diff merge_pcr_duplicates.py @ 8:17ef0e0dae68 draft

Uploaded

--- a/merge_pcr_duplicates.py	Tue Nov 10 08:12:25 2015 -0500
+++ b/merge_pcr_duplicates.py	Tue Nov 10 09:13:44 2015 -0500
@@ -8,7 +8,7 @@
 
 Input:
 * bed6 file containing alignments with fastq read-id in name field
-* fasta library with fastq read-id as sequence ids
+* fastq library of random barcodes
 
 Output:
 * bed6 file with random barcode in name field and number of PCR duplicates as
@@ -61,6 +61,11 @@
 parser.add_argument(
     "-o", "--outfile",
     help="Write results to this file.")
+parser.add_argument(
+    "--fasta-library",
+    dest="fasta_library",
+    action="store_true",
+    help="Read random barcode library as fasta format.")
 # misc arguments
 parser.add_argument(
     "-v", "--verbose",
@@ -93,7 +98,10 @@
 
 # load barcode library into dictionary
 input_handle = open(args.bclib, "rU")
-input_seq_iterator = SeqIO.parse(input_handle, "fasta")
+if args.fasta_library:
+    input_seq_iterator = SeqIO.parse(input_handle, "fasta")
+else:
+    input_seq_iterator = SeqIO.parse(input_handle, "fastq")
 bcs = pd.DataFrame.from_records(
     data=fasta_tuple_generator(input_seq_iterator),
     columns=["read_id", "bc"])