Oneamplicon (#2) Added input data and minor fixes

* update info for 1amp * Add newest reference dataset without UTR * add new initdir * fix calculation
talnor · Feb 24, 2022 · 774f217 · 774f217
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diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ detail [here](data/README.md).
 Shiver initilisation directories are included in this repository. Information on these are 
 available [here](data/README.md). To create your own initilisation directory, run the following command:
 ```
-nextflow run main.nf --init -profile slurm,singularity --primers <primers.fasta> --adapters <adapters.fasta> --config <shiver_config.sh> --references <references.fasta>
+nextflow run main.nf --init -profile slurm,singularity --primers <primers.fasta> --adapters <adapters.fasta> --config <shiver_config.sh> --references <references.fasta> --outdir <outdir>
 ```
 
 ## Usage

diff --git a/bin/calculate_eti.py b/bin/calculate_eti.py
@@ -44,7 +44,7 @@
 def get_region_data(base_frequency_file, pos_start, start_base, pos_fin, step):
     """Return base count data for region of interest"""
     with open(base_frequency_file, "r") as f:
-        column_names = [
+        headers = [
             "HXB2_position",
             "Reference_position",
             "Reference_Base",
@@ -66,7 +66,7 @@ def get_region_data(base_frequency_file, pos_start, start_base, pos_fin, step):
             "gap": float,
             "N": float,
         }
-        all_data = pd.read_csv(f, header=0, names=column_names)
+        all_data = pd.read_csv(f, header=0, names=headers)
         all_data.astype(columns)
     positions_of_interest = range(pos_start + start_base - 1, pos_fin + 1, step)
     pol = all_data[all_data["HXB2_position"].isin(str(i) for i in positions_of_interest)]
@@ -130,7 +130,7 @@ def remove_low_coverage_positions(pol, min_cov):
 
 def calculate_theta(pol, diversity_threshold):
     """Calculate theta value for each position"""
-    major_base_frequency = pol[["A", "C", "G", "T"]].max(axis=1)
+    major_base_frequency = pol[["freq_A", "freq_C", "freq_G", "freq_T"]].max(axis=1)
     pol["freq_major_base"] = major_base_frequency.values
     theta_array = np.where((1 - pol["freq_major_base"]) > diversity_threshold, 1, 0)
     pol["theta"] = theta_array.tolist()

diff --git a/data/README.md b/data/README.md
@@ -41,6 +41,7 @@ Below follows a description of the files that are made available in this directo
 | ----------- | ----------- | ----------- |
 | 1 | original_config.sh | Default settings used in Shiver |
 | 2 | shiver_config_BQ30_notrimming.sh | TIME-study settings |
+| 3 | config_BQ30.sh | Older settings |
 
 #### Configuration file 2
 
@@ -53,16 +54,35 @@ The following options in Shiver are altered. For the full list of options see th
 | mpileupOptions      | --min-BQ 30 | --min-BQ 5 | Higher quality threshold for individual bases |
 | deduplicate      | true | false | Remove read pairs marked as duplicates? This can cause loss of diversity in the reads due to true biological variation as well sequencing error. |
 
+#### Configuration file 3
+
+The following options in Shiver are altered. For the full list of options see the default config.
+
+| Parameter   | Value       | Default     | Description |
+| ----------- | ----------- | ----------- | ----------- |
+| mpileupOptions      | --min-BQ 30 | --min-BQ 5 | Higher quality threshold for individual bases |
+| deduplicate      | true | false | Remove read pairs marked as duplicates? This can cause loss of diversity in the reads due to true biological variation as well sequencing error. |
+
+
 ### Shiver init directory
 | Version     | InitDir     | Description | 
 | ----------- | ----------- | ----------- |
-| 1 | InitDirShiver190405_BQ30 |  |
-| 1 | InitDirShiver220128_BQ30_1amp | 1 amplicon primers, 2020 references |
+| 1 | InitDirShiver220223_BQ30_1amp | 1 amplicon primers, 2020 references, no UTRs |
+| 2 | InitDirShiver220128_BQ30_1amp | 1 amplicon primers, 2020 references |
+| 3 | InitDirShiver190405_BQ30 |  |
+| 4 | InitDirShiver191022_BQ30_PANHIV | 1 amplicon primers, 2018 references |
 
 #### Shiver init directory 1
 
-**Name**: InitDirShiver190405_BQ30
-**Created**: 2019-04-05
+**Name**: InitDirShiver220223_BQ30_1amp 
+**Created**: 2022-02-23
+
+| Content     | Description     |
+| ----------- | ----------- |
+| Primer      | primers_1_amplicon_PCR1_190620.fasta | 
+| Adapter      | NexteraPE-PE.fa | 
+| Configurations      | shiver_config_BQ30_notrimming.sh |
+| References      | HIV1_COM_2020_547-9592_DNA.fasta |
 
 #### Shiver init directory 2
 
@@ -71,17 +91,35 @@ The following options in Shiver are altered. For the full list of options see th
 
 | Content     | Description     |
 | ----------- | ----------- |
-| Primer      | primers_1_amplicon_PCR1_190620.fasta
+| Primer      | primers_1_amplicon_PCR1_190620.fasta | 
 | Adapter      | NexteraPE-PE.fa | 
 | Configurations      | shiver_config_BQ30_notrimming.sh |
-| References      | HIV1_COM_2020_genome_DNA.fasta' |
+| References      | HIV1_COM_2020_genome_DNA.fasta |
+
+#### Shiver init directory 3
+
+**Name**: InitDirShiver190405_BQ30
+**Created**: 2019-04-05
+
+#### Shiver init directory 4
+
+**Name**: InitDirShiver191022_BQ30_PANHIV 
+**Created**: 2019-10-22
+
+| Content     | Description     |
+| ----------- | ----------- |
+| Primer      | primers_1_amplicon_PCR1-2_190620.fasta | 
+| Adapter      | NexteraPE-PE.fa | 
+| Configurations      | config_BQ30.sh |
+| References      | HIV1_COM_2017_547-9592_DNA_2018Compendium.fasta |
 
 ### References to use in Shiver alignments
 Reference compendiums with representative genomes can be downloaded from the 
 [LANL HIV database](http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html).
 
 | Reference  file                | Description                                                          |
 | ------------------------------ | -------------------------------------------------------------------- |
-| HIV1_COM_2020_genome_DNA.fasta | Represenative genome alignment with references from 2020 and earlier |
-
+| HIV1_COM_2020_genome_DNA.fasta | Represenative genome alignment with references from 2020 and earlier. |
+| HIV1_COM_2020_547-9592_DNA.fasta | Represenative genome alignment with references from 2020 and earlier. Genomic positions 547-9592 included. |
+| HIV1_COM_2017_547-9592_DNA_2018Compendium.fasta | Represenative genome alignment with references from 2018 and earlier. Genomic positions 547-9592 included. |