Change mesa to splicedice in .py files, file names and directories

I confirmed that these changes do not change results

mesa/MESA.py → splicedice/SPLICEDICE.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 """
-Mutually Exclusive Splicing Analysis (MESA) main quantification step
+Mutually Exclusive Splicing Analysis (SPLICEDICE) main quantification step
 
 """
 
@@ -25,7 +25,7 @@ def __init__(self,manifestLine):
             with open(self.filename) as bedfile:
                 info = bedfile.readline().split('\t')[3].split(';')
                 if info[0].startswith("e:") and info[1].startswith("o:"):
-                    self.type = "mesabed"
+                    self.type = "splicedicebed"
         elif self.filename.upper().endswith("SJ.OUT.TAB"):
             self.type = "SJ"
         elif self.filename.upper().endswith(".BAM"):
@@ -68,7 +68,7 @@ def check(self):
 
 
 
-class MESA:
+class SPLICEDICE:
     """Main algorithm for Mutually Exclusive Splicing Analysis"""
     def __init__(self,manifestFilename,outputPrefix,args):
         """Call methods to get input, process, and write output"""
@@ -79,7 +79,7 @@ def __init__(self,manifestFilename,outputPrefix,args):
         self.manifestFilename = manifestFilename
         self.outputPrefix = outputPrefix
 
-        # Construct MESA
+        # Construct SPLICEDICE
         timer = Timer()
         print("Parsing manifest...")
         self.manifest = self.parseManifest()
@@ -106,7 +106,7 @@ def __init__(self,manifestFilename,outputPrefix,args):
         self.writeJunctionBed()
         print("\tDone",timer.check())
 
-        # Quantify MESA
+        # Quantify SPLICEDICE
         print("Gathering junction counts...")
         self.counts, self.low = self.getJunctionCounts()
         print("\tDone",timer.check())
@@ -180,7 +180,7 @@ def getAllJunctions(self):
                             intronMotif in validMotifs):
                             junctions.add((chromosome,left,right,strand))
 
-                elif sample.type == "mesabed":
+                elif sample.type == "splicedicebed":
                     for line in junctionFile:
                         row = line.rstrip().split("\t")
 
@@ -263,7 +263,7 @@ def getJunctionCounts(self):
 
             with open(sample.filename,"r") as sampleFile:
 
-                if sample.type == "bed" or sample.type == "mesabed" or sample.type == "leafcutter":
+                if sample.type == "bed" or sample.type == "splicedicebed" or sample.type == "leafcutter":
                     for line in sampleFile:
                         row = line.rstrip().split("\t")
 
@@ -402,11 +402,11 @@ def add_parser(parser):
                         help="Shannon's diversity index associated with a junction, minumum required for inclusion [Default 1]")
 
 def run_with(args):
-    """ Main program which calls MESA algorithm class"""
+    """ Main program which calls SPLICEDICE algorithm class"""
     manifestFilename = args.manifest
     outputPrefix = args.output_prefix
 
-    MESA(manifestFilename,outputPrefix,args)
+    SPLICEDICE(manifestFilename,outputPrefix,args)
 
 if __name__ == "__main__":
     import argparse 

mesa/__main__.py → splicedice/__main__.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
-"""This script is the main entry point for the different MESA commands."""
+"""This script is the main entry point for the different SPLICEDICE commands."""
 import argparse
 
-from . import MESA as quant
+from . import SPLICEDICE as quant
 from . import bam_to_junc_bed as bjb
 from . import pairwise_fisher as pf
 from . import compareSampleSets as css
@@ -17,9 +17,9 @@
 def add_cmd(name, arg_parser_fn, run_with, subparser):
     """Adds a subparser command to the parser.  name is a string that denotes
     name of the command being added. This function helps a) simplify adding new
-    commands to the mesa tool b) also allows for using each python file as its
+    commands to the splicedice tool b) also allows for using each python file as its
     own script instead of relying on the __main__.py parser solely.
-    ie allows for `mesa quant` and `python quantMESA.py` to be easier to use.
+    ie allows for `splicedice quant` and `python quantSPLICEDICE.py` to be easier to use.
 
     arg_parser_fn is a function that takes a subparser and adds arguments based
     on the command. Modules typically expose an add_parser() function that does

mesa/compareSampleSets.py → splicedice/compareSampleSets.py

@@ -104,7 +104,7 @@ def getColIndexFromArray(x, y):
 
 def returnSamplesFromManifest(x):
     """
-    reads in mesa formatted manifest
+    reads in splicedice formatted manifest
     returns list of samples
     """
     s = list()
@@ -123,10 +123,10 @@ def returnSamplesFromManifest(x):
 
 def add_parser(parser):
     parser.add_argument(
-        "--psiMESA",
+        "--psiSPLICEDICE",
         type=str,
         required=True,
-        help="Compressed NPZ formatted PSI matrix from 'mesa quant'.",
+        help="Compressed NPZ formatted PSI matrix from 'splicedice quant'.",
     )
     parser.add_argument(
         "-m1",
@@ -167,7 +167,7 @@ def run_with(args):
     Values are assumed to not be normall distributed, thus
     we invoke the wilcoxon ranksum test as the statistical analysis.
     """
-    pmesa = args.psiMESA
+    psplicedice = args.psiSPLICEDICE
     group1 = args.manifest1
     group2 = args.manifest2
 
