Fixed polya-trimming rule

In labkey_to_snakemake.py fixed the parameters so that there is 3p as well 5p polya
feature for every mate, which can be matched to the -a -g -A and -G options of cutadapt
depending on which is the sense or antisense mate the appropriate variable is populated
and the rest of variables are filled with 'XXXXXXXXXXXX' which leads to no trimming by
cutadapt. The poly-A trimming rules are fixed to contain all -a -g -A -G options.

scripts/labkey_to_snakemake.py

@@ -228,9 +228,13 @@ def main():
         snakemake_table.loc[index, 'soft_clip'] = options.soft_clip
         snakemake_table.loc[index, 'pass_mode'] = options.pass_mode
         snakemake_table.loc[index, 'libtype'] = options.libtype
+
         if options.trim_polya is True:
-            snakemake_table.loc[index, 'fq1_polya'] = trim_polya(
+            fq1_polya_3p, fq1_polya_5p = trim_polya(
                 row[input_dict.loc['mate1_direction', 'labkey']])
+            snakemake_table.loc[index, 'fq1_polya_3p'] = fq1_polya_3p
+            snakemake_table.loc[index, 'fq1_polya_5p'] = fq1_polya_5p
+
         snakemake_table.loc[index, 'kallisto_directionality'] = \
             get_kallisto_directionality(
                 row[input_dict.loc['mate1_direction', 'labkey']])
@@ -247,8 +251,10 @@ def main():
                 input_dict.loc['fq2_5p', 'labkey']]
 
             if options.trim_polya is True:
-                snakemake_table.loc[index, 'fq2_polya'] = trim_polya(
+                fq2_polya_3p, fq2_polya_5p = trim_polya(
                     row[input_dict.loc['mate2_direction', 'labkey']])
+                snakemake_table.loc[index, 'fq2_polya_3p'] = fq2_polya_3p
+                snakemake_table.loc[index, 'fq2_polya_5p'] = fq2_polya_5p
 
     snakemake_table.fillna('XXXXXXXXXXXXX', inplace=True)
     snakemake_table = snakemake_table.astype(
@@ -322,14 +328,15 @@ def get_kallisto_directionality(directionality):
 
 def trim_polya(sense):
     if sense == 'SENSE':
-        polya = 'AAAAAAAAAAAAAAAAA'
+        polya_3p = 'AAAAAAAAAAAAAAAAA'
+        polya_5p = 'XXXXXXXXXXXXXXXXX'
     elif sense == 'ANTISENSE':
-        polya = 'TTTTTTTTTTTTTTTTT'
-    elif sense == 'RANDOM':
-        polya = 'AAAAAAAAAAAAAAAAA'
+        polya_3p = 'XXXXXXXXXXXXXXXXX'
+        polya_5p = 'TTTTTTTTTTTTTTTTT'
     else:
-        polya = 'XXXXXXXXXXXXXXXXX'
-    return polya
+        polya_3p = 'XXXXXXXXXXXXXXXXX'
+        polya_5p = 'XXXXXXXXXXXXXXXXX'
+    return polya_3p, polya_5p
 
 
 if __name__ == '__main__':

workflow/rules/paired_end.snakefile.smk

@@ -143,9 +143,13 @@ rule pe_remove_polya_cutadapt:
 
     params:
         polya_3_mate1 = lambda wildcards:
-            samples_table.loc[wildcards.sample, 'fq1_polya'],
+            samples_table.loc[wildcards.sample, 'fq1_polya_3p'],
+        polya_5_mate1 = lambda wildcards:
+            samples_table.loc[wildcards.sample, 'fq1_polya_5p'],
         polya_3_mate2 = lambda wildcards:
-            samples_table.loc[wildcards.sample, 'fq2_polya']
+            samples_table.loc[wildcards.sample, 'fq2_polya_3p'],
+        polya_5_mate2 = lambda wildcards:
+            samples_table.loc[wildcards.sample, 'fq2_polya_5p']
 
     singularity:
         "docker://zavolab/cutadapt:1.16-slim"
@@ -173,7 +177,9 @@ rule pe_remove_polya_cutadapt:
         -e 0.1 \
         -O 1 \
         -a {params.polya_3_mate1} \
+        -g {params.polya_5_mate1} \
         -A {params.polya_3_mate2} \
+        -G {params.polya_5_mate2} \
         -o {output.reads1} \
         -p {output.reads2} \
         {input.reads1} \

workflow/rules/single_end.snakefile.smk

@@ -108,7 +108,9 @@ rule remove_polya_cutadapt:
 
     params:
         polya_3 = lambda wildcards:
-            samples_table.loc[wildcards.sample, "fq1_polya"]
+            samples_table.loc[wildcards.sample, "fq1_polya_3p"],
+        polya_5 = lambda wildcards:
+            samples_table.loc[wildcards.sample, "fq1_polya_5p"]
 
     singularity:
         "docker://zavolab/cutadapt:1.16-slim"
@@ -135,6 +137,7 @@ rule remove_polya_cutadapt:
         -O 1 \
         -m 10  \
         -a {params.polya_3} \
+        -g {params.polya_5} \
         -o {output.reads} \
         {input.reads};) \
         1> {log.stdout} 2> {log.stderr}"