From 14e32d71b4735a96a7326a3a416cde368f0b04c7 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Thu, 26 Oct 2023 09:27:59 +1030 Subject: [PATCH] fix issue #37 with the index error --- src/plassembler/utils/plass_class.py | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/src/plassembler/utils/plass_class.py b/src/plassembler/utils/plass_class.py index 753e319..4870ee3 100644 --- a/src/plassembler/utils/plass_class.py +++ b/src/plassembler/utils/plass_class.py @@ -272,11 +272,7 @@ def identify_chromosome_process_flye(self, chromosome_len): else: dna_header = "plasmid_" + str(i) dna_description = "" - # get length for bed file - le = info_df.length.loc[ - info_df["seq_name"] == dna_record.id - ] - plas_len = int(le.iloc[0]) + # write the updated record dna_record = SeqRecord( dna_record.seq, @@ -287,7 +283,7 @@ def identify_chromosome_process_flye(self, chromosome_len): # get length for bed file # make bed file bed_file.write( - f"{dna_header}\t1\t{plas_len}\n" + f"{dna_header}\t1\t{contig_len}\n" ) # Write read name i += 1 @@ -367,11 +363,6 @@ def identify_chromosome_process_flye_long(self, chromosome_len): else: dna_header = "plasmid_" + str(i) dna_description = "" - # get length for bed file - le = info_df.length.loc[ - info_df["seq_name"] == dna_record.id - ] - plas_len = int(le.iloc[0]) # write the updated record dna_record = SeqRecord( dna_record.seq, @@ -382,7 +373,7 @@ def identify_chromosome_process_flye_long(self, chromosome_len): # get length for bed file # make bed file bed_file.write( - f"{dna_header}\t1\t{plas_len}\n" + f"{dna_header}\t1\t{contig_len}\n" ) # Write read name i += 1 # add to object