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mhegde / base-editor-design-tool

This tool designs guides for use with the base editor technology.
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Mysterious error #2

Closed kiddo18 closed 1 year ago

kiddo18 commented 1 year ago

Hi Mudra,

I'm just wondering if you know what this error is. I simply just git clone your repo and ran python base_editing_guide_designs.py --input-file ./Sample_data/GFP.fasta --variant-file ../ClinVar/variant_summary.txt --input-type nuc --be-type BE3 --output-name GFP

But it showed this error. I tried looking through the file, but don't really understand where the bug is coming from. Are you familiar with this by any chance? Thank you! :)

/Users/base_editor_screen/base-editor-design-tool/base_editing_guide_designs.py:446: FutureWarning: In a future version of pandas all arguments of StringMethods.split except for the argument 'pat' will be keyword-only. parsed_variant_df.loc[:,'RefSeqID'] = parsed_variant_df.loc[:,'Name'].str.split('(',1).str[0] Designing for GFP Traceback (most recent call last): File "/Users/base_editor_screen/base-editor-design-tool/base_editing_guide_designs.py", line 1215, in <module> val = design_sgrnas(gene_name, assembly, chromosome, gene_id, w, tr_seq, abs_pos_map, fs, cds_map, utr, tr, pam, exons, gene_strand, edit, window, cds_sequence, len(pam), sg_len, cds_start_exon, w_error, w_clin, gene_variant_df, aa_map, input_type, intron_buffer, filter_gc) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/base_editor_screen/base-editor-design-tool/base_editing_guide_designs.py", line 971, in design_sgrnas context_for_trans, cds_pos, i_count = get_context_for_trans(ct_index, pos+sg_len+pam_len+3, abs_pos, cds_map, fs, sgrna_context) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/base_editor_screen/base-editor-design-tool/base_editing_guide_designs.py", line 832, in get_context_for_trans gen_pos = abs_pos.keys()[abs_pos.values().index(ct_index)] ^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'dict_values' object has no attribute 'index'

kiddo18 commented 1 year ago

python version 3.11 biopython version v1.81

mhegde commented 1 year ago

Hi, please use Python 2.7. That should resolve the error. The syntax is slightly different in Python3.

kiddo18 commented 1 year ago

That works! Thank you for sharing this tool!