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v6.2
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with some corrections to some of our infinite typos.
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@meren
meren committed Apr 1, 2020
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Showing 1 changed file with 26 additions and 25 deletions.
51 changes: 26 additions & 25 deletions anvio/__init__.py
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Expand Up @@ -200,7 +200,7 @@ def get_args(parser):
"freedom to the user to adjust the resolution of their display when necessary. The default value is "
"(%(default)d). If you are planning to use your contigs database for metagenomic binning, we advise you "
"to not go below 10,000 (since the lower the split size is, the more items to show in the display, and "
"decrasing the split size does not really help much to binning). But if you are thinking about using this "
"decreasing the split size does not really help much to binning). But if you are thinking about using this "
"parameter for ad hoc investigations other than binning, you should ignore our advice, and set the split "
"size as low as you want. If you do not want your contigs to be split, you can set the split size to '0' "
"or any other negative integer (lots of unnecessary freedom here, enjoy!)."}
Expand Down Expand Up @@ -441,7 +441,7 @@ def get_args(parser):
'help': "Data group to focus. Anvi'o misc data tables support associating a set of data keys "
"with a data group. If you have no idea what this is, then probably you don't need it, "
"and anvi'o will take care of you. Note: this flag is IRRELEVANT if you are working with "
"additioanl order data tables."}
"additional order data tables."}
),
'target-data-table': (
['-t', '--target-data-table'],
Expand Down Expand Up @@ -486,7 +486,7 @@ def get_args(parser):
'fields': (
['-f', '--fields'],
{'metavar': 'FIELD(S)',
'help': "Fields to report. USe --list-tables parameter with a table name to see available "
'help': "Fields to report. Use --list-tables parameter with a table name to see available "
"fields You can list fields using this notation: --fields 'field_1, field_2, ... field_N'."}
),
'list': (
Expand Down Expand Up @@ -584,7 +584,8 @@ def get_args(parser):
'metavar': 'PATH',
'help': "Path to the directory that contains the BLAST databases for single-copy core "
"genes. You will almost never need to use this parameter unless you are "
"trying something very fancy. Anvi'o will know where its database files are."}
"trying something very fancy. But when you do, you can tell anvi'o where "
"to look for database files through this parameter."}
),
'scgs-taxonomy-data-dir': (
['--scgs-taxonomy-data-dir'],
Expand Down Expand Up @@ -930,7 +931,7 @@ def get_args(parser):
{'metavar': 'FILE_PATH',
'default': None,
'type': str,
'help': "Some commonly used software for phylogenetic analyeses (e.g., IQ-TREE, RAxML, etc) allow users to "
'help': "Some commonly used software for phylogenetic analyses (e.g., IQ-TREE, RAxML, etc) allow users to "
"specify/test different substitution models for each gene of a concatenated multiple sequence alignments. For "
"this, they use a special file format called a 'partition file', which indicates the site for each gene in the "
"alignment. You can use this parameter to declare an output path for anvi'o to report a NEXUS format partition "
Expand Down Expand Up @@ -983,7 +984,7 @@ def get_args(parser):
'help': "If in --flank-mode, anvi-export-locus will extract a locus based on the coordinates "
"of flanking genes. You MUST provide 2 flanking genes in the form of TWO "
"--search-term, --gene-caller-ids, or --hmm-sources. The --flank-mode option is "
"appropriate for extracting loci of variable gene number lengths, but are consistantly "
"appropriate for extracting loci of variable gene number lengths, but are consistently "
"located between the same flanking genes in the genome(s) of interest."}
),
'num-genes': (
Expand All @@ -994,33 +995,33 @@ def get_args(parser):
"a block of genes will be saved. The block could include either genes only in the forward direction of the gene (defined "
"according to the direction of transcription of the gene) or reverse or both. "
"If you wish to get both direction use a comma (no spaces) to define the block "
"For example, \"-n 4,5\" will give you four genes before and five genes after. "
"Whereas, \"-n 5\" will give you five genes after (in addition to the gene that matched). "
"To get only genes preceeding the match use \"-n 5,0\". "
"If the number of genes requested exceeds the length of the contig, then the output "
"will include the sequence until the end of the contig."}
"For example, '-n 4,5' will give you four genes before and five genes after. "
"Whereas, '-n 5' will give you five genes after (in addition to the gene that matched). "
"To get only genes preceding the match use '-n 5,0'. If the number of genes requested "
"exceeds the length of the contig, then the output will include the sequence until the end "
"of the contig."}
),
'gene-mode': (
['--gene-mode'],
{'default': False,
'action': 'store_true',
'help': "Initiate the interactive interface in \"gene mode\". In this mode, the items are genes (instead of "
'help': "Initiate the interactive interface in 'gene mode'. In this mode, the items are genes (instead of "
"splits of contigs). The following views are available: detection (the detection value of each gene "
"in each sample). The mean_coverage (the mean coverage of genes). The non_outlier_mean_coverage "
"(the mean coverage of the non-outlier nucleotide positions of each gene in each sample (median absolute "
"deviation is used to remove outliers per gene per sample)). The non_outlier_coverage_std view (standard deviation "
"of the coverage of non-outlier positions of genes in samples). You can also choose to order items "
"and layers according to each one of the aforementioned views. In addition, all layer ordering "
"that are available in the regular mode (i.e. the full mode where you have contigs/splits) are also "
