changeset 5:e370df93715d draft

Uploaded

--- a/UMI_riboseq_processing/UMI.py	Tue Jun 21 08:32:44 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-import gzip
-from mimetypes import guess_type
-from functools import partial
-from Bio import SeqIO
-from sys import argv, exit
-
-def copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output):
-    # find wheather its plain or gzipped fastq
-    encoding = guess_type(pathToFastaFile)[1]  # uses file extension
-    _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open
-    # output file will be in gz format
-    output = gzip.open(output,"wt")
-    # open and parse
-    with _open(pathToFastaFile) as f:
-        for record in SeqIO.parse(f, 'fastq'):
-            lines = record.format('fastq').split('\n') # list of each record: id, seq, '+', quality
-            header = lines[0]
-            seq = lines[1]
-            sep = lines[2]
-            qual = lines[3]
-            trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode
-            UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN
-            split_header = header.split(" ")
-            new_header = split_header[0]+"_"+UMI+" "+split_header[1]
-            if qual[-1:] == "\n":
-                new_qual = qual[2:-6]+"\n"
-            else:
-                new_qual = qual[2:-6]
-            output.write(new_header+'\n')
-            output.write(trimmed_seq)
-            output.write(sep+'\n')
-            output.write(new_qual+'\n')
-
-    output.close()
-
-def main():
-    if len(argv) != 3:
-        exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")
-
-    # Get paths
-    pathToFastaFile = argv[1]
-    output = argv[2]
-    copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output)
-
-if __name__ == "__main__":
-    main()

--- a/UMI_riboseq_processing/UMI_riboseq.xml	Tue Jun 21 08:32:44 2022 +0000
+++ b/UMI_riboseq_processing/UMI_riboseq.xml	Tue Jun 21 09:22:37 2022 +0000
@@ -1,6 +1,5 @@
-<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.4">
+<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.5">
 <requirements>
-  <requirement type="package" version="1.75">biopython</requirement>
 </requirements>
 <command detect_errors="exit_code">
 <![CDATA[ python3 '$__tool_directory__/UMI.py' $reads $output ]]>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/UMI_riboseq_processing/UMI_test.py	Tue Jun 21 09:22:37 2022 +0000
@@ -0,0 +1,56 @@
+import gzip
+from mimetypes import guess_type
+from functools import partial
+from sys import argv, exit
+import itertools
+from itertools import zip_longest
+
+
+def grouper(iterable, n, fillvalue=None):
+    args = [iter(iterable)] * n
+    return zip_longest(*args, fillvalue=fillvalue)
+
+
+chunk_size=4
+
+def copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output):
+    # find wheather its plain or gzipped fastq
+    encoding = guess_type(pathToFastaFile)[1]  # uses file extension
+    _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open
+    # output file will be in gz format
+    output = gzip.open(output,"wt")
+    # open and parse
+    with _open(pathToFastaFile) as f:
+        for lines in grouper(f, chunk_size, ""):
+            #lines = record.format('fastq').split('\n') # list of each record: id, seq, '+', quality
+            header = lines[0]
+            seq = lines[1]
+            sep = lines[2]
+            qual = lines[3]
+            trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode
+            UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN
+            split_header = header.split(" ")
+            new_header = split_header[0]+"_"+UMI+" "+split_header[1]
+            if qual[-1:] == "\n":
+                new_qual = qual[2:-6]+"\n"
+            else:
+                new_qual = qual[2:-6]
+            output.write(new_header)
+            output.write(trimmed_seq)
+            output.write(sep)
+            output.write(new_qual)
+
+    output.close()
+
+    
+def main():
+    if len(argv) != 3:
+        exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")
+
+    # Get paths
+    pathToFastaFile = argv[1]
+    output = argv[2]
+    copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output)
+
+if __name__ == "__main__":
+    main()