8000 start bug fix · fmalmeida/pythonScripts@4e34f20 · GitHub
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‎build_conda.sh

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@@ -9,6 +9,7 @@ conda convert -p osx-64 $(find build -name "falmeida-py*.tar.bz2")
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# upload osx
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anaconda upload $(find osx-64 -name "falmeida-py*.tar.bz2") --force
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sleep 140
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anaconda upload $(find build/linux-64 -name "falmeida-py*.tar.bz2") --force
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# rm dirs

‎conda.recipe/meta.yaml

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package:
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name: falmeida-py
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version: '1.2.3'
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version: '1.2.4'
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source:
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path: ..

‎docs/align2subsetgbk_help.txt

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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.
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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'

‎docs/help_message.txt

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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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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'

‎docs/splitgbk_help.txt

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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.
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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'

‎docs/tsv2markdown_help.txt

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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 EF5E 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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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'

‎falmeida_py/general_stats_function.py

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# save annotation stats
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bacannot_summary[sample]['general_annotation'] = {}
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bacannot_summary[sample]['general_annotation']['mlst'] = str(mlst_results[2].item()).replace('-', 'null')
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bacannot_summary[sample]['general_annotation']['cds'] = general_results['CDS']
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bacannot_summary[sample]['general_annotation']['rrna'] = general_results['rRNA']
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bacannot_summary[sample]['general_annotation']['trna'] = general_results['tRNA']
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bacannot_summary[sample]['general_annotation']['tmrna'] = general_results['tmRNA']
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bacannot_summary[sample]['general_annotation']['cds'] = general_results.get('CDS', 0)
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bacannot_summary[sample]['general_annotation']['rrna'] = general_results.get('rRNA', 0)
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bacannot_summary[sample]['general_annotation']['trna'] = general_results.get('tRNA', 0)
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bacannot_summary[sample]['general_annotation']['tmrna'] = general_results.get('tmRNA', 0)
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bacannot_summary[sample]['general_annotation']['closest_reference'] = {}
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bacannot_summary[sample]['general_annotation']['closest_reference']['strain'] = refseq_masher_results.head(1)['top_taxonomy_name'].item()

‎falmeida_py/version.py

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If not, see <http://www.gnu.org/licenses/>.
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"""
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__version__ = '1.2.3'
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__version__ = '1.2.4'
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def get_version():
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return __version__

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