Mercurial > repos > rliterman > csp2

comparison CSP2/bin/screenSNPDiffs.py @ 39:93393808f415

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 13:53:15 -0500
parents 893a6993efe3
children
comparison
equal deleted inserted replaced
38:ee512a230a1e 39:93393808f415
500 else: 500 else:
501 filtered_snp_df = filterSNPs(snp_df,bed_df,log_file, min_len, min_iden, ref_edge, query_edge, density_windows, max_snps) 501 filtered_snp_df = filterSNPs(snp_df,bed_df,log_file, min_len, min_iden, ref_edge, query_edge, density_windows, max_snps)
502 502
503 # Write filtered SNP data to file 503 # Write filtered SNP data to file
504 snp_file = log_file.replace(".log","_SNPs.tsv") 504 snp_file = log_file.replace(".log","_SNPs.tsv")
505 filtered_snp_df.to_csv(snp_file, sep="\t", index=False) 505 with open(snp_file,"w") as f:
506 filtered_snp_df.to_csv(f, sep="\t", index=False)
506 507
507 csp2_screen_snps = filtered_snp_df[filtered_snp_df.Cat == "SNP"].shape[0] 508 csp2_screen_snps = filtered_snp_df[filtered_snp_df.Cat == "SNP"].shape[0]
508 509
509 purged_length = filtered_snp_df[filtered_snp_df.Cat == "Purged_Length"].shape[0] 510 purged_length = filtered_snp_df[filtered_snp_df.Cat == "Purged_Length"].shape[0]
510 purged_identity = filtered_snp_df[filtered_snp_df.Cat == "Purged_Identity"].shape[0] 511 purged_identity = filtered_snp_df[filtered_snp_df.Cat == "Purged_Identity"].shape[0]
628 'Filtered_Query_Edge','Filtered_Ref_Edge','Filtered_Both_Edge', 629 'Filtered_Query_Edge','Filtered_Ref_Edge','Filtered_Both_Edge',
629 'Kmer_Similarity','Shared_Kmers','Query_Unique_Kmers','Reference_Unique_Kmers', 630 'Kmer_Similarity','Shared_Kmers','Query_Unique_Kmers','Reference_Unique_Kmers',
630 'MUMmer_gSNPs','MUMmer_gIndels'] 631 'MUMmer_gSNPs','MUMmer_gIndels']
631 632
632 results_df = pd.DataFrame([item.result() for item in results], columns = output_columns) 633 results_df = pd.DataFrame([item.result() for item in results], columns = output_columns)
633 results_df.to_csv(output_file, sep="\t", index=False) 634 with open(output_file,"w") as f:
635 results_df.to_csv(f, sep="\t", index=False)
634 except: 636 except:
635 run_failed = True 637 run_failed = True
636 print("Exception occurred:\n", traceback.format_exc()) 638 print("Exception occurred:\n", traceback.format_exc())
637 finally: 639 finally:
638 helpers.cleanup(verbose=False, remove_all=False) 640 helpers.cleanup(verbose=False, remove_all=False)