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jhawkey / IS_mapper

IS mapping software
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create_typing_out.py returns "ValueError: More than one record found in handle" #23

Closed necoli1822 closed 7 years ago

necoli1822 commented 7 years ago

Hello, nice to see you. I stuck with the error "ValueError: More than one record found in handle" during the command create_typing_out.py.

Below is the traceback.

Traceback (most recent call last): File "/usr/local/bin/create_typing_out.py", line 543, in main() File "/usr/local/bin/create_typing_out.py", line 320, in main is_length = insertion_length(args.seq) File "/usr/local/bin/create_typing_out.py", line 48, in insertion_length sequence = SeqIO.read(insertion, "fasta") File "/usr/local/lib/python2.7/dist-packages/Bio/SeqIO/init.py", line 674, in read raise ValueError("More than one record found in handle") ValueError: More than one record found in handle

The command is

$: create_typing_out.py --intersect /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_contig1_ICEberg_seq_intersect.bed --closest /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_contig1_ICEberg_seq_closest.bed --left_bed /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_5_contig1_ICEberg_seq_merged.sorted.bed --right_bed /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_3_contig1_ICEberg_seq_merged.sorted.bed --left_unpaired /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_contig1_ICEberg_seq_left_unpaired.bed --right_unpaired /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_contig1_ICEberg_seq_right_unpaired.bed --seq ICEberg_seq.fas --ref contig1.gbk --temp /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_ICEberg_seq_temp/ --cds locus_tag gene product --trna locus_tag product --rrna locus_tag product --min_range 0.2 --max_range 1.1 --output /media/necoli/Data/Genomes/AB_BL_Result/ICEberg_db/BL2_ICEberg_seq --igv 1 --chr_name not_specified

This is the query file. https://drive.google.com/open?id=0B9L_dB5U6nHZWDBoZ0dLcnRYSzg

The reference is unpublished yet, thus if you need the sequence, please notify me to e-mail you.

Thank you for your sincere and fantastic work.

jhawkey commented 7 years ago

Hi, This error is occurring because you are supplying a multifasta file as your query sequence. At this stage, ISMapper can only take single entry fasta files - however you can supply multiple single entry fasta files, and ISMapper will loop through these.

A coming update of ISMapper will allow multifasta files to be used as query sequences - I'm hoping to push this update in the next few months.

necoli1822 commented 7 years ago

Thank you for your kind answer.

I read the info last night and got it with "'a' fasta file".

Hope it will be added for the next update, thank you again for your fantastic work. 2017년 2월 15일 (수) 오후 1:15, Jane Hawkey notifications@github.com님이 작성:

Closed #23 https://github.com/jhawkey/IS_mapper/issues/23.

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