Remove deepBlue support from plotFingerprint, in prep for merging

deeptools/plotFingerprint.py

@@ -16,7 +16,6 @@
 
 import deeptools.countReadsPerBin as countR
 from deeptools import parserCommon
-import deeptools.deepBlue as db
 
 old_settings = np.seterr(all='ignore')
 
@@ -27,10 +26,9 @@ def parse_arguments(args=None):
     output_args = get_output_args()
     optional_args = get_optional_args()
     read_options_parser = parserCommon.read_options()
-    deepBlue_optional_parser = parserCommon.deepBlueOptionalArgs()
     parser = argparse.ArgumentParser(
         parents=[required_args, output_args, read_options_parser,
-                 optional_args, deepBlue_optional_parser, parent_parser],
+                 optional_args, parent_parser],
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description='This tool samples indexed BAM files '
         'and plots a profile of cumulative read coverages for each. '
@@ -346,32 +344,6 @@ def getExpected(mu):
 def main(args=None):
     args = process_args(args)
 
-    # Preload deepBlue files, which need to then be deleted
-    deepBlueFiles = []
-    for idx, fname in enumerate(args.bamfiles):
-        if db.isDeepBlue(fname):
-            deepBlueFiles.append([fname, idx])
-    if len(deepBlueFiles) > 0:
-        sys.stderr.write("Preloading the following deepBlue files: {}\n".format(",".join([x[0] for x in deepBlueFiles])))
-        foo = db.deepBlue(deepBlueFiles[0][0], url=args.deepBlueURL, userKey=args.userKey)
-        regs = db.makeChromTiles(foo)
-        for x in deepBlueFiles:
-            x.extend([args, regs])
-        if len(deepBlueFiles) > 1 and args.numberOfProcessors > 1:
-            pool = multiprocessing.Pool(args.numberOfProcessors)
-            res = pool.map_async(db.preloadWrapper, deepBlueFiles).get(9999999)
-        else:
-            res = list(map(db.preloadWrapper, deepBlueFiles))
-
-        # substitute the file names with the temp files
-        for (ftuple, r) in zip(deepBlueFiles, res):
-            if ftuple[1] == 0:
-                args.bigwig1 = r
-            else:
-                args.bigwig2 = r
-        deepBlueFiles = [[x[0], x[1]] for x in deepBlueFiles]
-        del regs
-
     cr = countR.CountReadsPerBin(
         args.bamfiles,
         args.binSize,
@@ -454,14 +426,6 @@ def main(args=None):
             args.outQualityMetrics.write("\n")
         args.outQualityMetrics.close()
 
-    # Clean up temporary bigWig files, if applicable
-    if not args.deepBlueKeepTemp:
-        for k, v in deepBlueFiles:
-            os.remove(args.bamfiles[v])
-    else:
-        for k, v in deepBlueFiles:
-            print("{} is stored in {}".format(k, args.bamfiles[v]))
-
 
 if __name__ == "__main__":
     main()