Fix Bam-deam-stats-script (update version v2.5)

Author: merszym

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
     - Create a table that shows substitutions-rates for the first 10 and last 10 positions of each alignment.
     - Create a table that shows the 95% confidence-intervals for the first and last 10 positions of each alignment
     - the are saved to the `stats/` directory under `{RG}_04_deamination_positions/`
+- Add the `--ancientness_threshold` flag to specify the threshold used for reporting ancientness levels ('++' and '+')
 
 ### Bugfixes
 

assets/pipeline/help.txt

@@ -42,6 +42,9 @@ process arguments:
   --bamfilter_quality_cutoff    N    Quality filter for extracted bam (default: 25)
   --krakenuniq_min_kmers        N    Filter: minimal required unique kmers (krakenuniq) assigned to a family (default: 129)
   --krakenuniq_min_reads        N    Filter: minimal required number of reads assigned to a family by krakenuniq (default: 3)
+  --ancientness_threshold       N    Threshold for reporting 'Ancientness' values of '++' or '+' (default: 9.5)
+                                        - (++): Substitution frequencies on both ends of sequences are significantly higher than N %
+                                        -  (+): Substitution frequencies on either the 5’ or the 3’ end of sequences are significantly higher than N %
   --reportfilter_percentage     N    For the 'filtered_report.tsv', Specify a FamPercentage threshold
   --reportfilter_breadth        N    For the 'filtered_report.tsv', Specify a ProportionExpectedBreadth threshold
 

docs/source/flags.rst

@@ -272,6 +272,17 @@ Optional flags
 
           --bamfilter_quality_cutoff 25
 
+  * - --ancientness_threshold
+    - N
+    - | Threshold for reporting 'Ancientness' values of '++' or '+' (default: 9.5)
+      |    (++): Substitution frequencies on both ends of sequences are significantly higher than N %
+      |     (+): Substitution frequencies on either the 5’ or the 3’ end of sequences are significantly higher than N %
+      ::
+
+          Example:
+
+          --ancientness_threshold 5
+
   * - --reportfilter_percentage
     - N
     - | For the creation of the filtered_report.tsv file

modules/local/bam_deam_stats/resources/usr/bin/bam_deam_stats.py

@@ -15,7 +15,7 @@ def binomial_ci(x, n, alpha=0.05):
     return f"{round(lower*100,1):.1f},{round(upper*100,1):.1f}"
 
 
-def main(bamfile, threshold=threshold, positions=3, stats_only=False, doublestranded=False):
+def main(bamfile, threshold=9.5, positions=3, stats_only=False, doublestranded=False):
     #store all reference bases
     all_first = []
     all_last = []