[typos] Proof-reading

Co-authored-by: Ivan Blagoev Topolsky <[email protected]>
Co-authored-by: Jonathan Waehrer <[email protected]>

README.md

@@ -23,9 +23,9 @@ Here are the available command-line tools:
 | `cojac cooc-colourmut`  | display a JSON or YAML file as a coloured output on the terminal |
 | `cojac cooc-pubmut`     | render a JSON or YAML file to a table as in the publication |
 | `cojac cooc-tabmut`     | export a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio) |
-| `cojac cooc-curate`     | an (experimental) tool to assist evaluating the quality of variant definitions by looking at mutations' or cooccurences' frequencies from [covSPECTRUM](https://cov-spectrum.org) |
+| `cojac cooc-curate`     | an (experimental) tool to assist evaluating the quality of variant definitions by looking at mutations' or cooccurrences' frequencies from [covSPECTRUM](https://cov-spectrum.org) |
 | `cojac phe2cojac`       | a tool to generate new variant definition YAMLs for cojac using YMLs available at [UK Health Security Agency (UKHSA) _Standardised Variant Definitions_](https://github.com/ukhsa-collaboration/variant_definitions/) |
-| `cojac sig-generate`    | a tool to generate list of mutations by querying [covSPECTRUM](https://lapis.cov-spectrum.org/) and assist writing variant definition YAMLs for cojac |
+| `cojac sig-generate`    | a tool to generate a list of mutations by querying [covSPECTRUM](https://lapis.cov-spectrum.org/) and assist writing variant definition YAMLs for cojac |
 
 Use option `-h` / `--help` to see available command-line options:
 
@@ -58,7 +58,7 @@ Options:
                                   ref\tstart\tstop\tamp_num\tpool\tstrand
   --sort / --no-sort             sort the bedfile by 'reference name' and
                                   'start position' (default: sorted)
-  -#, --cooc COOC                 minimum number of cooccurences to search for
+  -#, --cooc COOC                 minimum number of cooccurrences to search for
   -Q, --amplicons, --in-amp, --in-amplicons YAML
                                   use the supplied YAML file to query
                                   amplicons instead of building it from BED +
@@ -68,9 +68,9 @@ Options:
   --comment / --no-comment        add comments in the out amplicon YAML with
                                   names from BED file (default: comment the
                                   YAML)
-  -j, --json JSON                 output results to as JSON file
-  -y, --yaml YAML                 output results to as yaml file
-  -t, --tsv TSV                   output results to as (raw) tsv file
+  -j, --json JSON                 output results to a JSON file
+  -y, --yaml YAML                 output results to a yaml file
+  -t, --tsv TSV                   output results to a (raw) tsv file
   -d, --dump                      dump the python object to the terminal
   --help                          Show this message and exit.
 
@@ -143,11 +143,11 @@ Options:
 $ cojac cooc-curate --help
 Usage: cojac cooc-curate [OPTIONS] [VOC]...
 
-  Helps determining specific mutations and cooccurences by querying CoV-
+  Helps determining specific mutations and cooccurrences by querying CoV-
   Spectrum
 
 Options:
-  -u, --url URL               url to use when contact covspectrum (e.g.
+  -u, --url URL               url to use when querying covspectrum (e.g.
                               https://lapis.cov-spectrum.org/open/v1,
                               https://lapis.cov-spectrum.org/gisaid/v1, etc.)
   -a, --amplicons YAML        use the YAML file generated by mutbamscan to
@@ -159,10 +159,10 @@ Options:
   -l, --low FLOAT             Fraction under which a mutation must be found
                               among other lineages
   --collapse / --no-collapse  combine counts of all sublineages together and
-                              consider a signle value that corresponds to a
+                              consider a single value that corresponds to a
                               lineages family (e.g.: count all B.1.612.2*
                               together). This is especially useful for
-                              assessing signature of old variants that have
+                              assessing signatures of old variants that have
                               branched out by now.
   --colour / --no-colour      use coloured output
   --help                      Show this message and exit.
@@ -192,7 +192,7 @@ Usage: cojac  sig-generate [OPTIONS]
   querying covSPECTRUM
 
