Mercurial > repos > bornea > saint_preproc

changeset 17:40c88c39f8d7 draft

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Uploaded
author bornea
date Tue, 17 Nov 2015 12:14:10 -0500
parents 413ffa0e80e7
children b230824e1a0e
files SAINT_preprocessing_v6.py
diffstat 1 files changed, 17 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/SAINT_preprocessing_v6.py	Tue Nov 17 11:05:54 2015 -0500
+++ b/SAINT_preprocessing_v6.py	Tue Nov 17 12:14:10 2015 -0500
@@ -26,7 +26,6 @@
 
 
 baits = make_bait.split()
-print baits
 i = 0
 bait_file_tmp = open("bait.txt", "wr")
 order = [] 
@@ -135,6 +134,7 @@
     count = 0
     for i in lines:           
         if ">sp" in i:
+            namer = i.split("|")[2]
             if uniprot_accession_in == i.split("|")[1]:
                 match = count+1
                 if 'GN=' in i:
@@ -150,6 +150,21 @@
                     else:
                         break
                 return ReturnValue1(seqlength, genename)
+            elif uniprot_accession_in == namer.split(" "):
+                match = count+1
+                if 'GN=' in i:
+                    lst = i.split('GN=')
+                    lst2 = lst[1].split(' ')
+                    genename = lst2[0]
+                if 'GN=' not in i:
+                    genename = 'NA'
+                while ">sp" not in lines[match]:
+                    if match <= db_len:
+                        seqlength = seqlength + len(lines[match].strip())
+                        match = match + 1
+                    else:
+                        break
+                return ReturnValue1(seqlength, genename)
         count = count + 1
         
 
@@ -242,5 +257,5 @@
 if __name__ == '__main__':
     main(infile, baitfile)
 
-os.rename('inter.txt', sys.argv[4])
+os.rename("inter.txt", sys.argv[4])
 os.rename("bait.txt", sys.argv[7])