updated index pipeline with latest index locations

cribbslab · Jul 25, 2023 · 3da74a7 · 3da74a7
1 parent 683c4ee
commit 3da74a7
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Showing 3 changed files with 64 additions and 44 deletions.
diff --git a/tallytrin/pipeline_index.py b/tallytrin/pipeline_index.py
@@ -110,13 +110,14 @@ def seperate_by_barcode(infile, outfile):
     '''
     Identify barcode and save to different samples
     '''
-
+    primer = PARAMS['primer']
     name = outfile.replace("seperate_samples.dir/", "")
     name = name.replace(".fastq", "")
 
     PYTHON_ROOT = os.path.join(os.path.dirname(__file__), "python/")
 
-    statement = '''python %(PYTHON_ROOT)s/identify_index.py --infile=%(infile)s --name=%(name)s'''
+    statement = '''python %(PYTHON_ROOT)s/identify_index.py --infile=%(infile)s --name=%(name)s
+                   --primer=%(primer)s'''
 
     P.run(statement)
 

diff --git a/tallytrin/pipeline_index/pipeline.yml b/tallytrin/pipeline_index/pipeline.yml
@@ -7,4 +7,6 @@ copyright: cribbslab (2021)
 
 split: 400000
 
-job_options: -t 48:00:00
+job_options: -t 48:00:00
+
+primer: AAGCAGTGGTAT
diff --git a/tallytrin/python/identify_index.py b/tallytrin/python/identify_index.py
@@ -26,7 +26,8 @@
                     help='infile fastq  file')
 parser.add_argument("--name", default=None, type=str,
                     help='name of sample')
-
+parser.add_argument("--primer", default=None, type=str,
+                    help='primer')
 args = parser.parse_args()
 
 L.info("args:")
@@ -113,15 +114,20 @@ def remove_indels(x, umi, first):
         'CCCTTTCCCTTT': '12'}
 
 
+tab = str.maketrans("ACTG", "TGAC")
+
+def reverse_complement(seq):
+    return seq.translate(tab)[::-1]
 
 
 with pysam.FastxFile(args.infile) as fh:
 
     for record in fh:
 
         seq_nano = record.sequence
+        primer = "(%s){e<=0}" % (args.primer)
 
-        m=regex.finditer("(AAGCAGTGGT){e<=1}", str(seq_nano))
+        m=regex.finditer(str(primer), str(seq_nano[:150]))
 
 
         for i in m:
@@ -156,46 +162,57 @@ def remove_indels(x, umi, first):
                 fname = name + '' + "Unidentified.fastq"
 
             if fname == name + '' + 'Unidentified.fastq':
-                m=regex.finditer("(ACCACTGCTT){e<=1}", str(seq_nano))
-                for i in m:
-                    barcode = seq_nano[int(i.end()):int(i.end()+12)]
-                    barcode = remove_point_mutations(barcode)[0]
-                    barcode = barcode[::3]
-                    if barcode == 'GCAT':
-                        fname = name + '' + "Sample1.fastq"
-                    elif barcode == 'CTGA':
-                        fname = name + '' + "Sample2.fastq"
-                    elif barcode == 'AGTC':
-                        fname = name + '' + "Sample3.fastq"
-                    elif barcode == 'TACG':
-                        fname = name + '' + "Sample4.fastq"
-                    elif barcode == 'TCGT':
-                        fname = name + '' + "Sample5.fastq"
-                    elif barcode == 'ATCA':
-                        fname = name + '' + "Sample6.fastq"
-                    elif barcode == 'CGAC':
-                        fname = name + '' + "Sample7.fastq"
-                    elif barcode == 'GATG':
-                        fname = name + '' + "Sample8.fastq"
-                    elif barcode == 'CTCT':
-                        fname = name + '' + "Sample9.fastq"
-                    elif barcode == 'TATA':
-                        fname = name + '' + "Sample10.fastq"
-                    elif barcode == 'GCGC':
-                        fname = name + '' + "Sample11.fastq"
-                    elif barcode == 'CTCT':
-                        fname = name + '' + "Sample12.fastq"
-                    else:
-                        fname = name + '' + "Unidentified.fastq"
-                if os.path.exists('seperate_samples.dir/' + fname):
-
-                    with open('seperate_samples.dir/'+ fname, "a") as myfile:
-                        myfile.write("@%s\n%s\n+\n%s\n" % (record.name, record.sequence, record.quality))
-                else:
-                    with iotools.open_file('seperate_samples.dir/' + fname, "w") as myfile:
-                        myfile.write("@%s\n%s\n+\n%s\n" % (record.name, record.sequence, record.quality))
+                pass
+
+            if os.path.exists('seperate_samples.dir/' + fname):
+
+                with open('seperate_samples.dir/'+ fname, "a") as myfile:
+                    myfile.write("@%s\n%s\n+\n%s\n" % (record.name, record.sequence, record.quality))
+            else:
+                with iotools.open_file('seperate_samples.dir/' + fname, "w") as myfile:
+                    myfile.write("@%s\n%s\n+\n%s\n" % (record.name, record.sequence, record.quality))
+
+        primer2 = "(%s){e<=0}" % (reverse_complement(args.primer))
+
+        m=regex.finditer(str(primer2), str(seq_nano[:-150]))
+        for i in m:
+            barcode = seq_nano[int(i.end()):int(i.end()+12)]
+            barcode = remove_point_mutations(barcode)[0]
+            barcode = barcode[::3]
+            if barcode == 'GCAT':
+                fname = name + '' + "Sample1.fastq"
+            elif barcode == 'CTGA':
+                fname = name + '' + "Sample2.fastq"
+            elif barcode == 'AGTC':
+                fname = name + '' + "Sample3.fastq"
+            elif barcode == 'TACG':
+                fname = name + '' + "Sample4.fastq"
+            elif barcode == 'TCGT':
+                fname = name + '' + "Sample5.fastq"
+            elif barcode == 'ATCA':
+                fname = name + '' + "Sample6.fastq"
+            elif barcode == 'CGAC':
+                fname = name + '' + "Sample7.fastq"
+            elif barcode == 'GATG':
+                fname = name + '' + "Sample8.fastq"
+            elif barcode == 'CTCT':
+                fname = name + '' + "Sample9.fastq"
+            elif barcode == 'TATA':
+                fname = name + '' + "Sample10.fastq"
+            elif barcode == 'GCGC':
+                fname = name + '' + "Sample11.fastq"
+            elif barcode == 'CTCT':
+                fname = name + '' + "Sample12.fastq"
+            else:
+                fname = name + '' + "Unidentified.fastq"
 
+            if os.path.exists('seperate_samples.dir/' + fname):
+
+                with open('seperate_samples.dir/'+ fname, "a") as myfile:
+                    myfile.write("@%s\n%s\n+\n%s\n" % (record.name, record.sequence, record.quality))
             else:
-                break
+                with iotools.open_file('seperate_samples.dir/' + fname, "w") as myfile:
+                    myfile.write("@%s\n%s\n+\n%s\n" % (record.name, record.sequence, record.quality))
+