 Options:
-  -u, --url URL           url to use when contact covspectrum (e.g.
+  -u, --url URL           url to use when querying covspectrum (e.g.
                           https://lapis.cov-spectrum.org/open/v1,
                           https://lapis.cov-spectrum.org/gisaid/v1, etc.)
   --var, --variant PANGO  Pangolineage of the root variant to list  [required]
@@ -237,9 +237,9 @@ curl -o SARS-CoV-2.v532.primer.bed 'https://raw.githubusercontent.com/artic-netw
 # convert it into an *insert* BED file
 scheme-convert SARS-CoV-2.v532.primer.bed --to bed --bed-type cojac -o SARS-CoV-2.v532.cojac_insert.bed
 ```
-> - for an useful application of *primer* BED files to searching for possible drop-outs, see [section _Mutations affecting primers_ below](#mutations-affecting-primers).
+> - for a useful application of *primer* BED files to searching for possible drop-outs, see [section _Mutations affecting primers_ below](#mutations-affecting-primers).
 
-These protocols produces ~400bp long amplicons, and thus needs to be sequenced with, e.g., paired end sequencing with read length 250.
+These protocols produce ~400bp long amplicons, and thus needs to be sequenced with, e.g., paired end sequencing with read length 250.
 
 Select the desired bedfile using the `-b` / `--bedfile` option.
 
@@ -265,7 +265,7 @@ cojac phe2cojac --shortname 'om2' --yaml voc/omicron_ba2_mutations.yaml variant_
 cojac cooc-curate voc/omicron_ba2_mutations.yaml
 # adjust the content of the YAML files to your needs
 ```
-> - Another possibility is obtaining an exhausive list of mutations from covSpectrum or [covariants.org's repository](https://github.com/hodcroftlab/covariants/tree/master/defining_mutations)
+> - Another possibility is obtaining an exhaustive list of mutations from covSpectrum or [covariants.org's repository](https://github.com/hodcroftlab/covariants/tree/master/defining_mutations)
 ```bash
 # display the exhaustive list of all mutations known to appear on Omicron BA.1 on covSPECTRUM:
 cojac sig-generate --url https://lapis.cov-spectrum.org/open/v1 --variant BA.1 | tee list_ba1.yaml
@@ -319,11 +319,11 @@ cojac cooc-mutbamscan -b nCoV-2019.insert.V3.bed -m voc/ -t work/samples.tsv -p
 
 > ***Note:** Warning, it is much slower as each alignment is analyzed sequentially.
 
-#### Number of cooccurences
+#### Number of cooccurrences
 
 By default `cooc-mutbamscan` will look for cooccurrences of at least 2 mutations on the same amplicon. You can change that number using option `-#`/`--cooc`:
 
- - you can increase it to e.g.: 3 if the variants you study requires more stringent identification
+ - you can increase it to e.g.: 3 if the variants you study require more stringent identification
  - you can set it to 1, to also count isolated occurrences - in this case `cooc-mutbamscan` will also double as a generic (non coorcurrence-aware) variant caller, so you can get all counts with a single tool.
 
 #### Store the amplicon query
@@ -337,7 +337,7 @@ This is useful for sharing the exact same request accross multiple parallel COJA
 cojac cooc-mutbamscan -b nCoV-2019.insert.V3.bed -m voc/ -A amplicons.v3.yaml
 # adjust the content of amplicons.v3.yaml
 
-# now have a look at the frequencies of mutation cooccurences using covSPECTRUM
+# now have a look at the frequencies of mutation cooccurrences using covSPECTRUM
 cojac cooc-curate -a amplicons.v3.yaml voc/omicron_ba2_mutations.yaml voc/omicron_ba1_mutations.yaml voc/delta_mutations.yaml
 # reuse the amplicon
 cojac cooc-mutbamscan -Q amplicons.v3.yaml -a sam1.bam -y cooc-sam1.yaml
@@ -457,7 +457,7 @@ cojac cooc-mutbamscan --voc omicron_ba286_mutations_full.yaml --bedfile SARS-CoV
 ```
 
 
-This will yields entries like:
+This will yield entries like:
 ```yaml
 50_ombba286: [7819, 7850, 7512, 7738, {7842: G}] # SARS-CoV-2_25_RIGHT
 ```

cojac/cooc_curate.py

@@ -189,7 +189,7 @@ def freqperlineage(mutations, lineages):
 
 
 def rank(sublineages, freqs, limit=0.05):
-    """find ranks of occurence of:
+    """find ranks of occurrence of:
     - last sublineages still part of the seeked lineages
     - first other lineages which is not part of the seeked one
     - last member still above the limit
@@ -275,7 +275,7 @@ def curate_muts(
 
