Merge pull request #70 from oicr-gsi/GBS-5307

added optional lane number in input library file

README.md

@@ -61,7 +61,7 @@ This parameter appends the suffix to the run folder name containing the file lin
 
 - libraries `-l/ --libraries` :
 Optional parameter. Libraries approved for release.
-Tab-delimited file with 2 columns with library and run Ids. 
+Tab-delimited file with 2 or 3 columns, without header. The First column is always the library identifier, the last column (2nd or 3rd) is always the run identifier. The optional column is the lane number. The lane number is either omitted or specified for all libraries. If the lane number is omitted, all the lanes for a given library and run will be linked. 
 
 - exclude `-e/ --exclude`:
 Optional parameter. Libraries excluded from release.

dare.py

@@ -29,30 +29,43 @@ def get_libraries(library_file):
     '''
     (str) -> dict
     
-    Returns a dictionary with library, run key, value pairs.
+    Returns a dictionary with library, run or libray, lane, run key, value pairs.
     Note: runs need to be specified for all libraries
     
     Parameters
     ----------
     - sample_file (str): Path to sample file. Sample file is a tab delimited file
-                         that includes 2 columns. The first column is always 
-                         the library alias, and the second is run id
+                         that includes 2 or 3 columns columns. The first column is always 
+                         the library alias, and the second is lane or run id
     '''
     D = {}
 
     infile = open(library_file)
-    for line in infile:
-        line = line.rstrip()
-        if line != '':
-            line = line.split()
-            if len(line) != 2:
-                raise ValueError('Run id must be specified for all libraries')        
-            if line[0] in D:
-                D[line[0]].append(line[1])
-            else:
-                D[line[0]] = [line[1]]
+    content = infile.read().strip().split('\n')
+    for i in range(len(content)):
+        content[i] = content[i].split('\t')
     infile.close()
-
+
+    # check that all lines have the same number of columns
+    if all(map(lambda x: len(x) == 2 or len(x) == 3 , content)) == False:
+        raise ValueError('File must have 2 or 3 columns')
+    if all(map(lambda x: '_' in x[-1], content)) == False:
+        raise ValueError('Run id must be the last column')
+
+    for i in content:
+        library = i[0]
+        run = i[-1]
+        if len(i) == 2:
+            lane = ''
+        elif len(i) == 3:
+            lane = int(i[1])
+
+        if library not in D:
+            D[library] = {}
+        if run not in D[library]:
+            D[library][run] = []
+        D[library][run].append(lane)
+
     return D
 
 
@@ -325,18 +338,26 @@ def exclude_non_specified_libraries(files, valid_libraries):
     for file_swid in files:
         libraries = files[file_swid]['library']
         runs = files[file_swid]['run_id']
-        if len(libraries) != 1 and len(runs) != 1:
+        lanes = files[file_swid]['lane']
+        if len(libraries) != 1 and len(runs) != 1 and len(lanes) != 1:
             sys.exit('Use option -a to link merging-workflows output files')
-        library, run = libraries[0], runs[0]
+        library, run, lane = libraries[0], runs[0], int(lanes[0])
+        # exclude file if libraries is not included in the input sheet
         if library not in valid_libraries:
             exclude.append(file_swid)
+        # exclude file if run is not included in the input sheet
         elif run not in valid_libraries[library]:
             exclude.append(file_swid)
-
+        # exclude file if lane is specified but not included
+        elif '' not in valid_libraries[library][run] and lane not in valid_libraries[library][run]:
+            exclude.append(file_swid)
+
     exclude = list(set(exclude))    
+
     for file_swid in files:
         if file_swid not in exclude:
             D[file_swid] = files[file_swid]        
+
     return D
 
 
@@ -503,9 +524,10 @@ def collect_files_for_release(files, release_files, nomiseq, runs, libraries, ex
     - nomiseq (bool): Exclude MiSeq runs if True
     - runs (list | None): List of run IDs. Include one or more run Id separated by white space.
                           Other runs are ignored if provided
-    - libraries (str | None): Path to 1 or 2 columns tab-delimited file with library IDs.
-                              The first column is always the library alias (TGL17_0009_Ct_T_PE_307_CM).
-                              The second and optional column is the library aliquot ID (eg. LDI32439).
+    - libraries (str | None): Path to 2 or 3 columns tab-delimited file with library IDs.
+                              The first column is always the library alias.
+                              The second column is the lane number or the run identifier.
+                              The last column is always the run identifier
                               Only the samples with these library aliases are used if provided'
     - exclude (str | None): File with sample name or libraries to exclude from the release
     '''