@@ -183,7 +183,7 @@ def run_with(args):
         sys.exit(1)
 
     # load psi
-    #data = loadNPZ(pmesa)
+    #data = loadNPZ(psplicedice)
 
     # table has 3 arrays, cols, rows and data
     #cols, rows, matrix = data["cols"], data["rows"], data["data"]
@@ -192,7 +192,7 @@ def run_with(args):
     ######
     rows = []
     data = []
-    with open(pmesa) as tsv:
+    with open(psplicedice) as tsv:
         headers = tsv.readline().strip().split('\t')[1:]
         for line in tsv:
             row = line.strip().split('\t')

mesa/counts_to_ps.py → splicedice/counts_to_ps.py

@@ -82,13 +82,13 @@ def add_parser(parser):
     """ """
     parser.add_argument("--clusters","-c",
                         action="store",default=None,
-                       help="allClusters.tsv file from MESA")
+                       help="allClusters.tsv file from SPLICEDICE")
     parser.add_argument("--recluster","-r",
                         action="store_true",
                         help="Determine clusters from splice junctions in counts file")
     parser.add_argument("--inclusion_counts","-i",
                         action="store",required=True,
-                       help="inclusionCounts.tsv file from MESA")
+                       help="inclusionCounts.tsv file from SPLICEDICE")
     parser.add_argument("--output_prefix","-o",
                         action="store",required=True,
                        help="output filename path and prefix") 

mesa/findOutliers.py → splicedice/findOutliers.py

@@ -28,11 +28,11 @@
 def add_parser(parser):
     """Add command line argument parser for findOutliers module"""
     parser.add_argument(
-        "--psiMESA",
+        "--psiSPLICEDICE",
         type=str,
         action="store",
         required=True,
-        help="Compressed NPZ formatted PSI matrix from quantMESA.",
+        help="Compressed NPZ formatted PSI matrix from quantSPLICEDICE.",
     )
 
     parser.add_argument(
@@ -91,7 +91,7 @@ def loadNPZ(x):
 ########################################################################
 
 def run_with(args):
-    pmesa = args.psiMESA
+    psplicedice = args.psiSPLICEDICE
     man = args.manifest
     null = args.nullMan
     zthresh = args.outlierCutoff
@@ -114,7 +114,7 @@ def run_with(args):
         )
         sys.exit(1)
     # load psi
-    data = loadNPZ(pmesa)
+    data = loadNPZ(psplicedice)
     mSamps, mEvents, matrix = data["cols"], data["rows"], data["data"]
     # m is for matrix
     nullIndices = np.argwhere(np.isin(mSamps, nullSamps))[:, 0]

mesa/intron_coverage.py → splicedice/intron_coverage.py

@@ -2,7 +2,7 @@
 """
 Process alignment files (BAMs) to determine coverage at positions along introns, as defined in junction file.
 
-python3 intron_coverage.py -b bam_manifest.tsv  -m output_allPSI.tsv  -j mesa_junctions.bed
+python3 intron_coverage.py -b bam_manifest.tsv  -m output_allPSI.tsv  -j splicedice_junctions.bed
 """
 
 
@@ -20,12 +20,12 @@ def add_parser(parser):
     parser.add_argument('-b', '--bamManifest', 
                         action = 'store', required=True, 
                         help='tab-separated list of bam files for all samples')
-    parser.add_argument('-m', '--mesaTable', 
+    parser.add_argument('-m', '--splicediceTable', 
                         action = 'store', required=True, 
-                        help='mesa allPSI.tsv output from mesa')
+                        help='splicedice allPSI.tsv output from splicedice')
     parser.add_argument('-j', '--junctionFile', 
                         action = 'store', required=True, 
-                        help='mesa junction.bed output from mesa')
+                        help='splicedice junction.bed output from splicedice')
     parser.add_argument('-s', '--binSize', 
                         action='store', default=500000, type=int,
                         help='chromosome bins for processing (must exceed intron length)')
@@ -38,12 +38,12 @@ def add_parser(parser):
                         help='directory for outputting intron coverage count files')
 
 class IntronCoverage():
-    def __init__(self, manifest,mesa,junctionFile,binSize,numThreads,outputDir):
+    def __init__(self, manifest,splicedice,junctionFile,binSize,numThreads,outputDir):
         """
         Instantiate object attributes
         """
         self.manifest = manifest
-        self.mesa = mesa
+        self.splicedice = splicedice
         self.junctionFilename = junctionFile
         self.binSize = binSize
         self.numThreads = numThreads
@@ -249,7 +249,7 @@ def run_with(args):
     start_time = time.time()
 
     manifest = args.bamManifest
-    mesa = args.mesaTable
+    splicedice = args.splicediceTable
     junctionFile = args.junctionFile
     binSize = args.binSize
     numThreads = args.numThreads
@@ -258,7 +258,7 @@ def run_with(args):
     if not os.path.isdir(outputDir):
         os.mkdir(outputDir)
 
