diff gtf_to_position_file.py @ 0:be7c0c692879 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/infercnv commit 7e7abdef47fdf68f3ca69b75a8477dabc7bfa965

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf_to_position_file.py	Tue Jul 23 15:43:10 2024 +0000
@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+
+
+"""
+Converts GTF files to proprietary formats.
+"""
+
+
+# Import statements
+import argparse
+import csv
+import gzip
+import os
+
+
+__author__ = 'Timothy Tickle, Itay Tirosh, Brian Haas'
+__copyright__ = 'Copyright 2016'
+__credits__ = ["Timothy Tickle"]
+__license__ = 'BSD-3'
+__maintainer__ = 'Timothy Tickle'
+__email__ = '[e-mail]'
+__status__ = 'Development'
+
+
+def open_file(file_path):
+    """ Open a file, handling gzip if necessary.
+
+    :param file_path: Path to input file
+    :type file_path: String
+
+    :returns: File object
+    """
+    if file_path.endswith('.gz'):
+        return gzip.open(file_path, 'rt')
+    else:
+        return open(file_path, 'r')
+
+
+def convert_to_positional_file(input_gtf, output_positional, attribute_key):
+    """ Convert input GTF file to positional file.
+
+    :param input_gtf: Path to input gtf file
+    :type input_gtf: String
+    :param output_positional: Path to output positional file
+    :type output_positional: String
+    :param attribute_key: Key of the GTF attribute to use for feature/row names
+    :type attribute_key: String
+
+    :returns: Indicator of success (True) or Failure (False)
+    :rtype: boolean
+    """
+
+    if not input_gtf or not os.path.exists(input_gtf):
+        print("".join(["gtf_to_position_file.py:: ",
+                       "Could not find input file : " + input_gtf]))
+        return False
+
+    all_genes_found = set()
+
+    # Holds lines to output after parsing.
+    output_line = []
+    previous_gene = None
+    previous_chr = None
+    gene_positions = []
+
+    # Metrics for the file
+    i_comments = 0
+    i_duplicate_entries = 0
+    i_entries = 0
+    i_accepted_entries = 0
+    i_written_lines = 0
+
+    with open_file(input_gtf) as gtf:
+        gtf_file = csv.reader(gtf, delimiter="\t")
+        for gtf_line in gtf_file:
+            if gtf_line[0][0] == "#":
+                i_comments += 1
+                continue
+            i_entries += 1
+            # Clean up the attribute keys and match the one of interest.
+            attributes = gtf_line[8].split(";")
+            attributes = [entry.strip(" ") for entry in attributes]
+            attributes = [entry.split(" ") for entry in attributes if entry]
+            attributes = [[entry[0].strip('"'), entry[1].strip('"')] for entry in attributes]
+            attributes = dict([[entry[0].split("|")[0], entry[1]] for entry in attributes])
+            if attribute_key in attributes:
+                gene_name = attributes[attribute_key]
+            else:
+                print("Could not find an attribute in the GTF with the name '" + attribute_key + "'. Line=" + "\t".join(gtf_line))
+                exit(99)
+            if not gene_name == previous_gene:
+                if len(gene_positions) > 1 and previous_gene not in all_genes_found:
+                    i_accepted_entries += 1
+                    gene_positions.sort()
+                    output_line.append("\t".join([previous_gene,
+                                                  previous_chr,
+                                                  str(gene_positions[0]),
+                                                  str(gene_positions[-1])]))
+                    all_genes_found.add(previous_gene)
+                gene_positions = []
+            else:
+                i_duplicate_entries += 1
+            gene_positions += [int(gtf_line[3]), int(gtf_line[4])]
+            previous_gene = gene_name
+            previous_chr = gtf_line[0]
+        if previous_gene and previous_chr and len(gene_positions) > 1:
+            i_accepted_entries += 1
+            gene_positions.sort()
+            output_line.append("\t".join([previous_gene,
+                                          previous_chr,
+                                          str(gene_positions[0]),
+                                          str(gene_positions[-1])]))
+
+    with open(output_positional, "w") as positional_file:
+        i_written_lines += len(output_line)
+        positional_file.write("\n".join(output_line))
+
+    # Print metrics
+    print("Number of lines read: " + str(i_entries))
+    print("Number of comments: " + str(i_comments))
+    print("Number of entries: " + str(i_accepted_entries))
+    print("Number of duplicate entries: " + str(i_duplicate_entries))
+    print("Number of entries written: " + str(i_written_lines))
+
+
+if __name__ == "__main__":
+
+    # Parse arguments
+    prsr_arguments = argparse.ArgumentParser(prog='gtf_to_position_file.py',
+                                             description='Convert a GTF file to a positional file.',
+                                             formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # Add positional argument
+    prsr_arguments.add_argument("input_gtf",
+                                metavar="input_gtf",
+                                help="Path to the input GTF file.")
+    prsr_arguments.add_argument("--attribute_name",
+                                metavar="attribute_name",
+                                default="gene_id",
+                                help="The name of the attribute in the GTF attributes to use instead of gene name, for example 'gene_name' or 'transcript_id'.")
+    prsr_arguments.add_argument("output_positional",
+                                metavar="output_positional",
+                                help="Path for the output positional file.")
+    args = prsr_arguments.parse_args()
+
+    # Run Script
+    convert_to_positional_file(args.input_gtf, args.output_positional, args.attribute_name)