seq_intake.py initial commit

tests/test_seq_intake.py

@@ -0,0 +1,38 @@
+import os
+import locidex.classes.seq_intake
+from locidex.constants import BLAST_TABLE_COLS
+
+
+PACKAGE_ROOT = os.path.dirname(locidex.__file__)
+
+
+def seq_intake_class_init(input_file, file_type, perform_annotation):
+    return locidex.classes.seq_intake.seq_intake(input_file=input_file,
+                                      file_type=file_type,feat_key='CDS',translation_table=11,
+                                      perform_annotation=perform_annotation,num_threads=1,skip_trans=False)
+
+def test_read_fasta_file():
+    seq_intake_object = seq_intake_class_init(input_file=os.path.join(PACKAGE_ROOT, 'example/search/NC_003198.1.fasta'),
+                          file_type='fasta', perform_annotation=True)
+    assert seq_intake_object.file_type == 'fasta'
+    assert seq_intake_object.feat_key == 'CDS'
+    assert seq_intake_object.status == True
+    assert seq_intake_object.translation_table == 11
+    assert seq_intake_object.valid_types == ['genbank', 'gff', 'gtf', 'fasta']
+    assert len(seq_intake_object.seq_data) == 4653
+    assert sum([contig['aa_len'] for contig in seq_intake_object.seq_data]) == 2996811
+    assert all([True if 'NC_003198.1' in contig['parent_id'] else False  for contig in seq_intake_object.seq_data]) == True
+    assert all([True if 'NC_003198.1' in contig['locus_name'] else False  for contig in seq_intake_object.seq_data]) == True
+    assert all([True if 'NC_003198.1' in contig['seq_id'] else False  for contig in seq_intake_object.seq_data]) == True
+    assert len(seq_intake_object.seq_data[0]['dna_seq']) == 2463
+    assert seq_intake_object.seq_data[0]['dna_len'] == 2463
+    assert seq_intake_object.seq_data[0]['dna_hash'] == 'd1681ad4c3c1b07a5d0afc5a893afb1b'
+    assert seq_intake_object.seq_data[0]['start_codon'] == 'atg'
+    assert seq_intake_object.seq_data[0]['stop_codon'] == 'taa'
+    assert seq_intake_object.seq_data[0]['count_internal_stop'] == 0
+    assert all([ True if contig['dna_ambig_count'] == 0 else False  for contig in seq_intake_object.seq_data]) == True
+
+
+
+
+