start bug fix

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

conda.recipe/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: falmeida-py
-  version: '1.2.3'
+  version: '1.2.4'
 
 source:
   path: ..

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 <in_gbk> --fasta <fasta> --out <out_gbk> --minid <int> --mincov <int> --culling_limit <int> --extension <int> ]
-
-Options:
-    -h --help                      Show this screen.
-    -g --gbk=<in_gbk>              Gbk file for subset
-    -f --fasta=<fasta>             FASTA (nucl) file for querying the gbk
-    -o --out=<out_gbk>             Gbk filtered output file [Default: out.gbk].
-    --extension=<int>              Base pair length to extend the flank regions in the alignment [Default: 0].
-    --minid=<int>                  Min. Identity percentage for gene annotation [Default: 80].
-    --mincov=<int>                 Min. Covereage for gene annotation [Default: 80].
-    --culling_limit=<int>          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 <command> [ -h|--help ] [ <args>... ]
-
-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 <commmand> -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 <module>
+    from falmeida_py.__main__ import main
+  File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
+    from docopt import docopt
+ModuleNotFoundError: No module named 'docopt'

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 <command> [ -h|--help ] [ <args>... ]
-
-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 <commmand> -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 <module>
+    from falmeida_py.__main__ import main
+  File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
+    from docopt import docopt
+ModuleNotFoundError: No module named 'docopt'

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 <file> ] [ --outdir <outdir> ]
-
-options:
-    -h --help                               Show this screen.
-    -g --gbk=<file>                         Input genbank file to split into multiple individual files.
-    -o --outdir=<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 <command> [ -h|--help ] [ <args>... ]
-
-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 <commmand> -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 <module>
+    from falmeida_py.__main__ import main
+  File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
+    from docopt import docopt
+ModuleNotFoundError: No module named 'docopt'

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 <file> --csv <file> --header <list> ]
-
-options:
-    -h --help                               Show this screen.
-    --tsv=<file>                            Input tsv file to print as markdown table
-    --csv=<file>                            Input csv file to print as markdown table
-    --header=<list>                         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 <command> [ -h|--help ] [ <args>... ]
-
-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 <commmand> -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 <module>
+    from falmeida_py.__main__ import main
+  File "/home/falmeida/Documents/GitHub/pythonScripts/falmeida_py/__main__.py", line 47, in <module>
+    from docopt import docopt
+ModuleNotFoundError: No module named 'docopt'

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()

falmeida_py/version.py

@@ -14,7 +14,7 @@
 If not, see <http://www.gnu.org/licenses/>.
 """
 
-__version__ = '1.2.3'
+__version__ = '1.2.4'
 
 def get_version():
     return __version__