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jambler24 / GenGraph

A repository for the GenGraph toolkit for the creation and manipulation of graph genomes
GNU General Public License v3.0
52 stars 16 forks source link

Novice to python #12

Closed Devinaseeruttun closed 4 years ago

Devinaseeruttun commented 4 years ago

I am having this problem can you help please? Thank you devina@devina-HP-ProBook-450-G3:~/GenGraph$ python3 gengraphTool.py make_genome_graph --seq_file analysis.txt --out_file_name test --recreate_check Traceback (most recent call last): File "gengraphTool.py", line 83, in parsed_input_dict = parse_seq_file(args.seq_file) File "/home/devina/GenGraph/gengraph.py", line 548, in parse_seq_file A_seq_label_dict[a_seq_file['aln_name']] = a_seq_file['seq_name'] KeyError: 'seq_name'

jambler24 commented 4 years ago

copy and paste the analysis.txt file here? I think something in the formatting is causing trouble

mvtullius commented 4 years ago

I had the same issue. The problem was the text file had some hidden characters at the start of the file that weren't showing up in the text editor. I think this was because I originally copied the text from the website. When I made a new text file it worked without the error.

jambler24 commented 4 years ago

Thanks for the comment @mvtullius, adding in some input checking to try catch problems like this.

jambler24 commented 4 years ago

Closing this for now, if it happens again please let me know so I can improve the input checking.

Thanks!