8000 added ICEberg database blastp results · fmalmeida/pythonScripts@bc006d6 · GitHub
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added ICEberg database blastp results
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‎falmeida_py/mges_function.py

Lines changed: 57 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,6 +3,7 @@
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##################################
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import pandas as pd
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import os
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from .utils import load_and_subset_gff
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####################################
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### check MGEs annotations stats ###
@@ -14,6 +15,9 @@ def mges_stats(bacannot_summary):
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# load dir of samples' results
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results_dir = bacannot_summary[sample]['results_dir']
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# load gff_file
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gff_file = f"{results_dir}/gffs/{sample}.gff"
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# integron_finder
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if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff") and os.stat(f"{results_dir}/integron_finder/{sample}_integrons.gff").st_size > 0:
@@ -54,4 +58,56 @@ def mges_stats(bacannot_summary):
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bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end']
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bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1]
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bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source']
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bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type']
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bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type']
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# ICE database
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ice_db_blastp = f"{results_dir}/ICEs/{sample}_iceberg_blastp_onGenes.summary.txt"
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if os.path.exists(ice_db_blastp) and os.stat(ice_db_blastp).st_size > 0:
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# init MGE annotation dictionary
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if 'MGE' not in bacannot_summary[sample]:
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bacannot_summary[sample]['MGE'] = {}
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# init iceberg annotation dictionary
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if 'ICE' not in bacannot_summary[sample]['MGE']:
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bacannot_summary[sample]['MGE']['ICEberg'] = {}
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# init iceberg blastp annotation dictionary
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'] = {}
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# load integron_finder results
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results = pd.read_csv(
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ice_db_blastp,
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sep='\t'
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)
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# load gff
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gff = load_and_subset_gff(gff_file, 'source', 'ICE')
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# number of integron_finder annotations
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total_number = len(results.index)
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bacannot_summary[sample]['MGE']['ICEberg']['blastp']['total'] = total_number
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# per gene info
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if int(results.shape[0]) > 0:
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for seq in [ str(x) for x in results['SEQUENCE'].unique() ]:
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# details missing in output but available in gff
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gff_row = gff[gff['attributes'].str.contains(seq)]
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contig = gff_row['seq'].item()
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start = gff_row['start'].item()
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end = gff_row['end'].item()
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {}
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for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows():
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id] = {}
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['id'] = row['ICEBERG_ID']
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['contig'] = contig
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['start'] = start
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['end'] = end
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['accession'] = row['ACCESSION']
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['product'] = row['PRODUCT']
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['description'] = row['DESCRIPTION']
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['blast_start'] = row['START']
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['blast_end'] = row['END']
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bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq][id]['strand'] = row['STRAND']

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