diff scripts/functions.py @ 4:6709645eff5d draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/functions.py	Wed Jan 17 08:53:53 2018 -0500
@@ -0,0 +1,229 @@
+import string
+
+# Used in S05 and
+def split_file(path_in, keyword):
+
+    file_in = open(path_in, "r")    
+    RUN = ''
+    BASH1={}
+    
+    with open(path_in, "r") as file_in:    
+        for nextline in file_in.readlines():       
+
+            ##################################
+            ###  [A] FORMATTING QUERY NAME ###
+
+            # Get query name
+            if nextline[0:6]=='Query=':
+                L1 = string.split(nextline, "||")
+                L2 = string.split(L1[0], " ")
+                query = L2[1]
+                if query[-1] == "\n":
+                    query = query[:-1]
+
+            ###  [A] END FORMATTING QUERY NAME ###
+            ######################################
+            
+
+            ### split the file with keyword ###
+            if keyword in nextline:
+                # Two cases here:
+                #1# If it is the first "RUN" in the block (i.e. the first occurence of "BLASTN" in the file), we have just to add the new lines in the "RUN" list ... 2nd , we have also to detect the 'key' of bash1, which is the "query" name ... and third we will have to save this "RUN" in the bash1, once we will have detected a new "RUN" (i.e. a new line beginning with "BLASTN".
+                #2# If it isn't the first run, we have the save the previous "RUN" in the "bash1", before to re-initialize the RUN list (RUN =[]), before to append lines to the new "RUN"
+
+                if RUN == '':                          # case #1#
+                    RUN = RUN + nextline     # we just added the first line of  the file
+
+                else:                                # case #2# (there was a run before)
+                    BASH1[query] = RUN    # add the previous run to the bash
+                    RUN = ''                           # re-initialize the "RUN"
+                    RUN = RUN + nextline    # add the line starting with the keyword ("BLASTN") (except the first line of the file (the first "RUN")
+
+            else:                          # Treatment of the subsequent lines of the one starting with the keyword ("BLASTN")  (which is not treated here but previously)
+                RUN = RUN + nextline
+            
+
+        if RUN:                           
+            BASH1[query] = RUN                       # add the last "RUN"
+   
+    
+    return(BASH1)
+
+def detect_Matches(query, MATCH, WORK_DIR, bash1):
+    F5 = open("%s/blastRun2.tmp" %WORK_DIR, 'w')
+    F5.write(bash1[query])
+    F5.close()
+
+    F6 = open("%s/blastRun2.tmp" %WORK_DIR, 'r')
+    list1 =[]
+    list2 =[]
+
+    while 1:
+        nexteu = F6.readline()
+
+        if not nexteu : break
+
+        if "***** No hits found ******" in nexteu :
+            hit = 0
+            break
+        
+        if 'Sequences producing significant alignments:' in nexteu:
+            hit = 1
+            F6.readline() # jump a line
+
+            while 1:
+                nexteu2 = F6.readline()
+            
+                if nexteu2[0]==">": break
+
+                ######################################
+                ### [B] FORMAT MATCH NAME 1st STEP ###
+               
+                if nexteu2 != '\n':
+                    LL1 = string.split(nexteu2, " ") # specific NORTH database names !!!!!!!
+                    match = LL1[0]                     #### SOUTH databank // NORTH will have "|" separators
+                    list1.append(match)
+
+                    match2 = ">" + LL1[0]        # more complete name // still specific NORTH database names !!!!!!!
+                    list2.append(match2)         #### SOUTH databank // NORTH will have "|" separators
+
+                    if MATCH == 0:        ## Only read the 1rst line (i.e. the First Match)
+                        break                
+                    else:                 ## Read the other lines (i.e. All the Matches)
+                        continue
+
+                ### [B] END FORMAT MATCH NAME 1st STEP ###
+                ##########################################     
+      
+            break
+    
+    F6.close()
+    return(list1, list2, hit)    # list1 = short name // list2 = more complete name
+
+def get_information_on_matches(list_of_line):
+
+    for line in list_of_line:
+
+        ## Score and Expect
+        if "Score" in line:
+            line = line[:-1]  # remove "\n"
+            S_line = string.split(line, " = ") 
+            Expect = S_line[-1]  ## ***** Expect
+            S_line2 = string.split(S_line[1], " bits ")
+            Score = string.atof(S_line2[0])
+
+        ## Identities/gaps/percent/divergence/length_matched
+        elif "Identities" in line:
+            line = line[:-1]  # remove "\n"
+            g = 0
+
+            if "Gaps" in line:
+                pre_S_line = string.split(line, ",")
+                identity_line = pre_S_line[0]
+                gaps_line = pre_S_line[1]
+                g = 1
+            else:
+                identity_line = line
+                g = 0
+
+            ## treat identity line
+            S_line = string.split(identity_line, " ")
+
+            identities = S_line[-2]  ## ***** identities
+
+            S_line2 = string.split(identities, "/")
+            hits = string.atof(S_line2[0])                 ## ***** hits
+            length_matched = string.atof(S_line2[1])       ## ***** length_matched
+            abs_nb_differences = length_matched - hits     ## ***** abs_nb_differences
+
+            identity_percent =   hits/length_matched * 100  ## ***** identity_percent
+
+            divergence_percent = abs_nb_differences/length_matched*100  ## ***** divergence_percent
+
+            ## treat gap line if any
+            if g ==1:    # means there are gaps
+                S_line3 = string.split(gaps_line, " ")
+                gaps_part  = S_line3[-2]
+                S_line4 = string.split(gaps_part, "/")
+                gaps_number = string.atoi(S_line4[0])                                       ## ***** gaps_number
+                
+                real_differences = abs_nb_differences - gaps_number                         ## ***** real_differences
+                real_divergence_percent = (real_differences/length_matched)*100             ## ***** real_divergence_percent
+            else:
+                gaps_number = 0               
+                real_differences = 0
+                real_divergence_percent = divergence_percent
+
+        ## Frame
+        elif "Frame" in line:
+            line = line[:-1]  # remove "\n"
+            S_line = string.split(line, " = ")
+            frame = S_line[1]
+
+    list_informations=[length_matched, Expect, Score, identities, hits, identity_percent, divergence_percent,gaps_number, real_divergence_percent, frame, length_matched]
+
+    return(list_informations)
+
+# Used in S06, S09, S11
+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)
+
+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)
+
+def filter_redondancy(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])
+         l2 = string.split(match_name, "||")
+         short_match_name = l2[0][1:]
+         binom = "%s_%s" %(short_query_name, short_match_name)
+         
+         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)
\ No newline at end of file