diff --git a/build_conda.sh b/build_conda.sh index 76fc21a..d3d0571 100644 --- a/build_conda.sh +++ b/build_conda.sh @@ -9,6 +9,7 @@ conda convert -p osx-64 $(find build -name "falmeida-py*.tar.bz2") # upload osx anaconda upload $(find osx-64 -name "falmeida-py*.tar.bz2") --force +sleep 140 anaconda upload $(find build/linux-64 -name "falmeida-py*.tar.bz2") --force # rm dirs diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml index 2dfa0db..b1e862a 100644 --- a/conda.recipe/meta.yaml +++ b/conda.recipe/meta.yaml @@ -1,6 +1,6 @@ package: name: falmeida-py - version: '1.2.3' + version: '1.2.4' source: path: .. diff --git a/docs/align2subsetgbk_help.txt b/docs/align2subsetgbk_help.txt index 769c2b2..087e990 100644 --- a/docs/align2subsetgbk_help.txt +++ b/docs/align2subsetgbk_help.txt @@ -1,44 +1,6 @@ -A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file - ---- -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -Usage: - falmeida-py align2subsetgbk [ -h|--help ] - falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ] - -Options: - -h --help Show this screen. - -g --gbk= Gbk file for subset - -f --fasta= FASTA (nucl) file for querying the gbk - -o --out= Gbk filtered output file [Default: out.gbk]. - --extension= Base pair length to extend the flank regions in the alignment [Default: 0]. - --minid= Min. Identity percentage for gene annotation [Default: 80]. - --mincov= Min. Covereage for gene annotation [Default: 80]. - --culling_limit= Blast culling_limit for best hit only [Default: 1]. -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/help_message.txt b/docs/help_message.txt index 6ed5318..087e990 100644 --- a/docs/help_message.txt +++ b/docs/help_message.txt @@ -1,25 +1,6 @@ -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/splitgbk_help.txt b/docs/splitgbk_help.txt index f139033..087e990 100644 --- a/docs/splitgbk_help.txt +++ b/docs/splitgbk_help.txt @@ -1,38 +1,6 @@ -A very simple script to split multisequence genbank files into separate files -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py splitgbk - falmeida-py splitgbk [ -h|--help ] - falmeida-py splitgbk [ --gbk ] [ --outdir ] - -options: - -h --help Show this screen. - -g --gbk= Input genbank file to split into multiple individual files. - -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./]. -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/docs/tsv2markdown_help.txt b/docs/tsv2markdown_help.txt index 0b2b685..087e990 100644 --- a/docs/tsv2markdown_help.txt +++ b/docs/tsv2markdown_help.txt @@ -1,40 +1,6 @@ -A simple script to convert tsv (or csv) files to markdown tables using tabulate! -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py tsv2markdown - falmeida-py tsv2markdown [ -h|--help ] - falmeida-py tsv2markdown [ --tsv --csv --header ] - -options: - -h --help Show this screen. - --tsv= Input tsv file to print as markdown table - --csv= Input csv file to print as markdown table - --header= If file does not have a header, set a - custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)". -falmeida-py: a package to the simple distribution of my custom scripts. - -Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com) -License: Public Domain - -usage: - falmeida-py [ -h|--help ] [ -v|--version ] [ --license ] - falmeida-py [ -h|--help ] [ ... ] - -options: - -h --help Show this screen - -v --version Show version information - --license Show LEGAL LICENSE information - -commands: - tsv2markdown Command for rapid convertion of tsv or csv to markdown tables. - splitgbk Command to split multisequence genbank files into individual files. - align2subsetgbk Command to subset genbank files based on alignments to a FASTA file. - gbk2fasta Command to convert genbank files to fasta files. - blasts Command to execute automatized blast commands. - replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file - mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file - bacannot2json Command to summarize main bacannot annotation results into JSON file - -Use: `falmeida-py -h` to get more help and see examples. +Traceback (most recent call last): + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida-py-runner.py", line 18, in + from falmeida_py.__main__ import main + File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in + from docopt import docopt +ModuleNotFoundError: No module named 'docopt' diff --git a/falmeida_py/general_stats_function.py b/falmeida_py/general_stats_function.py index 74e0893..80e2590 100644 --- a/falmeida_py/general_stats_function.py +++ b/falmeida_py/general_stats_function.py @@ -37,10 +37,10 @@ def general_stats(bacannot_summary): # save annotation stats bacannot_summary[sample]['general_annotation'] = {} bacannot_summary[sample]['general_annotation']['mlst'] = str(mlst_results[2].item()).replace('-', 'null') - bacannot_summary[sample]['general_annotation']['cds'] = general_results['CDS'] - bacannot_summary[sample]['general_annotation']['rrna'] = general_results['rRNA'] - bacannot_summary[sample]['general_annotation']['trna'] = general_results['tRNA'] - bacannot_summary[sample]['general_annotation']['tmrna'] = general_results['tmRNA'] + bacannot_summary[sample]['general_annotation']['cds'] = general_results.get('CDS', 0) + bacannot_summary[sample]['general_annotation']['rrna'] = general_results.get('rRNA', 0) + bacannot_summary[sample]['general_annotation']['trna'] = general_results.get('tRNA', 0) + bacannot_summary[sample]['general_annotation']['tmrna'] = general_results.get('tmRNA', 0) bacannot_summary[sample]['general_annotation']['closest_reference'] = {} bacannot_summary[sample]['general_annotation']['closest_reference']['strain'] = refseq_masher_results.head(1)['top_taxonomy_name'].item() diff --git a/falmeida_py/version.py b/falmeida_py/version.py index 304580c..e524e2d 100644 --- a/falmeida_py/version.py +++ b/falmeida_py/version.py @@ -14,7 +14,7 @@ If not, see . """ -__version__ = '1.2.3' +__version__ = '1.2.4' def get_version(): return __version__