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smirarab / pasta

PASTA (Practical Alignment using SATe and Transitivity)
GNU General Public License v3.0
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small issue with run_pasta_gui.py and run_pasta.py -h or -i options. #38

Closed kibet-gilbert closed 5 years ago

kibet-gilbert commented 5 years ago

Here are some errors:

$ python run_pasta_gui.py Traceback (most recent call last): File "run_pasta_gui.py", line 45, in from pasta.configure import get_invoke_run_pasta_command File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/configure.py", line 35, in from pasta.tools import get_external_tool_classes File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/tools.py", line 41, in from sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations ModuleNotFoundError: No module named 'sequence_lib'

and:

$ python run_pasta.py -h Traceback (most recent call last): File "run_pasta.py", line 27, in from pasta.mainpasta import pasta_main File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/mainpasta.py", line 33, in from pasta.configure import get_configuration File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/configure.py", line 35, in from pasta.tools import get_external_tool_classes File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/tools.py", line 41, in from sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations ModuleNotFoundError: No module named 'sequence_lib'

Bug easily fixed by: changing :

File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/tools.py", line 41, in from sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations

to:

from pasta.sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations

More info: I am working on Ubuntu lts 18.04, Installed pasta and sate-tools-linux as described in tutorial

smirarab commented 5 years ago

Fixed. Sorry for the careless commits of unfinished work. Can you check now?

On Fri, Jan 4, 2019 at 3:42 AM Kibet Gilbert notifications@github.com wrote:

Here are some errors:

$ python run_pasta_gui.py Traceback (most recent call last): File "run_pasta_gui.py", line 45, in from pasta.configure import get_invoke_run_pasta_command File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/configure.py", line 35, in from pasta.tools import get_external_tool_classes File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/tools.py", line 41, in from sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations ModuleNotFoundError: No module named 'sequence_lib'

and:

$ python run_pasta.py -h Traceback (most recent call last): File "run_pasta.py", line 27, in from pasta.mainpasta import pasta_main File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/mainpasta.py", line 33, in from pasta.configure import get_configuration File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/configure.py", line 35, in from pasta.tools import get_external_tool_classes File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/tools.py", line 41, in from sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations ModuleNotFoundError: No module named 'sequence_lib'

Bug easily fixed by: changing :

File "/home/kibet/bioinformatics/tools/pasta_code/pasta/pasta/tools.py", line 41, in from sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations

to:

from pasta.sequence_lib import read_fasta, write_fasta, replace, replace_back, merge_rep_locations

More info: I am working on Ubuntu lts 18.04, Installed pasta and sate-tools-linux as described in tutorial https://github.com/smirarab/pasta/blob/master/pasta-doc/pasta-tutorial.md#installation

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kibet-gilbert commented 5 years ago

thanks