 
 @click.command(
-    help="Helps determining specific mutations and cooccurences by querying covSPECTRUM",
+    help="Helps determining specific mutations and cooccurrences by querying covSPECTRUM",
     epilog="This tool queries LAPIS, see https://lapis-docs.readthedocs.io/en/latest/",
 )
 @click.option(
@@ -285,7 +285,7 @@ def curate_muts(
     required=False,
     default=None,
     type=str,
-    help="url to use when contact covspectrum (e.g. https://lapis.cov-spectrum.org/open/v1, https://lapis.cov-spectrum.org/gisaid/v1, etc.)",
+    help="url to use when querying covspectrum (e.g. https://lapis.cov-spectrum.org/open/v1, https://lapis.cov-spectrum.org/gisaid/v1, etc.)",
 )
 @click.option(
     "-a",
@@ -325,7 +325,7 @@ def curate_muts(
     "--collapse/--no-collapse",
     required=False,
     default=True,
-    help="combine counts of all sublineages together and consider a signle value that corresponds to a lineages family (e.g.: count all B.1.612.2* together). This is especially useful for assessing signature of old variants that have branched out by now.",
+    help="combine counts of all sublineages together and consider a single value that corresponds to a lineages family (e.g.: count all B.1.612.2* together). This is especially useful for assessing signatures of old variants that have branched out by now.",
 )
 @click.option(
     "--colour/--no-colour",

cojac/cooc_mutbamscan.py

@@ -157,7 +157,7 @@ def make_amplicons_dict(amp_bed, mut_dict, voc_name="", cooc=2):
     Returns:
             amplicons_dict: dict() with entries of the form:
                     *amplicon_number*_*voc_name* : [start, stop, {position1 : mutation1, position2 : mutation2 , ...}]
-                    for each amplicon where cooccurences could be found
+                    for each amplicon where cooccurrences could be found
     """
     mut_df = pd.DataFrame({"position": mut_dict.keys(), "mutation": mut_dict.values()})
     amplicons_dict = {}
@@ -490,7 +490,7 @@ def flowseq_rep(dumper, data):
     required=False,
     default=2,
     type=int,
-    help="minimum number of cooccurences to search for",
+    help="minimum number of cooccurrences to search for",
 )
 # TODO: use mutually exclusive groups
 @click.option(
@@ -530,7 +530,7 @@ def flowseq_rep(dumper, data):
     required=False,
     default=None,
     type=str,
-    help="output results to as JSON file",
+    help="output results to a JSON file",
 )
 @click.option(
     "-y",
@@ -540,7 +540,7 @@ def flowseq_rep(dumper, data):
     required=False,
     default=None,
     type=str,
-    help="output results to as yaml file",
+    help="output results to a yaml file",
 )
 @click.option(
     "-t",
@@ -549,7 +549,7 @@ def flowseq_rep(dumper, data):
     required=False,
     default=None,
     type=str,
-    help="output results to as (raw) tsv file",
+    help="output results to a (raw) tsv file",
 )
 @click.option(
     "-d",

cojac/sig_generate.py

@@ -27,7 +27,7 @@
     required=False,
     default=None,
     type=str,
-    help="url to use when contact covspectrum (e.g. https://lapis.cov-spectrum.org/open/v1, https://lapis.cov-spectrum.org/gisaid/v1, etc.)",
+    help="url to use when querying covspectrum (e.g. https://lapis.cov-spectrum.org/open/v1, https://lapis.cov-spectrum.org/gisaid/v1, etc.)",
 )
 @click.option(
     "--var",
@@ -64,7 +64,7 @@
     metavar="FREQ",
     default=None,
     type=float,
-    help="Use a different minimum frequency for deletions (useful early on when there are few sequences and some of those were produced by pipeline that don't handle deletions)",
+    help="Use a different minimum frequency for deletions (useful early on when there are few sequences and some of those were produced by pipelines that don't handle deletions)",
 )
 @click.option(
     "-s",