPG2_24H:G12', 'LJP008_NPC.CAS9_24H:G10', 'LPROT002_NPC.TAK_6H:O12', 'LJP008_NPC.TAK_24H:G10', 'LJP008_SKL_24H:A03', 'LJP008_SKL.C_24H:G11', 'LPROT001_NPC.TAK_6H:O10', 'LJP008_HCC515_24H:G11', 'LJP008_SKL.C_24H:G12', 'LJP008_ASC.C_24H:G12', 'LJP008_NPC_24H:A03', 'LJP007_NPC_24H:A03', 'LJP008_NPC.TAK_24H:G12', 'LPROT002_A549_6H:O11', 'LJP008_NPC.TAK_24H:A03', 'LJP008_HME1_24H:G11', 'LJP007_ASC.C_24H:A03', 'LJP008_MCF7_24H:G08', 'LJP007_HA1E_24H:A03', 'LJP008_MCF7_24H:G09', 'LJP008_ASC.C_24H:A03', 'LJP008_SKL_24H:G11', 'LJP008_A549_24H:G12', 'LPROT003_PC3_6H:O09', 'LJP007_HUVEC_24H:A03', 'LJP008_NPC_24H:G11', 'LPROT003_A549_6H:O10', 'LJP008_NPC.TAK_24H:G09', 'LJP008_HUVEC_24H:G09', 'LPROT001_NPC.TAK_6H:O08', 'LJP007_NEU_24H:A03', 'LJP008_NPC_24H:G10', 'LJP008_HA1E_24H:G09', 'LJP008_HEPG2_24H:G07', 'LJP008_A375_24H:G07', 'LJP008_MCF7_24H:G12', 'LJP008_NPC.TAK_24H:G07', 'LJP008_HEPG2_24H:G10', 'LPROT001_NPC.TAK_6H:O12', 'LJP007_JURKAT_24H:A03', 'LJP009_A549_24H:A03', 'LJP007_PC3_24H:A03', 'LPROT002_A375_6H:P09', 'LPROT002_NPC.TAK_6H:O08', 'LJP007_NPC.CAS9_24H:A03', 'LPROT002_MCF7_6H:P10', 'LJP008_HA1E_24H:G12', 'LJP009_NEU_24H:A03', 'LJP008_CD34_24H:G10', 'LJP007_HCC515_24H:A03', 'LJP008_ASC_24H:G12', 'LJP008_A549_24H:G10'}