Mercurial > repos > iuc > anndata_import
view tsv_to_loompy.py @ 6:00712416fdaa draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
author | iuc |
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date | Wed, 22 Jul 2020 12:21:43 -0400 |
parents | b5c7ba11401d |
children |
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#!/usr/bin/env python """This module converts a tsv file into a binary loom file""" import argparse import os 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('--rowfile', '-r', help="File of row attributes & values") parser.add_argument('--colfile', '-c', help="File of column attributes and values") parser.add_argument('--output', '-o', help="Output file name") parser.add_argument('--files', '-f', nargs='*', help="Input tsv files. First file becomes main layer.") args = parser.parse_args() colsfile = args.colfile rowsfile = args.rowfile if args.output: filename = args.output else: filename = "converted.loom" alldata = args.files alayers = [] layernames = [] rowdict = {} coldict = {} # Creates dictionary based on row file # For each attribute: # Attribute: [attribute values] with open(rowsfile, "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]) # Same as above, but for columns with open(colsfile, "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]) # Finding dimensions for the loom layers rowshape = len(rowdict[list(rowdict.keys())[0]]) colshape = len(coldict[list(coldict.keys())[0]]) # Creates a list with each element being entire matrix of # each layer file as floats for file in range(0, len(alldata)): layer = alldata[file][:-4] layer = layer.split("/")[-1] if layer == "": raise Exception("Please only use named files") layernames.append(layer) cfile = alldata[file] with open(cfile, "r") as tsv: cmatrix = [] for line in tsv: line = line.strip().split("\t") line = [float(i) for i in line] cmatrix += line alayers.append(cmatrix) # Loompy cannot overwright existing files. If somehow it finds # a second file with the same name, it must be deleted if os.path.isfile(filename): os.remove(filename) # To create the file properly, the first row and column attributes must be # added separately in the form of individual dictionaries row_attrs = {row_attributes[0]: np.asarray(rowdict[row_attributes[0]])} col_attrs = {col_attributes[0]: np.asarray(coldict[col_attributes[0]])} matrix = np.asarray(alayers[0]) matrix = matrix.astype(float) matrix = matrix.reshape(rowshape, colshape) # Creation of initial loom file if "loom" not in filename[-5:]: filename = filename + ".loom" loompy.create(filename, matrix, row_attrs, col_attrs) # Adding all row and column attributes, then all layers with loompy.connect(filename) as loomfile: for x in row_attributes: loomfile.ra[x] = rowdict[x] for y in col_attributes: loomfile.ca[y] = coldict[y] for z in range(1, len(alayers)): matrix = np.asarray(alayers[z]) matrix = matrix.astype(float) matrix = matrix.reshape(rowshape, colshape) loomfile[layernames[z]] = matrix