add scaling factor from spike-in to bedcov before seacr

workflow/rules/compute_scaling_factor.rules

+#########################################################################
+# ChIPflow: Standardize and reproducible ChIP-seq analysis from raw     #
+#           data to differential analysis                               #
+# Authors: Rachel Legendre, Maelle Daunesse                             #
+# Copyright (c) 2019-2020  Institut Pasteur (Paris) and CNRS.           #
+#                                                                       #
+# This file is part of ChIPflow workflow.                               #
+#                                                                       #
+# ChIPflow is free software: you can redistribute it and/or modify      #
+# it under the terms of the GNU General Public License as published by  #
+# the Free Software Foundation, either version 3 of the License, or     #
+# (at your option) any later version.                                   #
+#                                                                       #
+# ChIPflow is distributed in the hope that it will be useful,           #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          #
+# GNU General Public License for more details .                         #
+#                                                                       #
+# You should have received a copy of the GNU General Public License     #
+# along with ChIPflow (LICENSE).                                        #
+# If not, see <https://www.gnu.org/licenses/>.                          #
+#########################################################################
+
+
+rule compute_scaling_factor:
+	input:
+		bam = compute_scaling_factor_input
+	output:
+		txt = temp(compute_scaling_factor_output)
+	run:
+		import pysam
+
+		samfile = pysam.AlignmentFile(input.bam, "rb")
+		nb_reads = samfile.mapped
+		try:
+			S = "{0:.2f}".format(10000 / (samfile.mapped))
+		except ZeroDivisionError:
+			S = 1
+		
+		with open(output.txt, 'w') as file_fp:
+			file_fp.write(S)
+
+		
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