diff profrep_masking.py @ 0:a5f1638b73be draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/profrep_masking.py	Wed Jun 26 08:01:42 2019 -0400
@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+
+import argparse
+from Bio import SeqIO
+from Bio.Seq import MutableSeq
+from Bio.Alphabet import generic_dna
+import sys
+
+
+def main(args):
+    # Command line arguments
+    QUERY = args.query
+    MODE = args.mode
+    REPEAT_GFF = args.repeat_gff
+    MASKED = args.output_masked
+
+    repeats_all = get_indices(REPEAT_GFF)
+
+    if MODE == "lowercase":
+        lower_mask(QUERY, repeats_all, MASKED)
+    else:
+        N_mask(QUERY, repeats_all, MASKED)
+
+
+def get_indices(REPEAT_GFF):
+    '''
+	Get indices of repeats from GFF file to mask
+	'''
+    repeats_all = {}
+    with open(REPEAT_GFF, "r") as repeats_gff:
+        for line in repeats_gff:
+            if not line.startswith("#"):
+                seq_id = line.split("\t")[0]
+                start_r = line.split("\t")[3]
+                end_r = line.split("\t")[4]
+                if seq_id in repeats_all.keys():
+                    repeats_all[seq_id].append([int(start_r), int(end_r)])
+                else:
+                    repeats_all[seq_id] = [[int(start_r), int(end_r)]]
+    return repeats_all
+
+
+def lower_mask(QUERY, repeats_all, MASKED):
+    allSeqs = list(SeqIO.parse(QUERY, 'fasta'))
+    for singleSeq in allSeqs:
+        mutable = MutableSeq(str(singleSeq.seq), generic_dna)
+        for index in repeats_all[singleSeq.id]:
+            for item in range(index[0] - 1, index[1]):
+                mutable[item] = mutable[item].lower()
+        singleSeq.seq = mutable
+    with open(MASKED, "w") as handle:
+        SeqIO.write(allSeqs, handle, 'fasta')
+
+
+def N_mask(QUERY, repeats_all, MASKED):
+    allSeqs = list(SeqIO.parse(QUERY, 'fasta'))
+    for singleSeq in allSeqs:
+        mutable = MutableSeq(str(singleSeq.seq), generic_dna)
+        for index in repeats_all[singleSeq.id]:
+            for item in range(index[0] - 1, index[1]):
+                mutable[item] = "N"
+        singleSeq.seq = mutable
+    with open(MASKED, "w") as handle:
+        SeqIO.write(allSeqs, handle, 'fasta')
+
+
+if __name__ == "__main__":
+
+    # Command line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-q',
+                        '--query',
+                        type=str,
+                        required=True,
+                        help='query sequence to be processed')
+    parser.add_argument('-rg',
+                        '--repeat_gff',
+                        type=str,
+                        required=True,
+                        help='query sequence to be processed')
+    parser.add_argument('-m',
+                        '--mode',
+                        default="lowercase",
+                        choices=['lowercase', 'N'],
+                        help='query sequence to be processed')
+    parser.add_argument('-o',
+                        '--output_masked',
+                        type=str,
+                        default="output_masked",
+                        help='query sequence to be processed')
+
+    args = parser.parse_args()
+    main(args)