Add click decorators

.gitignore

@@ -3,4 +3,5 @@ tmpdata/*
 .vscode
 *.bed
 *.tad
-*.bedpe
+*.bedpe
+*.sizes

convert_to_bedpe.py

@@ -16,6 +16,5 @@
         # Load to pandas:
         df = pd.read_csv(csvfile, sep="\t", header=None)
         df[3] = df[0]
-        df = df.drop(columns=[4,5,8])
+        df = df.drop(columns=[4, 5, 8])
         df.to_csv(filename[:-4]+".bedpe", header=None, index=False, sep="\t")
-

create_dense_matrix.py

@@ -1,3 +1,5 @@
+"""Command line interface for OnTAD preprocessing"""
+import click
 import os
 import cooler
 # import cooltools
@@ -12,22 +14,30 @@
 
 # get chromosomal arms
 
-chromsizes = bioframe.fetch_chromsizes('hg19')
+chromsizes = bioframe.fetch_chromsizes("hg19")
 arms = HT.getArmsHg19()
 
 # load in data
 
-HICPATH = "/groups/gerlich/experiments/Experiments_004800/004812/Sequencing_data/Pooled_FC_1_2/cooler/"
-
-BINSIZE = 50000
-BARCODE = "G2.fc_1_2.wOldG2"
-clrs = {interType:
-        cooler.Cooler(
-            os.path.join(HICPATH, f'{BARCODE}.{interType}.1000.mcool::/resolutions/{BINSIZE}'))
-        for interType in ["cis", "trans"]}
-
-
-cis_cooler = clrs['cis']
-cis_matrix = cis_cooler.matrix(balance=True).fetch("chr18")
-cis_matrix = np.nan_to_num(cis_matrix)
-np.savetxt("tmpdata/G2.fc_1_2.wOldG2.chr18.cis.matrix", cis_matrix, fmt='%1.4f', delimiter="\t")
+# fileP = "testdata/G2.fc_1_2.wOldG2.cis.1000.mcool"
+# binsize = 50000
+
+
+@click.command()
+@click.argument('filep', type=click.Path(exists=True))
+@click.option('--binsize', '-b', 'binsize', default=50000,
+              help='Resulution size.',
+              show_default=True)
+def create_dense_matrix(filep, binsize):
+    cooler_obj = cooler.Cooler(f'{filep}::/resolutions/{binsize}')
+    filename = os.path.basename(filep)
+    filename_base = filename[:-6]
+    for chr_name in chromsizes.index:
+        matrix = cooler_obj.matrix(balance=True).fetch(chr_name)
+        matrix = np.nan_to_num(matrix)
+        print(chr_name)
+        print("tmpdata/%s.%s.matrix" % (filename_base, chr_name))
+        np.savetxt("tmpdata/%s.%s.matrix" % (filename_base, chr_name), matrix, fmt='%1.8f', delimiter="\t")
+
+if __name__ == "__main__":
+    create_dense_matrix()

readme.md

@@ -1,12 +1,13 @@
  OnTAD repo:
  https://github.com/anlin00007/OnTAD
 
- Create Imput with:
- create_dense_matrix.py
+Create Input with:
+python create_dense_matrix.py testdata/G2.fc_1_2.wOldG2.cis.1000.mcool -b 50000
+
 
  Use there docker:
  singularity run docker://anlin00007/ontad:v1.2
 
  Run there tool with following parameters:
 
- OnTAD tmpdata/G2.fc_1_2.wOldG2.chr18.cis.matrix -penalty 0.1 -maxsz 200 -bedout 18 78077248 50000 -o OnTAD_cis_chr18
+ OnTAD tmpdata/G2.fc_1_2.wOldG2.chr18.cis.matrix -penalty 0.1 -maxsz 200 -bedout 18 78077248 50000 -o OnTAD_cis_chr18