Merge pull request #1282 from deeptools/plotheatmap_ymax_mpl

drop deepblue support, heatmapper constrained layout,

CHANGES.txt

@@ -1,3 +1,15 @@
+3.5.5
+* drop support for python 3.7
+* doc fixes (argparse properly displayed, minor changes in installation instructions)
+* deepblue support stops
+* initiate deprecation of tight_layout in plotheatmap, in favor of constrained_layout. Minor changes in paddings, etc can occur (but for the better).
+
+3.5.4
+* error handling and cases for bwAverage with >2 samples
+* Tick.label deprecation for mpl 3.8
+* minimal mpl version is 3.5
+* cicd update for pypi push
+
 3.5.3
 * requirement cap for matplotlib lifted (changes in plotting can occur)
 * nose has been deprecated in favor of pytests

deeptools/bigwigAverage.py

@@ -1,23 +1,19 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import argparse  # to parse command line arguments
+import argparse
 import sys
-import multiprocessing
-import os
 import numpy as np
 from deeptools import parserCommon
 from deeptools import writeBedGraph_bam_and_bw
-import deeptools.deepBlue as db
 
 debug = 0
 
 
 def parse_arguments(args=None):
     parentParser = parserCommon.getParentArgParse()
     outputParser = parserCommon.output()
-    dbParser = parserCommon.deepBlueOptionalArgs()
     parser = argparse.ArgumentParser(
-        parents=[parentParser, outputParser, dbParser],
+        parents=[parentParser, outputParser],
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description='This tool average multiple bigWig files based on the number '
         'of mapped reads. To average the bigWig files, the genome is '
@@ -59,7 +55,7 @@ def parse_arguments(args=None):
 
 def getType(fname):
     """
-    Tries to determine if a file is a wiggle file from deepBlue or a bigWig file.
+    Tries to determine if a file is a wiggle file a bigWig file.
     Returns 'wiggle' if the file name ends with .wig, otherwise 'bigwig'
     """
     if fname.endswith(".wig") or fname.endswith(".wiggle"):
@@ -119,29 +115,6 @@ def main(args=None):
     FUNC = average
     function_args = {'scaleFactors': scaleFactors}
 
-    # Preload deepBlue files, which need to then be deleted
-    deepBlueFiles = []
-    for idx, fname in enumerate(args.bigwigs):
-        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):
-            args.bigwigs[ftuple[1]] = r
-        deepBlueFiles = [[x[0], x[1]] for x in deepBlueFiles]
-        del regs
-
     writeBedGraph_bam_and_bw.writeBedGraph(
         [(b, getType(b)) for b in args.bigwigs],
         args.outFileName, 0, FUNC,
@@ -154,12 +127,3 @@ def main(args=None):
         smoothLength=False,
         missingDataAsZero=not args.skipNonCoveredRegions,
         extendPairedEnds=False)
-
-    # Clean up temporary bigWig files, if applicable
-    if not args.deepBlueKeepTemp:
-        for k, v in deepBlueFiles:
-            os.remove(args.bigwigs[v])
-    else:
-        for k, v in deepBlueFiles:
-            foo = args.bigwigs[v]
-            print("{} is stored in {}".format(k, foo))

deeptools/bigwigCompare.py

@@ -1,23 +1,18 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
-import argparse  # to parse command line arguments
-import sys
-import multiprocessing
-import os
+import argparse
 from deeptools import parserCommon
 from deeptools.getRatio import getRatio
 from deeptools import writeBedGraph_bam_and_bw
-import deeptools.deepBlue as db
 
 debug = 0
 
 
 def parse_arguments(args=None):
     parentParser = parserCommon.getParentArgParse()
     outputParser = parserCommon.output()
-    dbParser = parserCommon.deepBlueOptionalArgs()
     parser = argparse.ArgumentParser(
-        parents=[parentParser, outputParser, dbParser],
+        parents=[parentParser, outputParser],
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
         description='This tool compares two bigWig files based on the number '
         'of mapped reads. To compare the bigWig files, the genome is '
@@ -104,7 +99,7 @@ def parse_arguments(args=None):
 
 def getType(fname):
     """
-    Tries to determine if a file is a wiggle file from deepBlue or a bigWig file.
+    Tries to determine if a file is a wiggle file or a bigWig file.
     Returns 'wiggle' if the file name ends with .wig, otherwise 'bigwig'
     """
     if fname.endswith(".wig") or fname.endswith(".wiggle"):
@@ -136,32 +131,6 @@ def main(args=None):
                      'scaleFactors': scaleFactors,
                      'pseudocount': args.pseudocount}
 