"available in \"gene mode\", so that, for example, you can choose to order the layers according to \"detection\", and that "
"would be the order according to the detection values of splits, whereas if you choose \"genes_detections\" "
"available in 'gene mode', so that, for example, you can choose to order the layers according to 'detection', and that "
"would be the order according to the detection values of splits, whereas if you choose 'genes_detections' "
"then the order of layers would be according to the detection values of genes. Inspection and sequence "
"functionality are available (through the right-click menu), except now sequences are of the specific gene. "
"Inspection has now two options available: \"Inspect Context\", which brings you to the inspection page of the split "
"to which the gene belongs where the inspected gene will be highlighted in yellow in the bottom, and \"Inspect Gene\", "
"Inspection has now two options available: 'Inspect Context', which brings you to the inspection page of the split "
"to which the gene belongs where the inspected gene will be highlighted in yellow in the bottom, and 'Inspect Gene', "
"which opens the inspection page only for the gene and 100 nts around each side of it (the purpose of this option "
"is to make the inspection page load faster if you only want to look at the nucleotide coverage of a specific gene). "
"NOTICE: You can't store states or collections in \"gene mode\". However, you still can make fake selections, and create "
"NOTICE: You can't store states or collections in 'gene mode'. However, you still can make fake selections, and create "
"fake bins for your viewing convenience only (smiley). Search options are available, and you can even search for functions "
"if you have them in your contigs database. ANOTHER NOTICE: loading this mode might take a while if your bin "
"has many genes, and your profile database has many samples, this is because the gene coverages stats are "
Expand Down Expand Up @@ -1323,7 +1324,7 @@ def get_args(parser):
'default': 0,
'type': float,
'help': "Takes a value between 0 and 1, where 1 is maximum divergence from the consensus for a given position. The "
"default is %(default)f. The consensus is the most frequent observation at a given positon."}
"default is %(default)f. The consensus is the most frequent observation at a given position."}
),
'max-departure-from-consensus': (
['-a', '--max-departure-from-consensus'],
Expand Down Expand Up @@ -1376,7 +1377,7 @@ def get_args(parser):
{'default': 'NT',
'metavar': 'ENGINE',
'type': str,
'help': "Varaibility engine. The default is '%(default)s'."}
'help': "Variability engine. The default is '%(default)s'."}
),
'driver': (
['--driver'],
Expand Down Expand Up @@ -1811,7 +1812,7 @@ def get_args(parser):
'help': "Single profiles are rarely used for genome binning or visualization, and since "
"clustering step increases the profiling runtime for no good reason, the default "
"behavior is to not cluster contigs for individual runs. However, if you are "
"planning to do binning on one sample, you must use this flag to tell anvio to "
"planning to do binning on one sample, you must use this flag to tell anvi'o to "
"run cluster configurations for single runs on your sample."}
),
'num-clusters-requested': (
Expand Down Expand Up @@ -1841,7 +1842,7 @@ def get_args(parser):
"nucleotide positions. Usually it does not report every variable position, since "
"not every variable position is genuine variation. Say, if you have 1,000 coverage, "
"and all nucleotides at that position are Ts and only one of them is a C, the "
"confidence of that C being a real variation is quite low. anvio has a simple "
"confidence of that C being a real variation is quite low. anvi'o has a simple "
"algorithm in place to reduce the impact of noise. However, using this flag "
"you can disable it and ask profiler to report every single variation (which "
"may result in very large output files and millions of reports, but you are the "
Expand Down Expand Up @@ -1913,7 +1914,7 @@ def get_args(parser):
{'metavar': 'INT',
'default': 10,
'type': int,
'help': "Minimum coverage of a nucleotide position to be subjected to SNV profiling. By default, anvio will "
'help': "Minimum coverage of a nucleotide position to be subjected to SNV profiling. By default, anvi'o will "
"not attempt to make sense of variation in a given nucleotide position if it is covered less than "
"%(default)dX. You can change that minimum using this parameter."}
),
Expand Down Expand Up @@ -2130,7 +2131,7 @@ def get_args(parser):
'dump-dir': (
['--dump-dir'],
{'required': False,
'help': "Modelling and annotating structures requires a lot of moving parts, each which have "
'help': "Modeling and annotating structures requires a lot of moving parts, each which have "
"their own outputs. The output of this program is a structure database containing the "
"pertinent results of this computation, however a lot of stuff doesn't make the cut. "
"By providing a directory for this parameter you will get, in addition to the structure "
Expand Down Expand Up @@ -2192,7 +2193,7 @@ def get_args(parser):
"Any parameter that is accepted by snakemake should be fair game here, but it is your "
"responsibility to make sure that whatever you added makes sense. To see what parameters are "
"available please refer to the snakemake documentation. For example, you could use this to set "
"up cluster submission using --additional-params --cluster \"YOUR-CLUSTER-SUBMISSION-CMD\""}
"up cluster submission using --additional-params --cluster 'YOUR-CLUSTER-SUBMISSION-CMD'."}
),
'self-key': (
['--self-key'],
Expand All @@ -2210,7 +2211,7 @@ def get_args(parser):
['--no-variability'],
{'required': False,
'action': 'store_true',
'help': "If provided, no measures of sequence heterogeneity (from short read data) will be overlayed "
'help': "If provided, no measures of sequence heterogeneity (from short read data) will be overlaid "
"on structures."}
),
'compute-gene-coverage-stats': (
Expand Down

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