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‎docs/align2subsetgbk_help.txt‎

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Traceback (most recent call last):
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in <module>
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from falmeida_py.__main__ import main
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
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from docopt import docopt
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ModuleNotFoundError: No module named 'docopt'
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A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file
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---
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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Usage:
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falmeida-py align2subsetgbk [ -h|--help ]
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falmeida-py align2subsetgbk [ --gbk <in_gbk> --fasta <fasta> --out <out_gbk> --minid <int> --mincov <int> --culling_limit <int> --extension <int> ]
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Options:
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-h --help Show this screen.
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-g --gbk=<in_gbk> Gbk file for subset
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-f --fasta=<fasta> FASTA (nucl) file for querying the gbk
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-o --out=<out_gbk> Gbk filtered output file [Default: out.gbk].
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--extension=<int> Base pair length to extend the flank regions in the alignment [Default: 0].
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--minid=<int> Min. Identity percentage for gene annotation [Default: 80].
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--mincov=<int> Min. Covereage for gene annotation [Default: 80].
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--culling_limit=<int> Blast culling_limit for best hit only [Default: 1].
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falmeida-py: a package to the simple distribution of my custom scripts.
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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usage:
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falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
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falmeida-py <command> [ -h|--help ] [ <args>... ]
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options:
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-h --help Show this screen
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-v --version Show version information
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--license Show LEGAL LICENSE information
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commands:
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tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
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splitgbk Command to split multisequence genbank files into individual files.
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align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
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gbk2fasta Command to convert genbank files to fasta files.
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blasts Command to execute automatized blast commands.
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replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
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mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
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bacannot2json Command to summarize main bacannot annotation results into JSON file
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Use: `falmeida-py <commmand> -h` to get more help and see examples.

‎docs/help_message.txt‎

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Traceback (most recent call last):
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in <module>
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from falmeida_py.__main__ import main
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
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from docopt import docopt
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ModuleNotFoundError: No module named 'docopt'
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falmeida-py: a package to the simple distribution of my custom scripts.
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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usage:
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falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
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falmeida-py <command> [ -h|--help ] [ <args>... ]
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options:
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-h --help Show this screen
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-v --version Show version information
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--license Show LEGAL LICENSE information
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commands:
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tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
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splitgbk Command to split multisequence genbank files into individual files.
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align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
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gbk2fasta Command to convert genbank files to fasta files.
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blasts Command to execute automatized blast commands.
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replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
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mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
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bacannot2json Command to summarize main bacannot annotation results into JSON file
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Use: `falmeida-py <commmand> -h` to get more help and see examples.

‎docs/splitgbk_help.txt‎

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Traceback (most recent call last):
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in <module>
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from falmeida_py.__main__ import main
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
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from docopt import docopt
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ModuleNotFoundError: No module named 'docopt'
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A very simple script to split multisequence genbank files into separate files
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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usage:
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falmeida-py splitgbk
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falmeida-py splitgbk [ -h|--help ]
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falmeida-py splitgbk [ --gbk <file> ] [ --outdir <outdir> ]
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options:
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-h --help Show this screen.
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-g --gbk=<file> Input genbank file to split into multiple individual files.
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-o --outdir=<outdir> Directory (must already exist) in which to write the splitted files [Default: ./].
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falmeida-py: a package to the simple distribution of my custom scripts.
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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usage:
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falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
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falmeida-py <command> [ -h|--help ] [ <args>... ]
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options:
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-h --help Show this screen
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-v --version Show version information
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--license Show LEGAL LICENSE information
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commands:
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tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
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splitgbk Command to split multisequence genbank files into individual files.
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align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
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gbk2fasta Command to convert genbank files to fasta files.
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blasts Command to execute automatized blast commands.
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replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
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mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
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bacannot2json Command to summarize main bacannot annotation results into JSON file
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Use: `falmeida-py <commmand> -h` to get more help and see examples.

‎docs/tsv2markdown_help.txt‎

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Traceback (most recent call last):
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in <module>
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from falmeida_py.__main__ import main
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File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
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from docopt import docopt
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ModuleNotFoundError: No module named 'docopt'
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A simple script to convert tsv (or csv) files to markdown tables using tabulate!
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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usage:
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falmeida-py tsv2markdown
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falmeida-py tsv2markdown [ -h|--help ]
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falmeida-py tsv2markdown [ --tsv <file> --csv <file> --header <list> ]
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options:
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-h --help Show this screen.
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--tsv=<file> Input tsv file to print as markdown table
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--csv=<file> Input csv file to print as markdown table
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--header=<list> If file does not have a header, set a
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custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)".
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falmeida-py: a package to the simple distribution of my custom scripts.
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Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
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License: Public Domain
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usage:
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falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
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falmeida-py <command> [ -h|--help ] [ <args>... ]
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options:
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-h --help Show this screen
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-v --version Show version information
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--license Show LEGAL LICENSE information
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commands:
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tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
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splitgbk Command to split multisequence genbank files into individual files.
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align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
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gbk2fasta Command to convert genbank files to fasta files.
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blasts Command to execute automatized blast commands.
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replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
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mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
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bacannot2json Command to summarize main bacannot annotation results into JSON file
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Use: `falmeida-py <commmand> -h` to get more help and see examples.

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