changeset 1:b25b0f210e10 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_fasta.py	Thu Aug 04 12:08:49 2016 -0400
@@ -0,0 +1,90 @@
+# -*- coding: utf-8 -*-
+"""
+Python-code: Merge Scaffold Samples Report files
+@author = Brent Kuenzi
+@email = [e-mail]
+"""
+#######################################################################################
+## Description: ##
+#    This program will filter a fasta file using a data file
+#    containing an "Accession" or "Accession Number" column
+## Required input: ##
+# 1) fasta file to be filtered
+# 2) data file containing a "Accession" or "Accession Number" column
+
+
+import sys
+import os
+def readtab(infile): # read in tab-delim text
+    with open(infile,'r') as x:
+        output = []
+        for line in x:
+            line = line.strip()
+            temp = line.split('\t')
+            output.append(temp)
+    return output
+def getAccessions(infile): # get list of protein accessions from your data
+    data = readtab(infile)
+    cnt = 0
+    header_start = 0
+    prot_start = 0
+    for i in data:
+        if "Accession" in i: # finds the start of header
+            header_start = cnt
+            break
+        cnt += 1
+    header = data[header_start]
+    if "Accession Number" in header:
+        prot_start = header.index("Accession Number")
+    elif "Accession" in header:
+        prot_start = header.index("Accession")
+    proteins = []
+    for protein in data[1:]:
+        proteins.append(protein[prot_start])
+    return proteins
+def FilterFastaSeq(infile,accession): # fasta file and UniprotID/SwissprotID
+    input_data = readtab(infile)
+    seq=[]
+    header=[]
+    temp=[]
+    flag = 0
+    cnt = 0
+    for i in input_data:
+        cnt+=1
+        if flag == 1: # once we have a hit, start adding the sequences
+            if ">" not in i[0]: # don't add the headers to the sequence
+                temp.append(i[0])
+                #print temp
+        if i[0].startswith(">"): # is it a fasta header?    
+            if temp != []: # if it is a continued fasta header, add old sequences to the sequence list
+            # will this cutoff the last on of the file?
+                merged = "\n".join(temp)
+                if merged!="":
+                    seq.append(merged)
+                    temp=[]
+            lst = i[0].split('|')
+            ID1 = lst[1]
+            lst2 = lst[2].split(' ')
+            ID2 = lst2[0]
+            flag = 0
+            if ID1 in accession: # are the IDs part of your data?
+                flag+=1
+                header.append(i[0]) # if it is then append it
+            if ID2 in accession: # are the IDs part of your data?
+                flag+=1
+                header.append(i[0]) # if it is then append it
+        if cnt == len(input_data): # account for last fasta sequence in file
+            if temp != []:
+                merged = "\n".join(temp)
+                if merged!="":
+                    seq.append(merged)
+    cnt=0
+    with open("output.fasta","wt") as x:
+        for i in header:
+            x.write(i+'\n'+seq[cnt]+'\n')
+            cnt+=1
+fasta = sys.argv[1] # fasta file to filter
+data = sys.argv[2] # scaffold report #2 -- filename
+
+FilterFastaSeq(fasta,getAccessions(data))
+os.rename("output.fasta", sys.argv[3])
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