changed to hash novel mature names

dmnfarrell · Apr 24, 2017 · 9f799e4 · 9f799e4
1 parent 1d0394a
commit 9f799e4
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Showing 3 changed files with 24 additions and 12 deletions.
diff --git a/smallrnaseq/app.py b/smallrnaseq/app.py
@@ -193,7 +193,8 @@ def map_mirnas(self):
                 return
             new.to_csv(os.path.join(out,'novel_mirna.csv'), index=False)
             #pad mature novel and write to fasta for counting
-            novpad = base.get_mature_padded(new, idkey='id', seqkey='mature')
+            novpad = base.get_mature_padded(new, idkey='mature_id', seqkey='mature')
+            novpad = novpad.drop_duplicates('name')
             utils.dataframe_to_fasta(novpad,os.path.join(out,'novel.fa'),
                                      seqkey='sequence', idkey='name')
             novel.create_report(new, cl, self.species, outfile=os.path.join(out, 'novel.html'))

diff --git a/smallrnaseq/data/styles.css b/smallrnaseq/data/styles.css
@@ -129,7 +129,7 @@ a:active { color: red; }
 	margin-right: 5px;
 	float: right;
 	height: 650px;
-	width: 20%;
+	width: 15%;
 	position: fixed;
 	overflow:hidden;
 	top: 30;
@@ -139,14 +139,15 @@ a:active { color: red; }
 	border: 0px solid transparent;
 	font-family: monospace, sans-serif;
 	overflow-y: auto;
-	height: 600px;
-	width: 400px;
-   display:block;
+	overflow-x: auto;
+	height: 640px;
+	width: 300px;
+    display: block;
 }
 
 .sidebar td, th {
   text-align: left;
-	font-size: 14px;
+	font-size: 12px;
 }
 
 .main, .aside

diff --git a/smallrnaseq/novel.py b/smallrnaseq/novel.py
@@ -589,11 +589,11 @@ def find_mirnas(reads, ref_fasta, score_cutoff=.8, read_cutoff=50, species='',
         anchor = df.iloc[0]
         st = anchor.start
         end = anchor.end
-        m = df.loc[(abs(df.start-st)<=3) & (abs(df.end-end)<=5)]
+        m = df.loc[(abs(df.start-st)<=3) & (abs(df.end-end)<=5)].copy()
         m['mature'] = True
         X.append(m)
         #remainder of reads assigned as non-mature
-        o = df.loc[-df.index.isin(m.index)]
+        o = df.loc[-df.index.isin(m.index)].copy()
         o['mature'] = False
         X.append(o)
 
@@ -638,9 +638,19 @@ def assign_names(df, species=''):
     """Assign name to novel mirna, precursor/mature ids should allow consistent
        identification across datasets"""
 
-    df['id'] = df.apply( lambda x: species+'_novel_'+x.chrom+'_'+str(x.start),1 )
+    df['precursor_id'] = df.apply( lambda x: species+'_novel_'+x.chrom+'_'+str(x.start),1 )
+    df['mature_id'] = df.apply( lambda x: species+'_'+encode_name(x.mature), 1 )
     return
 
+def encode_name(s):
+    """hash a sequence into a short string"""
+
+    import hashlib
+    h = hashlib.md5(s.encode())
+    s = h.digest().encode('base64')[:8]
+    s.replace('/','x')
+    return s
+
 def forna_url(precursor, mature, star=None, struct=None):
     """Create link to view mirna structure in forna web app"""
 
@@ -688,13 +698,13 @@ def create_report(df, reads, species=None, outfile='report.html'):
     h += '<h3>novel miRNA predictions</h3>'
     h += '</div>'
     h += '<div class="sidebar">'
-    links = df[['id','mature_reads']].copy()
-    links['id'] = links.id.apply(lambda x: ('<a href=#%s > %s </a>' %(x,x)))
+    links = df[['mature_id','mature_reads','chrom']].copy()
+    links['mature_id'] = links.mature_id.apply(lambda x: ('<a href=#%s > %s </a>' %(x,x)))
     h += links.to_html(escape=False, classes='sidebar', index=False)
     h += '</div>'
 
     df = df.copy()
-    df = df.set_index('id')
+    df = df.set_index('mature_id')
 
     ens_sp = pd.read_csv(os.path.join(datadir, 'ensembl_names.csv'), index_col=0)
     if species in ens_sp.index: