--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify_loom.py	Mon Jan 06 13:45:13 2020 -0500
@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+"""This program adds layers, row attributes or column attributes for loom files"""
+
+import argparse
+
+import loompy
+import numpy as np
+
+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('--file', '-f',
+                    help="Loom file to which data will be added")
+parser.add_argument('--rowfile', '-r', help="File of row attributes & values")
+parser.add_argument('--colfile', '-c',
+                    help="File of column attributes and values")
+parser.add_argument('--layers', '-l', nargs='*',
+                    help="Input tsv files. First file becomes main layer.")
+parser.add_argument('--add', '-a', choices=["rows", "cols", "layers"],
+                    help="Selects rows, columns or layers to be added to file")
+args = parser.parse_args()
+
+lfile = args.file
+if args.rowfile:
+    rowfile = args.rowfile
+if args.colfile:
+    colfile = args.colfile
+if args.layers:
+    alllayers = args.layers
+addselect = args.add
+# Check proper flags for chosen attributes are being added
+if addselect == "cols" and not args.colfile:
+    raise Exception("To add column attributes, column flag and file must be provided")
+if addselect == "rows" and not args.rowfile:
+    raise Exception("To add row attributes, row flag and file must be provided")
+if addselect == "layers" and not args.layers:
+    raise Exception("To add layers, a layer flag and file(s) must be provided")
+
+layernames = []
+rowdict = {}
+coldict = {}
+
+with loompy.connect(lfile) as loomfile:
+    # Loom file dimensions
+    nrow = loomfile.shape[0]
+    ncol = loomfile.shape[1]
+    if addselect == "layers":
+        layernames = []
+        # Generate layer names based on file names
+        for x in range(0, len(alllayers)):
+            layer = alllayers[x]
+            layer = layer.split("/")[-1].split(".")[-2]  # Takes away path, takes off extension
+            layernames.append(layer)
+        # Add in the layers themselves
+        for layer in range(0, len(alllayers)):
+            matrix = ""
+            with open(alllayers[layer], "r") as infile:
+                rows = 0
+                count = 0
+                for line in infile:
+                    if count == 0:
+                        cols = len(line.split("\t"))
+                        if cols != ncol:
+                            raise Exception("Dimensions of new matrix incorrect for this loom file. New matrices must be %d by %d" % (nrow, ncol))
+                    matrix = matrix + line + "\t"
+                    rows += 1
+                if rows != nrow:
+                    raise Exception("Dimensions of new matrix incorrect for this loom file. New matrices must be %d by %d")
+            matrix = matrix.split("\t")
+            matrix = [float(n) for n in matrix[:-1]]
+            matrix = np.asarray(matrix).reshape(nrow, ncol)
+            loomfile[layernames[layer]] = matrix
+    elif addselect == "rows":
+        with open(rowfile, "r") as rows:
+            count = 0
+            for line in rows:
+                line = line.strip().split("\t")
+                if count == 0:  # First time through
+                    row_attributes = line
+                    for x in row_attributes:
+                        rowdict[x] = []
+                    count += 1
+                else:
+                    for x in range(0, len(line)):
+                        rowdict[row_attributes[x]].append(line[x])
+        for x in row_attributes:
+            if len(rowdict[x]) != nrow:
+                raise Exception("Incorrect length of row. Row length must be: %d" % nrow)
+            loomfile.ra[x] = rowdict[x]
+    elif addselect == "cols":
+        with open(colfile, "r") as cols:
+            count = 0
+            for line in cols:
+                line = line.replace('\"', "")
+                line = line.replace(' ', "")
+                line = line.strip().split("\t")
+                if count == 0:  # First time through
+                    col_attributes = line
+                    for x in col_attributes:
+                        coldict[x] = []
+                    count += 1
+                else:
+                    for x in range(0, len(line)):
+                        coldict[col_attributes[x]].append(line[x])
+        for y in col_attributes:
+            if len(coldict[y]) != ncol:
+                raise Exception("Incorrect length of column. Column length must be: %d" % ncol)
+            loomfile.ca[y] = coldict[y]