diff scripts/S06_post_processing_of_pairwise.py @ 1:c8af52875b0f draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/S06_post_processing_of_pairwise.py	Thu Apr 13 09:46:45 2017 -0400
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+## AUTHOR: Eric Fontanillas
+## LAST VERSION: 14/08/14 by Julie BAFFARD
+
+MINIMUM_LENGTH = 1    #bp
+
+
+############################
+##### DEF1 : Get Pairs #####
+############################
+def get_pairs(fasta_file_path):
+    F2 = open(fasta_file_path, "r")
+    list_pairwises = []
+    while 1:
+        next2 = F2.readline()
+        if not next2:
+            break
+        if next2[0] == ">":
+            fasta_name_query = next2[:-1]
+            next3 = F2.readline()
+            fasta_seq_query = next3[:-1]
+            next3 = F2.readline()    ## jump one empty line (if any after the sequence)
+            fasta_name_match = next3[:-1]
+            next3 = F2.readline()
+            fasta_seq_match = next3[:-1]
+            pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
+            
+            ## ADD pairwise with condition
+            list_pairwises.append(pairwise)
+    F2.close()
+
+    return(list_pairwises)
+##############################################
+
+#################################
+##### DEF2 : Extract length #####
+#################################
+def extract_length(length_string):   # format length string = 57...902
+    l3 = string.split(length_string, "...")
+    n1 = string.atoi(l3[0])
+    n2 = string.atoi(l3[1])
+    length = n2-n1
+
+    return(length)
+##############################################
+
+
+####################################
+##### DEF3 : Remove Redondancy ##### 
+####################################
+def filter_redondancy_and_length(list_paireu, MIN_LENGTH):
+    
+    bash1 = {}
+    list_pairout = []
+    
+    for pair in list_paireu:
+         query_name = pair[0]
+         query_seq = pair[1]
+         match_name = pair[2]
+         match_seq = pair[3]
+
+         l1 = string.split(query_name, "||")
+         short_query_name = l1[0][1:]
+         length_matched =  extract_length(l1[1])               ### DEF2 ###
+         l2 = string.split(match_name, "||")
+         short_match_name = l2[0][1:]
+         binom = "%s_%s" %(short_query_name, short_match_name)
+
+         ## TEST FOR REDONDANCY
+         ## REDONDANCY OF BINOME!!!! => MATCHE BETWEEN THE SAME 2 CONTIGS, BUT AT DIFFERENT POSITIONS ON THE CONTIG
+         ## REDONDANCY NOT REMOVED HERE:
+         ## 1/ Several "TERA" match with one "APN"  (Counted in script "09_formatMatch_getBackNucleotides.py")
+         ## 2/ Several "APN" match with one "TERA" (Counted
+         if binom not in bash1.keys():
+             bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
+         else:
+             old_length = bash1[binom][-1]
+             if length_matched > old_length:
+                 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
+
+    
+    for bino in bash1.keys():
+        length = bash1[bino][-1]
+        if length > MIN_LENGTH:
+            list_pairout.append(bash1[bino])
+
+    return(list_pairout)
+##############################################
+
+
+#######################
+##### RUN RUN RUN #####
+#######################
+import string, os, time, re, sys
+
+## 1 ## INPUT/OUTPUT
+SHORT_FILE = sys.argv[1] #short-name-query_short-name-db
+
+F_IN = "%s/06_PairwiseMatch_%s.fasta" %(SHORT_FILE, SHORT_FILE) 
+
+F_OUT = "%s/09_PairwiseMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE) 
+File_OUT = open(F_OUT, "w")
+
+F_OUT2 = "%s/09_onlyMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE) 
+File_OUT2 = open(F_OUT2, "w")
+
+## 2 ## RUN
+list_pairwises = get_pairs(F_IN)           ### DEF1 ###
+list_pairwises_filtered1 = filter_redondancy_and_length(list_pairwises, MINIMUM_LENGTH)                ### DEF3 ###
+
+i = 0
+for pair in list_pairwises_filtered1:
+     i = i+1
+
+     ## Write pairwise alignment
+     File_OUT.write("%s\n" %pair[0])
+     File_OUT.write("%s\n" %pair[1])
+     File_OUT.write("%s\n" %pair[2])
+     File_OUT.write("%s\n" %pair[3])
+
+     ## Write only "matches" [AND UNGAP THEM: needed before the 2nd run of blast]
+     File_OUT2.write("%s\n" %pair[2])
+     seq_match = pair[3]
+     seq_match_ungapped = string.replace(seq_match, "-", "")
+     File_OUT2.write("%s\n" %seq_match_ungapped)
+    
+File_OUT.close()
+File_OUT2.close()