-    # Preload deepBlue files, which need to then be deleted
-    deepBlueFiles = []
-    for idx, fname in enumerate([args.bigwig1, args.bigwig2]):
-        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
-
     writeBedGraph_bam_and_bw.writeBedGraph(
         [(args.bigwig1, getType(args.bigwig1)),
          (args.bigwig2, getType(args.bigwig2))],
@@ -176,17 +145,3 @@ def main(args=None):
         missingDataAsZero=not args.skipNonCoveredRegions,
         extendPairedEnds=False,
         fixedStep=args.fixedStep)
-
-    # Clean up temporary bigWig files, if applicable
-    if not args.deepBlueKeepTemp:
-        for k, v in deepBlueFiles:
-            if v == 0:
-                os.remove(args.bigwig1)
-            else:
-                os.remove(args.bigwig2)
-    else:
-        for k, v in deepBlueFiles:
-            foo = args.bigwig1
-            if v == 1:
-                foo = args.bigwig2
-            print("{} is stored in {}".format(k, foo))

deeptools/computeMatrix.py

@@ -3,14 +3,10 @@
 
 import argparse
 import sys
-import os
-import multiprocessing
-
 from deeptools.parserCommon import writableFile, numberOfProcessors
 from deeptools import parserCommon
 from deeptools import heatmapper
 import deeptools.computeMatrixOperations as cmo
-import deeptools.deepBlue as db
 from importlib.metadata import version
 
 
@@ -44,17 +40,16 @@ def parse_arguments(args=None):
         dest='command',
         metavar='')
 
-    dbParser = parserCommon.deepBlueOptionalArgs()
-
     # scale-regions mode options
     subparsers.add_parser(
         'scale-regions',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        parents=[computeMatrixRequiredArgs(),
-                 computeMatrixOutputArgs(),
-                 computeMatrixOptArgs(case='scale-regions'),
-                 parserCommon.gtf_options(),
-                 dbParser],
+        parents=[
+            computeMatrixRequiredArgs(),
+            computeMatrixOutputArgs(),
+            computeMatrixOptArgs(case='scale-regions'),
+            parserCommon.gtf_options()
+        ],
         help="In the scale-regions mode, all regions in the BED file are "
         "stretched or shrunken to the length (in bases) indicated by the user.",
         usage='An example usage is:\n  computeMatrix scale-regions -S '
@@ -67,8 +62,8 @@ def parse_arguments(args=None):
         parents=[computeMatrixRequiredArgs(),
                  computeMatrixOutputArgs(),
                  computeMatrixOptArgs(case='reference-point'),
-                 parserCommon.gtf_options(),
-                 dbParser],
+                 parserCommon.gtf_options()
+                 ],
         help="Reference-point refers to a position within a BED region "
         "(e.g., the starting point). In this mode, only those genomic"
         "positions before (upstream) and/or after (downstream) of the "
@@ -399,28 +394,6 @@ def main(args=None):
 
     hm = heatmapper.heatmapper()
 
-    # Preload deepBlue files, which need to then be deleted
-    deepBlueFiles = []
-    for idx, fname in enumerate(args.scoreFileName):
-        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])))
-        regs = db.makeRegions(args.regionsFileName, args)
-        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):
-            args.scoreFileName[ftuple[1]] = r
-        deepBlueFiles = [[x[0], x[1]] for x in deepBlueFiles]
-        del regs
-
     scores_file_list = args.scoreFileName
     hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
     if args.sortRegions not in ['no', 'keep']:
@@ -446,11 +419,3 @@ def main(args=None):
 
     if args.outFileSortedRegions:
         hm.save_BED(args.outFileSortedRegions)
-
-    # Clean up temporary bigWig files, if applicable
-    if not args.deepBlueKeepTemp:
-        for k, v in deepBlueFiles:
-            os.remove(args.scoreFileName[v])
-    else:
-        for k, v in deepBlueFiles:
-            print("{} is stored in {}".format(k, args.scoreFileName[v]))