fixed

aft_pipelines_analysis/aft_pipelines_main.py

@@ -57,7 +57,7 @@ def check_path(path):
         os.system('mkdir -p %s ' % path)
 
 
-for opath in [somatic_csv, germline_csv, vcf_path, final_csv, filtered_csv, pcgr_output, pack_result]:
+for opath in [somatic_csv, germline_csv, vcf_path, final_csv, filtered_csv, pcgr_output, pack_result,info_summary_path]:
     check_path(opath)
 
 
@@ -162,6 +162,10 @@ def remind_text(local_project_path):
     base_outpath, server_script_path, bed_file_path, REF_file_path)
     remind_run_command += '''for each in %s/XK_result/*/*recal_reads.bam; do python %s/pre_pipelines_analysis/cal_Cov_script_version.py -b $each -B %s -r %s & done''' % (
     base_outpath, server_script_path, bed_file_path, REF_file_path)
+    remind_run_command += '''
+        ##run script in order to generate accessment file. \n\n \
+        python %s/aft_pipelines_analysis/run_info_summary.py %s \n''' % (
+    server_script_path, server_setting_path)
     remind_run_command += '''
     ##run script which is fetch cov_info from .info file and add it into csvfile. \n\n \
     python2 Whole_pipelines/aft_pipelines_analysis/run_add_per_info_into_csv.py %s \n''' % server_setting_path
@@ -171,6 +175,7 @@ def remind_text(local_project_path):
 def draw_coverage_depths():
     from draw_quality_line import draw_coverage_depths as dcd
     dcd(info_summary_path, NORMAL_SIG, TUMOR_SIG)
+    print('finish drawing.')
 
 
 if __name__ == '__main__':
@@ -186,7 +191,7 @@ def draw_coverage_depths():
 
     server_setting_path = os.path.join(local_project_path, 'setting.py')
     if '1' in args:
-        if input('Download ? Y/y').upper() == 'Y':
+        if str(input('Download ? Y/y')).upper() == 'Y':
             download_scp()
         else:
             print('wrong command,just pass.')

aft_pipelines_analysis/draw_quality_line.py

@@ -5,6 +5,8 @@
 import sys
 
 def draw_coverage_depths(dir_info,NORMAL_SIG,TUMOR_SIG):
+    draw_data = []
+    layout = dict(yaxis=dict(exponentformat='e'))
     all_info = list(glob.glob(dir_info+'/*cov_summary.info'))
     for data_path in all_info:
         data_df = pd.read_csv(data_path,sep='\t',index_col=0)

aft_pipelines_analysis/filter_pipelines.py

@@ -3,7 +3,7 @@
 import pandas,time
 import argparse
 import os, sys, glob
-def filter_pipelines2(normal_germline,normal_somatic, tumor_somatic,pair_somatic,output_path,pp=[0,2,3,4,5,6]):
+def filter_pipelines2(normal_germline,normal_somatic, tumor_somatic,pair_somatic,output_path,pp=[0,2,3,4,5,6],snp_path='/home/liaoth/data/humandb/snp138Common.name.txt'):
     '''
     created at 2017-06-26 advances XK filter pipelines
 
@@ -15,7 +15,7 @@ def filter_pipelines2(normal_germline,normal_somatic, tumor_somatic,pair_somatic
     :return:
     '''
     t1 = time.time()
-    snp138_common = snp_138_common_init()
+    snp138_common = snp_138_common_init(snp_path)
     TUMOR_S = pd.read_csv(tumor_somatic, index_col=None)
     TUMOR_P = pd.read_csv(pair_somatic, index_col=None)
     NORMAL_S = pd.read_csv(normal_somatic, index_col=None)
@@ -71,7 +71,7 @@ def filter_pipelines2(normal_germline,normal_somatic, tumor_somatic,pair_somatic
         descriptions.append('Coverage')
         counts.append([len(TUMOR_S_filtered_index),len(TUMOR_P_filtered_index)])
     if 3 in pp:
-        TUMOR_S_filtered_index = snp_common(snp138_common, TUMOR_S.loc[TUMOR_S_filtered_index+special_S_index, :])
+        TUMOR_S_filtered_index = snp_common(snp138_common, TUMOR_S.loc[TUMOR_S_filtered_index+special_S_index, :],)
         TUMOR_P_filtered_index = snp_common(snp138_common, TUMOR_P.loc[TUMOR_P_filtered_index+special_P_index, :])
         print('finish snp common filter.....')
         descriptions.append('Snp_common')
@@ -168,8 +168,8 @@ def filter_pipelines2(normal_germline,normal_somatic, tumor_somatic,pair_somatic
         if not os.path.isdir(os.path.dirname(output_file)):
             os.makedirs(os.path.dirname(output_file))
         print("filter_pipelines2(%s,%s,%s,%s,%s,pp=[3,4,5,6])" % (germline,somatic_normal,somatic_tumor,somatic_pair,output_file))
-        filter_pipelines2(germline,somatic_normal,somatic_tumor,somatic_pair,output_file,pp=[3,4,5,6])
-        filter_pipelines2(germline, somatic_normal, somatic_tumor, somatic_pair, output_file.replace('except_AF_depth.csv','except_AF_depth_PASS.csv'), pp=[3, 4, 6])
+        filter_pipelines2(germline,somatic_normal,somatic_tumor,somatic_pair,output_file,pp=[3,4,5,6],snp_path=snp138_common_file)
+        filter_pipelines2(germline, somatic_normal, somatic_tumor, somatic_pair, output_file.replace('except_AF_depth.csv','except_AF_depth_PASS.csv'), pp=[3, 4, 6],snp_path=snp138_common_file)
         # print()
 
 

aft_pipelines_analysis/run_add_per_info_into_csv.py

@@ -46,7 +46,7 @@ def run_batch(input_path,tb_bam_path,nb_bam_path,NORMAL_SIG,TUMOR_SIG):
     nb_bam_path = "%s/output/XK_result/{nb}/{nb}.recal_reads.bam" % os.path.dirname(base_outpath.rstrip('/'))
 
     cmdlines = run_batch(input_path,tb_bam_path,nb_bam_path,NORMAL_SIG,TUMOR_SIG)
-    makesure = input("If your `num of processes >4`, Please be careful of memory. It may stalled whole server.\nUsing %s processes, prepare process listing files: \n . %sIf you make sure, please type y/Y." % (num_processes,'\n'.join(glob.glob(input_path))))
+    makesure = str(input("If your `num of processes >4`, Please be careful of memory. It may stalled whole server.\nUsing %s processes, prepare process listing files: \n . %sIf you make sure, please type y/Y." % (num_processes,'\n'.join(glob.glob(input_path)))))
 
     if makesure.strip().upper() == 'Y':
         pool = multiprocessing.Pool(num_processes)

aft_pipelines_analysis/run_info_summary.py

@@ -43,7 +43,10 @@ def cov_depth(cov_info):
     num_processes = 4
     parsing_path = '%s/XK_result/*/*cov.info' % base_outpath
 
-    makesure = input("If your `num of processes >4`, Please be careful of memory. It may stalled whole server.\nUsing %s processes, prepare process listing files: \n . %s\n\nIf you make sure, please type y/Y." % (num_processes,'\n'.join(glob.glob(parsing_path))))
+    makesure = str(input("If your `num of processes >4`, Please be careful of memory. It may stalled whole server.\nUsing %s processes, prepare process listing files: \n . %s\n\nIf you make sure, please type y/Y." %
+                         (num_processes,'\n'.join(glob.glob(parsing_path)))
+                         )
+                   )
 
     if makesure.strip().upper() == 'Y':
         pool = multiprocessing.Pool(num_processes)