💪 celseq2-to-st supports the csv result of celseq2

celseq2/support/st_pipeline.py

@@ -9,7 +9,7 @@ import argparse
 import pandas as pd
 
 
-def celseq2stpipeline(celseq2_hdf5, spatial_map, out,
+def celseq2stpipeline(celseq2_fpath, spatial_map, out,
                       exclude_empty_spots, exclude_nondetected_genes):
     fhout = open(out, 'w')
 
@@ -21,8 +21,10 @@ def celseq2stpipeline(celseq2_hdf5, spatial_map, out,
             row = row.strip().split()
             dict_spatial_seq2xy[row[0]] = (row[1], row[2])
 
-    expr = pd.read_hdf(celseq2_hdf5, 'table')  # genes x cells
-
+    if celseq2_fpath.endswith('h5') or celseq2_fpath.endswith('hdf5'):
+        expr = pd.read_hdf(celseq2_fpath, 'table')  # genes x cells
+    if celseq2_fpath.endswith('csv'):
+        expr = pd.read_csv(celseq2_fpath, index_col=0)
     # df.loc[(df.sum(axis=1) != 0), (df.sum(axis=0) != 0)]
     if (exclude_empty_spots) and (exclude_nondetected_genes):
         expr_valid = expr.loc[(expr.sum(axis=1) != 0), (expr.sum(axis=0) != 0)]
@@ -38,7 +40,8 @@ def celseq2stpipeline(celseq2_hdf5, spatial_map, out,
     fhout.write('{}\t{}\n'.format('', '\t'.join(genes)))  # header
 
     for colname in colnames:
-        spot_seq = colname.split('-')[-1]
+        tmp = colname.replace('.', '-')
+        spot_seq = tmp.split('-')[-1]
         spot_expr = expr_valid[colname].values
         spot_xy = dict_spatial_seq2xy.get(spot_seq, None)
         if not spot_xy:
@@ -56,7 +59,7 @@ def celseq2stpipeline(celseq2_hdf5, spatial_map, out,
 def main():
     parser = argparse.ArgumentParser(add_help=True)
     parser.add_argument('celseq2', metavar='FILENAME', type=str,
-                        help=('File path to expr.hdf5 generated by celseq2.'))
+                        help=('File path to expr.hdf5 (expr.h5 or expr.csv) generated by celseq2.'))
     parser.add_argument('spatial_map', metavar='FILENAME', type=str,
                         help='File path to spatial position dictionary.')
     parser.add_argument('out', metavar='FILENAME', type=str,