fixed typo

phagetermvirome/PhageTerm.py

@@ -142,7 +142,7 @@ def main():
                     host_whole_coverage    = return_dict[core_id][5]
                     list_hybrid            = return_dict[core_id][6]
                     insert                 = return_dict[core_id][7].tolist()
-                    paired_missmatch       = return_dict[core_id][8]
+                    paired_mismatch       = return_dict[core_id][8]
                     reads_tested           = return_dict[core_id][9]
                 else:
                     termini_coverage      += return_dict[core_id][0]
@@ -153,7 +153,7 @@ def main():
                     host_whole_coverage   += return_dict[core_id][5]
                     list_hybrid           += return_dict[core_id][6]
                     insert                += return_dict[core_id][7].tolist()
-                    paired_missmatch      += return_dict[core_id][8]
+                    paired_mismatch      += return_dict[core_id][8]
                     reads_tested          += return_dict[core_id][9]
 
             termini_coverage = termini_coverage.tolist()

phagetermvirome/functions_PhageTerm.py

@@ -88,7 +88,7 @@ def init_ws(p_res,refseq,hostseq):
         host_whole_coverage   = np.array([host_len*[0], host_len*[0]])
         list_hybrid           = np.array([0,0])
         insert                = []
-        paired_missmatch      = 0
+        paired_mismatch      = 0
         read_match            = 0
     else:
         termini_coverage=p_res.interm_res.termini_coverage
@@ -99,12 +99,12 @@ def init_ws(p_res,refseq,hostseq):
         host_whole_coverage=p_res.interm_res.host_whole_coverage
         list_hybrid=p_res.interm_res.list_hybrid
         insert=p_res.interm_res.insert
-        paired_missmatch=p_res.interm_res.paired_mismatch
+        paired_mismatch=p_res.interm_res.paired_mismatch
         k=int(p_res.interm_res.reads_tested)
         #count_line=p_res.count_line-1 # do that because readsCoverage will start by incrementing it of 1
         read_match=p_res.read_match
     return gen_len,host_len,termini_coverage,whole_coverage,paired_whole_coverage,phage_hybrid_coverage,host_hybrid_coverage, \
-           host_whole_coverage,list_hybrid,insert,paired_missmatch,k,count_line,read_match #TODO refactor that.
+           host_whole_coverage,list_hybrid,insert,paired_mismatch,k,count_line,read_match #TODO refactor that.
 
 
 
@@ -198,7 +198,7 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
                         position_end = matchPplus_end_paired
                         insert.append(insert_length)
                     else:
-                        paired_missmatch += 1
+                        paired_mismatch += 1
                         # Paired hybrid
                         if inDArgs.hostseq != "" and matchPplus_start_paired == -1:
                             matchHplus_start, matchHplus_end = applyCoverage(read_paired[:fParms.seed], inDArgs.hostseq)
@@ -258,7 +258,7 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
                             position_start = matchPminus_start_paired
                             insert.append(insert_length)
                         else:
-                            paired_missmatch += 1
+                            paired_mismatch += 1
                             # Paired hybrid
                             if inDArgs.hostseq != "" and matchPminus_start_paired == -1:
                                 matchHplus_start, matchHplus_end = applyCoverage(read_paired[:fParms.seed], inDArgs.hostseq)
@@ -318,7 +318,7 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
 
             chk_handler.check(count_line,core_id,idx_refseq,termini_coverage,whole_coverage,paired_whole_coverage,\
                  phage_hybrid_coverage, host_hybrid_coverage, \
-                 host_whole_coverage,list_hybrid,insert,paired_missmatch,k,read_match) # maybe time to create checkpoint
+                 host_whole_coverage,list_hybrid,insert,paired_mismatch,k,read_match) # maybe time to create checkpoint
 
         else:
             if line[0] == "@":
@@ -356,13 +356,13 @@ def readsCoverage(inRawDArgs,refseq,inDArgs,fParms,return_dict, core_id,line_sta
         host_hybrid_coverage   = correctEdge(host_hybrid_coverage, fParms.edge)
 
     if return_dict!=None and tParms.dir_cov_mm==None:
-        return_dict[core_id] = [termini_coverage, whole_coverage, paired_whole_coverage, phage_hybrid_coverage, host_hybrid_coverage, host_whole_coverage, list_hybrid, np.array(insert), paired_missmatch, k]
+        return_dict[core_id] = [termini_coverage, whole_coverage, paired_whole_coverage, phage_hybrid_coverage, host_hybrid_coverage, host_whole_coverage, list_hybrid, np.array(insert), paired_mismatch, k]
     elif return_dict==None and tParms.dir_cov_mm!=None:
         insert = np.array(insert)
         fic_name = os.path.join(tParms.dir_cov_mm, "coverage" + str(idx_refseq) + "_" + str(core_id))
         res=RCRes(termini_coverage,whole_coverage,paired_whole_coverage,\
                  phage_hybrid_coverage, host_hybrid_coverage, \
-                 host_whole_coverage,list_hybrid,insert,paired_missmatch,k)
+                 host_whole_coverage,list_hybrid,insert,paired_mismatch,k)
         res.save(fic_name)
     else:
         print("Error: readsCoverage must be used either with directory name or return_dict")
@@ -1087,7 +1087,7 @@ def CreateReport(phagename, seed, added_whole_coverage, draw, Redundant, P_left,
     report.append(Paragraph(ptext, styles["Left"]))
     report.append(Spacer(1, 10))
     
-    ptext = '<i><font size=10>PhageTerm software uses raw reads of a phage sequenced with a sequencing technology using random fragmentation and its genomic reference sequence to determine the termini position. The process starts with the alignment of NGS reads to the phage genome in order to calculate the starting position coverage (SPC), where a hit is given only to the position of the first base in a successfully aligned read (the alignment algorithm uses the lenght of the seed (default: 20) for mapping and does not accept gap or missmatch to speed up the process). Then the program apply 2 distinct scoring methods: i) a statistical approach based on the Gamma law; and ii) a method derived from LI and al. 2014 paper.</font></i>'
+    ptext = '<i><font size=10>PhageTerm software uses raw reads of a phage sequenced with a sequencing technology using random fragmentation and its genomic reference sequence to determine the termini position. The process starts with the alignment of NGS reads to the phage genome in order to calculate the starting position coverage (SPC), where a hit is given only to the position of the first base in a successfully aligned read (the alignment algorithm uses the lenght of the seed (default: 20) for mapping and does not accept gap or mismatch to speed up the process). Then the program apply 2 distinct scoring methods: i) a statistical approach based on the Gamma law; and ii) a method derived from LI and al. 2014 paper.</font></i>'
     report.append(Paragraph(ptext, styles["Justify"]))
     report.append(Spacer(1, 5))