Commit 4a309952 authored by Sam Nooij's avatar Sam Nooij
Browse files

Also import profile read counts and percentages

parent 377838d6
...@@ -3,6 +3,8 @@ ...@@ -3,6 +3,8 @@
# Import the output of Jovian, that is needed to screen for # Import the output of Jovian, that is needed to screen for
# species and sequences, into another directory. This includes # species and sequences, into another directory. This includes
# trimmed reads, filtered scaffolds and classification tables. # trimmed reads, filtered scaffolds and classification tables.
# It also import other useful output files, such as sample composition
# graphs, Krona charts, and tables of taxonomic abundances.
# #
# Example use: # Example use:
# $ python3 import_jovian_output.py -i ../Jovian/ -o ./ -m move # $ python3 import_jovian_output.py -i ../Jovian/ -o ./ -m move
...@@ -529,7 +531,8 @@ def main(): ...@@ -529,7 +531,8 @@ def main():
print("Trying to copy extra files:") print("Trying to copy extra files:")
print("pipeline_parameters.yaml, multiqc.html,") print("pipeline_parameters.yaml, multiqc.html,")
print("Sample_composition_graph.html, Krona.html and heatmaps.") print("Sample_composition_graph.html, Krona.html, heatmaps,")
print("and profile_read_counts.csv and profile_percentages.csv.")
try: try:
shutil.copy2( shutil.copy2(
...@@ -550,6 +553,14 @@ def main(): ...@@ -550,6 +553,14 @@ def main():
) )
for heatmap in list(Path(main_input / "results" / "heatmaps").glob("*.html")): for heatmap in list(Path(main_input / "results" / "heatmaps").glob("*.html")):
shutil.copy2(heatmap, Path(main_output / "data" / "raw" / "Jovian_report")) shutil.copy2(heatmap, Path(main_output / "data" / "raw" / "Jovian_report"))
shutil.copy2(
Path(main_input / "results" / "profile_read_counts.csv"),
Path(main_output / "data" / "raw" / "Jovian_report"),
)
shutil.copy2(
Path(main_input / "results" / "profile_percentages.csv"),
Path(main_output / "data" / "raw" / "Jovian_report")
)
except: except:
print("Could not copy all Jovian results files.") print("Could not copy all Jovian results files.")
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment