diff loompy_to_tsv.py @ 3:b5c7ba11401d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/loompy_to_tsv.py	Mon Jan 06 13:45:13 2020 -0500
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+"""Converts a loompy file to tsv file(s). Each layer becomes a new file."""
+
+import argparse
+
+import loompy
+
+parser = argparse.ArgumentParser(description="Loompy file converter flags")
+parser.add_argument('--version', action='version', version='%(prog)s 0.1.0',
+                    help="Displays tool version")
+parser.add_argument("-f", "--file", help="loom file to import")
+args = parser.parse_args()
+
+file = args.file
+
+matrices = []
+allcols = []
+colstrings = []
+allrows = []
+
+# Build background info for all attributes and layers
+loompyfile = loompy.connect(file)
+row_attributes = loompyfile.ra.keys()  # List of row attributes
+for row in row_attributes:  # Each list represents rownames for row_attributes
+    c_row = loompyfile.ra[row]
+    c_row = [str(r) for r in c_row]
+    allrows.append(c_row)
+col_attributes = loompyfile.ca.keys()  # List of column attributes
+for col in col_attributes:  # each list represents colnames for col_attributes
+    c_col = loompyfile.ca[col]
+    c_col = [str(c) for c in c_col]
+    allcols.append(c_col)
+layers = loompyfile.layers.keys()  # List of layers
+for layer in layers:  # List with each element being a loompy layer
+    c_layer = loompyfile[layer]
+    c_layer = c_layer[:, :]
+    c_layer = c_layer.astype(str)
+    matrices.append(c_layer)
+
+# Create column attribute output
+with open("attributes/col_attr.tsv", "w") as colout:
+    col_attributes = "\t".join(col_attributes) + "\n"
+    colout.write(col_attributes)
+    for length in range(0, len(c_col)):
+        attributestring = ""
+        for col in allcols:
+            attributestring = attributestring + col[length] + "\t"
+        while attributestring[-1] == "\t":
+            attributestring = attributestring[:-1]
+        colout.write(attributestring)
+        colout.write("\n")
+# Create row attribute output
+with open("attributes/row_attr.tsv", "w") as rowout:
+    row_attributes = "\t".join(row_attributes) + "\n"
+    rowout.write(row_attributes)
+    for length in range(0, len(c_row)):
+        attributestring = ""
+        for row in allrows:
+            attributestring = attributestring + row[length] + "\t"
+        while attributestring[-1] == "\t":
+            attributestring = attributestring[:-1]
+        rowout.write(attributestring)
+        rowout.write("\n")
+
+# Build output files for each layer
+for x in range(0, len(layers)):
+    # Output file name generation
+    if layers[x] in layers[0: x]:  # Different output names if layers have same names somehow
+        repeats = layers[0, x].count(layer[x])
+        outputname = "output/" + layers[x] + repeats + ".tsv"
+    elif layers[x] == "":  # Empty layer name
+        outputname = "output/mainmatrix.tsv"
+    else:
+        outputname = "output/" + str(layers[x]) + ".tsv"  # Usual case
+# Matrix output
+    with open(outputname, "w") as outputmatrix:
+        for line in matrices[x]:
+            line = "\t".join(line)
+            line += "\n"
+            line = line
+            outputmatrix.write(line)