update for gen_fusion_file

scripts/make_fusion_genes.py

@@ -0,0 +1,79 @@
+"""
+Generate a user-defined fusion file 
+
+Input file should be a text file containing 
+1. gene name and 
+2. transcript name (optional)
+
+For example:
+gene1   transcript1
+gene2
+gene3   transcript3
+"""
+__author__ = "Kai"
+__date__ = "20/05/2020"
+
+import argparse
+
+
+def read_genelist(inputf):
+    with open(inputf, "r") as fh:
+        for line in fh:
+            yield line.rstrip("\n").split()
+
+
+def make_fusion_gene(gene, fw, refflat):
+    # no transcript specified --> use the longest transcript
+    if len(gene) == 1:
+        transcripts = {}
+        with open(refflat, "r") as fh:
+            for line in fh:
+                if gene[0] not in line:
+                    continue
+                _, transcript, chrom, _, start, end, _, _, _, exonstart, exonend = line.rstrip("\n").split("\t")
+                transcripts[transcript] = (chrom, start, end, exonstart, exonend)
+        transcript = get_longest_transcript(transcripts.keys(), refflat)
+        chrom, start, end, exonstart, exonend  = transcripts[transcript]
+
+    # use user-specified transcript
+    elif len(gene) == 2:
+        with open(refflat, "r") as fh:
+            for line in fh:
+                if gene[1] not in line:
+                    continue
+                _, transcript, chrom, _, start, end, _, _, _, exonstart, exonend = line.rstrip("\n").split("\t")
+                break
+
+    # write to a file
+    header = f">{gene[0]}_{transcript},{chrom}:{start}-{end}\n"
+    fw.write(header)
+    exons = list(zip(exonstart.split(","), exonend.split(",")))[:-1]
+    for index, each_exon in enumerate(exons, start=1):
+        fw.write(f'{index},{each_exon[0]},{each_exon[1]}\n')
+    fw.write("\n")
+
+
+def get_longest_transcript(transcripts, refflat):
+    longest_length = 0
+    longest_transcript = ""
+    with open(refflat, "r") as fh:
+        for line in fh:
+            line = line.strip().split()
+            if line[1] in transcripts:
+                length = int(line[5]) - int(line[4])
+                if length > longest_length:
+                    longest_length = length
+                    longest_transcript = line[1]
+    return longest_transcript
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("input", help="Input filename")
+    parser.add_argument("-r", "--refflat", required=True, help="Path to the refFlat.txt file, need to be downloaded from UCSC in advance")
+    parser.add_argument("-o", "--output", required=True, help="The output filename")
+    args = parser.parse_args()
+
+    with open(args.output, "w") as fw:
+        for gene in read_genelist(args.input):
+            make_fusion_gene(gene, fw, args.refflat)