-    intronCoverage = IntronCoverage(manifest,mesa,junctionFile,binSize,numThreads,outputDir)
+    intronCoverage = IntronCoverage(manifest,splicedice,junctionFile,binSize,numThreads,outputDir)
     intronCoverage.parseManifest()
     intronCoverage.getIntronPercentiles()
     intronCoverage.getCoveragePool()

mesa/make_bed.py → splicedice/make_bed.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-Make a bed file from MESA's compare_sample_sets output file
+Make a bed file from SPLICEDICE's compare_sample_sets output file
 """
 
 def deltaColor(delta):
@@ -38,13 +38,13 @@ def makeBed(bedfilename,vsfilename,use_corrected,alpha):
 
 def get_args():
     import argparse
-    parser = argparse.ArgumentParser(description='Make bed file from output of mesa compare_sample_sets')
+    parser = argparse.ArgumentParser(description='Make bed file from output of splicedice compare_sample_sets')
     parser.add_argument('--alpha','-a',default=0.05,
                         help='Significance threshold for filtering based on p-value. Default 0.05')
     parser.add_argument('--use_corrected','-c',action='store_true',
                         help='Flag to use corrected p-value in filtering and output label. Default uses raw p-value')
     parser.add_argument('--input','-i',required=True,
-                        help='Comparison file from mesa compare_sample_sets')
+                        help='Comparison file from splicedice compare_sample_sets')
     parser.add_argument('--output','-o',required=True,
                         help='Output filename')
     return parser.parse_args()

mesa/pairwise_fisher.py → splicedice/pairwise_fisher.py

@@ -70,10 +70,10 @@ def getEventCounts(filename, filter_list=None):
 
 def add_parser(parser):
     parser.add_argument(
-        "--inclusionMESA",
+        "--inclusionSPLICEDICE",
         type=str,
         required=True,
-        help="Compressed NPZ formatted Inclusion count matrix from quantMESA.",
+        help="Compressed NPZ formatted Inclusion count matrix from quantSPLICEDICE.",
     )
 
     parser.add_argument(
@@ -120,7 +120,7 @@ def run_with(args):
     from statsmodels.stats.multitest import multipletests
 
     # Input file arguments
-    inclusionCounts = args.inclusionMESA
+    inclusionCounts = args.inclusionSPLICEDICE
     allClusters = args.clusters
     outfilename = args.output
 

mesa/select_samples.py → splicedice/select_samples.py

@@ -1,5 +1,5 @@
 """
-MESA select
+SPLICEDICE select
 """
 
 def parseManifest(manifest_filename):
@@ -64,10 +64,10 @@ def add_parser(parser):
     """ """
     parser.add_argument("--allps1","-a1",
                         action="store",
-                       help="First allPS file output from mesa quant")
+                       help="First allPS file output from splicedice quant")
     parser.add_argument("--allps2","-a2",
                         action="store",
-                       help="Second allPS file output from mesa quant")
+                       help="Second allPS file output from splicedice quant")
     parser.add_argument("--manifest","-m",
                         action="store",
                         help="File with list of allPS file paths (supercedes allPS1 and allPS2)")

mesa/similarity.py → splicedice/similarity.py

@@ -1,5 +1,5 @@
 """
-MESA similarity
+SPLICEDICE similarity
 """
 
 def readVsFile(vs_filename):
@@ -75,7 +75,7 @@ def add_parser(parser):
                        help="Output table from compare_sample_sets")
     parser.add_argument("--allps","-a",
                         action="store",required=True,
-                       help="Allps table from mesa quant")
+                       help="Allps table from splicedice quant")
     parser.add_argument("--output","-o",
                         action="store",required=True,
                        help="Output filename")
@@ -99,7 +99,7 @@ def run_with(args):
 
 if __name__ == "__main__":
     import argparse 
-    parser = argparse.ArgumentParser(description='Scores similarity of samples to a condition from mesa compare_sample_sets.')           
+    parser = argparse.ArgumentParser(description='Scores similarity of samples to a condition from splicedice compare_sample_sets.')           
     add_parser(parser)
     args = parser.parse_args()
     run_with(args)

mesa/subset.py → splicedice/subset.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 """
-For subsetting a percent-spliced table output from mesa (filename ending with allPS.tsv).
+For subsetting a percent-spliced table output from splicedice (filename ending with allPS.tsv).
 """
 
 
@@ -19,7 +19,7 @@ def add_parser(parser):
                         help='Text file of samples to include in subset, one per line [Default includes all samples]')
     parser.add_argument('-i', '--inputFilename',
                         required=True,
-                        help='Table of PS values from MESA quant (*_allPS.tsv)')
+                        help='Table of PS values from SPLICEDICE quant (*_allPS.tsv)')
     parser.add_argument('-o', '--outputFilename',
                         required=True,
                         help='Table of PS values for selected samples and junctions')