diff salmonKallistoMtxTo10x.py @ 0:fe0fd27aba50 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/salmonKallistoMtxTo10x.py	Thu Nov 07 05:12:10 2019 -0500
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+
+# Alevin and Kallisto currently output MTX files and gene labels in a manner
+# inconsistent with the old-style 10X conventions. In both cases the matrix
+# must be transposed, and gene indentifier columns duplicated
+
+from __future__ import print_function
+from collections import defaultdict
+from struct import Struct
+import pandas as pd
+import gzip
+import sys
+import os
+from scipy.io import mmread,mmwrite
+from scipy.sparse import *
+from shutil import copyfile
+import pathlib
+import numpy as np
+import argparse
+
+parser = argparse.ArgumentParser(description='Convert Alevin or Kallisto MTX outputs to 10X .mtx.')
+parser.add_argument('mtx', help = 'MTX-format matrix file')
+parser.add_argument('genes', help = 'Gene names text file')
+parser.add_argument('barcodes', help = 'Barcodes file')
+parser.add_argument('mtx_out', help = 'Output directory for converted results')
+parser.add_argument('--cell_prefix', dest='cell_prefix', default='', help = 'Prefix to apply to cell barcodes')
+args = parser.parse_args() 
+
+quant_file=args.mtx
+cb_file=args.barcodes
+gene_file=args.genes
+mtx_out=args.mtx_out
+cell_prefix=args.cell_prefix
+
+if not os.path.exists(quant_file):
+    print("quant file {} doesn't exist".format( quant_file ))
+    sys.exit(1)
+
+if not os.path.exists(cb_file):
+    print("cell barcodes file: {} doesn't exist".format( cb_file ))
+    sys.exit(1)
+
+if not os.path.exists(gene_file):
+    print("genes file: {} doesn't exist".format( gene_file))
+    sys.exit(1)
+
+# Read gene and cell labels, apply cell prefix
+
+cb_names = [cell_prefix + s for s in pd.read_csv(cb_file, header=None)[0].values]
+gene_names = pd.read_csv(gene_file, header=None)[0].values
+umi_counts = mmread( quant_file )
+    
+# Write outputs to a .mtx file readable by tools expecting 10X outputs.
+# Barcodes file works as-is, genes need to be two-column, duplicating the
+# identifiers. Matrix itself needs to have genes by row, so we transpose. 
+
+pathlib.Path(mtx_out).mkdir(parents=True, exist_ok=True)
+mmwrite('%s/matrix.mtx' % mtx_out, umi_counts.transpose()) 
+
+genes_frame = pd.DataFrame([ gene_names, gene_names]).transpose()
+genes_frame.to_csv(path_or_buf='%s/genes.tsv' % mtx_out, index=False, sep="\t", header = False)
+
+with open('%s/barcodes.tsv' % mtx_out, 'w') as f:
+    f.write("\n".join(cb_names))    
+    f.write("\n")