adding class and docstring

sequence_extractor/pre_bedtools.py

@@ -14,6 +14,36 @@ for x in range(len(feat)):
 
 
 bed = {"chr":exons[0],"start":exons[3],"end":exons[4],"transcript_id":superlist,"score":exons[5],"strand":exons[6],"gene_id":idlist}
+class bed:
+   def__init__(self, exons, chr, start, end, transcript_id, score, strand, gene_id):
+       self.exons = exons
+       self.chr = exons[0]
+       self.start = exons[3]
+       self.end = exons[4]
+       self.transcript_id = superlist
+       self.score = exons[5]
+       self.strand = exons[6]
+       self.gene_id = idList
+
+"""Creates BED from GTF for bedtools.
+
+    This class defines a BED from exon annotation from a GTF, for use in bedtools to get sequences with transcript ID as header.
+    Parameters
+    ----------
+    arg1 : GTF file.
+
+    Returns
+    -------
+    Class
+        A class which defines columns in standard BED format.
+
+
+
+    Raises
+    ------
+    TypeError
+        ValueError: Not all columns found in GTF.
+    """
 bed = pd.DataFrame(bed)
 bed.to_csv("bed_file.bed",sep="\t",index=False)
 bed[(bed["gene_id"]=="ENSG00000160072")|(bed["gene_id"]== "ENSG00000142611")|(bed["gene_id"]=="ENSG00000232596")].to_csv("test.bed",sep="\t",index=False,header=None)