changeset 8:10f70fea57b3 draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c

--- a/scripts/S04_find_orf.py	Wed Feb 28 06:03:31 2018 -0500
+++ b/scripts/S04_find_orf.py	Wed Feb 28 10:36:51 2018 -0500
@@ -3,70 +3,62 @@
 #python find_ORF.py file output
 
 def find_orf(entry):
-  orf={}
-  orf_length={}
-  stop=['TAA','TAG','TGA']
-  for i in range(0,3):
-    pos=i
-    orf[i]=[0]
-    while pos<len(entry):
-      if entry[pos:pos+3] in stop:
-        orf[i].append(pos-1)
-        orf[i].append(pos+3)
-      pos+=3
-    orf[i].append(len(entry)-1)
-    orf_length[i]=[]
-    for u in range(1,len(orf[i])):
-      orf_length[i].append(orf[i][u]-orf[i][u-1]+1)
-    orf[i]=[orf[i][orf_length[i].index(max(orf_length[i]))],orf[i][orf_length[i].index(max(orf_length[i]))+1]]
-  orf_max={0:max(orf_length[0]),1:max(orf_length[1]),2:max(orf_length[2])}
-  orf=orf[max(list(orf_max.keys()), key=(lambda k: orf_max[k]))]
-  if orf[0]==0:
-    orf[0]=orf[0]+max(list(orf_max.keys()), key=(lambda k: orf_max[k]))
-  return orf
+    orf={}
+    orf_length={}
+    stop=['TAA','TAG','TGA']
+    for i in range(0,3):
+        pos=i
+        orf[i]=[0]
+        while pos<len(entry):
+            if entry[pos:pos+3] in stop:
+                orf[i].append(pos-1)
+                orf[i].append(pos+3)
+            pos+=3
+        orf[i].append(len(entry)-1)
+        orf_length[i]=[]
+        for u in range(1,len(orf[i])):
+            orf_length[i].append(orf[i][u]-orf[i][u-1]+1)
+        orf[i]=[orf[i][orf_length[i].index(max(orf_length[i]))],orf[i][orf_length[i].index(max(orf_length[i]))+1]]
+    orf_max={0:max(orf_length[0]),1:max(orf_length[1]),2:max(orf_length[2])}
+    orf=orf[max(list(orf_max.keys()), key=(lambda k: orf_max[k]))]
+    if orf[0]==0:
+        orf[0]=orf[0]+max(list(orf_max.keys()), key=(lambda k: orf_max[k]))
+    return orf
 
 
 def reverse_seq(entry):
-  nt={'A':'T','T':'A','G':'C','C':'G', 'N':'N'}
-  seqlist=[]
-  for i in range(len(entry)-1,-1,-1):
-    seqlist.append(nt[entry[i]])
-  seq=''.join(seqlist)
-  return seq
-  
-
+    nt={'A':'T','T':'A','G':'C','C':'G', 'N':'N'}
+    seqlist=[]
+    for i in range(len(entry)-1,-1,-1):
+        seqlist.append(nt[entry[i]])
+    seq=''.join(seqlist)
+    return seq
 
 # RUN
 
-import string, os, sys, re
+import string, os, sys, re, itertools
 
 path_IN = sys.argv[1]
 file_OUT = open(sys.argv[2], "w")
-f_in = open(path_IN, "r")
 inc=1
 threshold=0 #minimal length of the ORF
-while 1:
-  line=f_in.readline()
-  if not line:
-    break
-  line=f_in.readline()
-  name=">"+path_IN[:2]+str(inc)+"_1/1_1.000_"
-  high_plus=find_orf(line[:-1])
-  reverse=reverse_seq(line[:-1])
-  high_minus=find_orf(reverse)
-  if high_plus[1]-high_plus[0]>threshold or high_minus[1]-high_minus[0]>threshold:
-    inc+=1
-    if high_plus[1]-high_plus[0]>high_minus[1]-high_minus[0]:
-      file_OUT.write("%s" %name)
-      file_OUT.write(str(high_plus[1]-high_plus[0]+1)+"\n")
-      file_OUT.write("%s" %line[high_plus[0]:high_plus[1]+1])
-      file_OUT.write("\n")
-    else:
-      file_OUT.write("%s" %name)
-      file_OUT.write(str(high_minus[1]-high_minus[0]+1)+"\n")
-      file_OUT.write("%s" %reverse[high_minus[0]:high_minus[1]+1])
-      file_OUT.write("\n")
-f_in.close()
-file_OUT.close()
 
-  
+with open (path_IN, "r") as f_in:
+    for ignored, line in itertools.izip_longest(*[f_in]*2):    
+        name=">"+path_IN[:2]+str(inc)+"_1/1_1.000_"
+        high_plus=find_orf(line[:-1])
+        reverse=reverse_seq(line[:-1])
+        high_minus=find_orf(reverse)
+        if high_plus[1]-high_plus[0]>threshold or high_minus[1]-high_minus[0]>threshold:
+            inc+=1
+            if high_plus[1]-high_plus[0]>high_minus[1]-high_minus[0]:
+                file_OUT.write("%s" %name)
+                file_OUT.write(str(high_plus[1]-high_plus[0]+1)+"\n")
+                file_OUT.write("%s" %line[high_plus[0]:high_plus[1]+1])
+                file_OUT.write("\n")
+            else:
+                file_OUT.write("%s" %name)
+                file_OUT.write(str(high_minus[1]-high_minus[0]+1)+"\n")
+                file_OUT.write("%s" %reverse[high_minus[0]:high_minus[1]+1])
+                file_OUT.write("\n")
+file_OUT.close()  

--- a/scripts/S05_filter.py	Wed Feb 28 06:03:31 2018 -0500
+++ b/scripts/S05_filter.py	Wed Feb 28 10:36:51 2018 -0500
@@ -2,33 +2,20 @@
 #filters the sequences depending on their length after cap3, makes the sequences names compatible with the phylogeny workflow
 #python filter.py file length_threshold_nucleotides output
 
-import string, os, sys, re
+import string, os, sys, re, itertools
 
 path_IN = sys.argv[1]
-threshold=int(sys.argv[2]) #minimum number of nucleotides for one sequence
+threshold = int(sys.argv[2]) #minimum number of nucleotides for one sequence
 file_OUT = open(sys.argv[3], "w")
-f_in = open(path_IN, "r")
-inc=1
-while 1:
-    line=f_in.readline()
-    if not line:
-        break
-    line=f_in.readline()
-    name=">"+path_IN[:2]+str(inc)+"_1/1_1.000_"
-    if len(line)-1>threshold-1:
-        inc+=1
-        file_OUT.write("%s" %name)
-        file_OUT.write(str(len(line)-1)+"\n")
-        file_OUT.write("%s" %line)
-f_in.close()
+inc = 1
+with open(path_IN, "r") as f_in:
+    for ignored, sequence in itertools.izip_longest(*[f_in]*2):
+        name=">"+path_IN[:2]+str(inc)+"_1/1_1.000_"
+        if len(sequence)-1>threshold-1:
+            inc+=1
+            file_OUT.write("%s" %name)
+            file_OUT.write(str(len(sequence)-1)+"\n")
+            file_OUT.write("%s" %sequence)
 file_OUT.close()
-    
-    
 
-#filtre eventuel sur les petits transcrits
-
-
-
-
-
-  
+#filtre eventuel sur les petits transcrits
\ No newline at end of file