Corrected fasta format output

aljpetri · Dec 4, 2023 · 7723b12 · 7723b12
1 parent 526427f
commit 7723b12
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Showing 4 changed files with 7 additions and 7 deletions.
diff --git a/isONform_parallel.py b/isONform_parallel.py
@@ -310,7 +310,7 @@ def main(args):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description="De novo reconstruction of long-read transcriptome reads",
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('--version', action='version', version='%(prog)s 0.3.1')
+    parser.add_argument('--version', action='version', version='%(prog)s 0.3.3')
     parser.add_argument('--fastq_folder', type=str, default=False,
                         help='Path to input fastq folder with reads in clusters')
     parser.add_argument('--t', dest="nr_cores", type=int, default=8, help='Number of cores allocated for clustering')

diff --git a/main.py b/main.py
@@ -586,7 +586,7 @@ def main(args):
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description="De novo error correction of long-read transcriptome reads",
                                      formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser.add_argument('--version', action='version', version='%(prog)s 0.3.1')
+    parser.add_argument('--version', action='version', version='%(prog)s 0.3.3')
     parser.add_argument('--fastq', type=str, default=False, help='Path to input fastq file with reads')
 
     parser.add_argument('--k', type=int, default=20, help='Kmer size')

diff --git a/modules/batch_merging_parallel.py b/modules/batch_merging_parallel.py
@@ -111,7 +111,7 @@ def write_final_output(all_infos_dict, outfolder, iso_abundance, cl_dir, folder,
                         consensus_file.write("@{0}\n{1}\n+\n{2}\n".format(new_id, all_infos_dict[batchid][id].sequence,
                                                                       "+" * len(all_infos_dict[batchid][id].sequence)))
                     else:
-                        consensus_file.write("@{0}\n{1}\n".format(new_id, all_infos_dict[batchid][id].sequence))
+                        consensus_file.write(">{0}\n{1}\n".format(new_id, all_infos_dict[batchid][id].sequence))
                     support_file.write("{0}: {1}\n".format(new_id, len(all_infos_dict[batchid][id].reads)))
                 else:
                     if write_low_abundance:
@@ -120,7 +120,7 @@ def write_final_output(all_infos_dict, outfolder, iso_abundance, cl_dir, folder,
                                                                            "+" * len(
                                                                                all_infos_dict[batchid][id].sequence)))
                         else:
-                            other_consensus.write("@{0}\n{1}\n".format(new_id, all_infos_dict[batchid][id].sequence))
+                            other_consensus.write(">{0}\n{1}\n".format(new_id, all_infos_dict[batchid][id].sequence))
                         if new_id in all_infos_dict:
                             other_support_file.write("{0}: {1}\n".format(new_id, len(all_infos_dict[new_id].reads)))
                         else:

diff --git a/setup.py b/setup.py
@@ -19,7 +19,7 @@
 setup(
 
     name='isONform',  # Required
-    version='0.3.1',  # Required
+    version='0.3.3',  # Required
     description='De novo construction of isoforms from long-read data ',  # Required
     long_description=long_description,  # Optional
     long_description_content_type='text/markdown',
@@ -102,5 +102,5 @@
     #         'IsoCon=IsoCon.__main__()',
     #     ],
     # },
-    scripts=['isONform_parallel.py'],
-)
+    scripts=['isONform_parallel.py','main.py'],
+)