Merge pull request #90 from pinellolab/v218

Fix off-targets search processes join

Author: ManuelTgn

PostProcess/pool_index_indels.py

@@ -10,13 +10,14 @@
 true_pam = sys.argv[3]
 ref_name = sys.argv[4]
 vcf_name = sys.argv[5]
-ncpus = sys.argv[6]
+bMax = sys.argv[6]
+ncpus = sys.argv[7]
 
 
 def index_indels(chrom):
     print("Indexing INDELs in", chrom)
     os.system(
-        f"crispritz.py index-genome {ref_name}+{vcf_name}_INDELS/{true_pam}_2_fake{chrom} {indels_folder}/fake_{vcf_name}_{chrom} {pam_file} -bMax 2 -th 1  >/dev/null"
+        f"crispritz.py index-genome {ref_name}+{vcf_name}_INDELS/{true_pam}_{bMax}_fake{chrom} {indels_folder}/fake_{vcf_name}_{chrom} {pam_file} -bMax {bMax} -th 1  >/dev/null"
     )  # {indels_folder}/fake_{vcf_name}_{chrom}
     print("Indexing ended for INDELs in", chrom)
 

PostProcess/pool_search_indels.py

@@ -32,10 +32,9 @@ def search_indels(f):
     print("Searching for INDELs in", chrom)
     if bDNA != "0" or bRNA != "0":
         os.system(
-            f"crispritz.py search {current_working_directory}/genome_library/{true_pam}_2_{ref_name}+{vcf_name}_INDELS/{true_pam}_2_fake{chrom}/ {pam_file} {guide_file} fake{chrom}_{pam_name}_{guide_name}_{mm}_{bDNA}_{bRNA} -index -mm {mm} -bDNA {bDNA} -bRNA {bRNA} -t -th 1 >/dev/null"
+            f"crispritz.py search {current_working_directory}/genome_library/{true_pam}_{bMax}_{ref_name}+{vcf_name}_INDELS/{true_pam}_{bMax}_fake{chrom}/ {pam_file} {guide_file} fake{chrom}_{pam_name}_{guide_name}_{mm}_{bDNA}_{bRNA} -index -mm {mm} -bDNA {bDNA} -bRNA {bRNA} -t -th 1 >/dev/null"
         )
     else:
-        print("faccio ricerca brute")
         os.system(
             f"crispritz.py search {current_working_directory}/Genomes/{ref_name}+{vcf_name}_INDELS/fake_{vcf_name}_{chrom}/ {pam_file} {guide_file} fake{chrom}_{pam_name}_{guide_name}_{mm}_{bDNA}_{bRNA} -mm {mm} -t -th 1 >/dev/null"
         )