@@ -24,9 +24,7 @@ def filter_entry(entry, tum_id, norm_id, tid_idx, nid_idx, v_idx, h_idx, maf_exc
2424 return None
2525
2626
27- def process_maf (
28- maf_fn , new_maf , maf_exc , tum_id , norm_id
29- ):
27+ def process_maf (maf_fn , new_maf , maf_exc , tum_id , norm_id ):
3028 """
3129 Iterate over maf file, skipping header lines since the files are being merged.
3230 With possiblility of mixed source, search headers
@@ -69,9 +67,7 @@ def process_maf(
6967 cur_maf .close ()
7068
7169
72- def process_tbl (
73- cbio_dx , file_meta_dict , print_head
74- ):
70+ def process_tbl (cbio_dx , file_meta_dict , print_head ):
7571 """
7672 Probaby a less likely scenario, but can split out into multiple projects based on dict
7773 """
@@ -84,28 +80,10 @@ def process_tbl(
8480 for cbio_tum_id in file_meta_dict [cbio_dx ]:
8581 cbio_norm_id = file_meta_dict [cbio_dx ][cbio_tum_id ]["cbio_norm_id" ]
8682 fname = file_meta_dict [cbio_dx ][cbio_tum_id ]["fname" ]
87- sys .stderr .write (
88- "Found relevant maf to process for "
89- + " "
90- + cbio_tum_id
91- + " "
92- + cbio_norm_id
93- + " "
94- + file_meta_dict [cbio_dx ][cbio_tum_id ]["kf_tum_id" ]
95- + " "
96- + file_meta_dict [cbio_dx ][cbio_tum_id ]["kf_norm_id" ]
97- + " "
98- + fname
99- + "\n "
100- )
101- sys .stderr .flush ()
102- process_maf (
103- maf_dir + fname ,
104- new_maf ,
105- maf_exc ,
106- cbio_tum_id ,
107- cbio_norm_id ,
108- )
83+ print ("Found relevant maf to process for {} {} {} {} {}" .format (
84+ cbio_tum_id , cbio_norm_id , file_meta_dict [cbio_dx ][cbio_tum_id ]["kf_tum_id" ], file_meta_dict [cbio_dx ][cbio_tum_id ]["kf_norm_id" ], fname ),
85+ file = sys .stderr )
86+ process_maf (maf_dir + fname , new_maf , maf_exc , cbio_tum_id , cbio_norm_id )
10987 x += 1
11088 sys .stderr .write (
11189 "Completed processing " + str (x ) + " entries in " + cbio_dx + "\n "
@@ -130,7 +108,7 @@ def process_tbl(
130108 "-i" , "--header" , action = "store" , dest = "header" , help = "File with maf header only"
131109 )
132110 parser .add_argument (
133- "-m" , "--maf-dir " , action = "store" , dest = "maf_dir " , help = "maf file directory "
111+ "-m" , "--maf-dirs " , action = "store" , dest = "maf_dirs " , help = "comma-separated list of maf file directories "
134112 )
135113 parser .add_argument (
136114 "-j" ,
@@ -155,10 +133,21 @@ def process_tbl(
155133 args = parser .parse_args ()
156134 with open (args .config_file ) as f :
157135 config_data = json .load (f )
158- # get maf file ext
159- maf_dir = args .maf_dir
160- if maf_dir [- 1 ] != "/" :
161- maf_dir += "/"
136+ # Create symlinks to mafs in one place for ease of processing
137+ maf_dir = "MAFS/"
138+ maf_dirs_in = args .maf_dirs
139+ print ("Symlinking maf files from {} to {}" .format (maf_dirs_in , maf_dir ), file = sys .stderr )
140+ os .makedirs ("MAFS" , exist_ok = True )
141+ for dirname in maf_dirs_in .split ("," ):
142+ abs_path = os .path .abspath (dirname )
143+ for fname in os .listdir (dirname ):
144+ try :
145+ src = os .path .join (abs_path , fname )
146+ dest = os .path .join (maf_dir , fname )
147+ os .symlink (src , dest )
148+ except Exception as e :
149+ print (e , file = sys .stderr )
150+ print ("Could not sym link {} in {}" .format (fname , dirname ))
162151 # If DGD maf only, else if both, dgd maf wil be handled separately, or not at all if no dgd and kf only
163152
164153 file_meta_dict = get_file_metadata (args .table , "DGD_MAF" )
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