From dcbb51e6aefa9f21843fb87513c10e93d03e9b4e Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Wed, 18 Mar 2020 13:38:03 +0100
Subject: [PATCH] included ALFA results for Unique reads. Fixes #93
---
Snakefile | 38 +++++++++++++------
tests/test_alfa/expected_output.md5 | 36 ++++++++++++------
tests/test_alfa/test.sh | 3 +-
.../expected_output.md5 | 24 +++++++-----
4 files changed, 67 insertions(+), 34 deletions(-)
diff --git a/Snakefile b/Snakefile
index 97db0e3..65c9b5e 100644
--- a/Snakefile
+++ b/Snakefile
@@ -101,16 +101,20 @@ rule finish:
"{seqmode}",
"{sample}",
"ALFA",
- "ALFA_plots.Biotypes.pdf"),
+ "{unique_type}",
+ "ALFA_plots.Categories.pdf"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [
samples_table.loc[i,"seqmode"]
- for i in list(samples_table.index.values)]),
- alfa_all_samples = os.path.join(
+ for i in list(samples_table.index.values)],
+ unique_type = ["Unique", "UniqueMultiple"]),
+ alfa_all_samples = expand(os.path.join(
config["output_dir"],
"ALFA",
- "ALFA_plots.Categories.pdf")
+ "{unique_type}",
+ "ALFA_plots.Categories.pdf"),
+ unique_type = ["Unique", "UniqueMultiple"]),
@@ -460,13 +464,13 @@ rule rename_star_rpm_for_alfa:
"{seqmode}",
"{sample}",
"STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str1.out.bg"),
+ "{sample}_Signal.{unique}.str1.out.bg"),
str2 = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"STAR_coverage",
- "{sample}_Signal.UniqueMultiple.str2.out.bg")
+ "{sample}_Signal.{unique}.str2.out.bg")
output:
plus = os.path.join(
@@ -474,13 +478,15 @@ rule rename_star_rpm_for_alfa:
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ "{unique}",
+ "{sample}_Signal.{unique}.out.plus.bg"),
minus = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.minus.bg")
+ "{unique}",
+ "{sample}_Signal.{unique}.out.minus.bg")
params:
orientation = lambda wildcards: samples_table.loc[wildcards.sample, "kallisto_directionality"]
@@ -825,13 +831,15 @@ rule alfa_qc:
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.plus.bg"),
+ "{unique}",
+ "{sample}_Signal.{unique}.out.plus.bg"),
minus = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
- "{sample}_Signal.UniqueMultiple.out.minus.bg"),
+ "{unique}",
+ "{sample}_Signal.{unique}.out.minus.bg"),
gtf = lambda wildcards: os.path.join(config["alfa_indexes"],
samples_table.loc[wildcards.sample, "organism"],
str(samples_table.loc[wildcards.sample, "index_size"]),
@@ -844,18 +852,21 @@ rule alfa_qc:
"{seqmode}",
"{sample}",
"ALFA",
+ "{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
+ "{unique}",
"ALFA_plots.Categories.pdf"),
table = os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
+ "{unique}",
"{sample}.ALFA_feature_counts.tsv")
params:
@@ -874,7 +885,7 @@ rule alfa_qc:
config["log_dir"],
"{seqmode}",
"{sample}",
- "alfa_qc.log"))
+ "alfa_qc.{unique}.log"))
shell:
"""
@@ -893,6 +904,7 @@ rule alfa_qc_all_samples:
samples_table.loc[sample1, "seqmode"],
str(sample1),
"ALFA",
+ "{unique}",
sample1 + ".ALFA_feature_counts.tsv")
for sample1 in list(samples_table.index.values)]
@@ -900,10 +912,12 @@ rule alfa_qc_all_samples:
biotypes = os.path.join(
config["output_dir"],
"ALFA",
+ "{unique}",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
"ALFA",
+ "{unique}",
"ALFA_plots.Categories.pdf")
params:
@@ -912,7 +926,7 @@ rule alfa_qc_all_samples:
log:
os.path.abspath(
os.path.join(config["log_dir"],
- "alfa_qc_all_samples.log"))
+ "alfa_qc_all_samples.{unique}.log"))
singularity:
"docker://zavolab/alfa:1.1.1"
diff --git a/tests/test_alfa/expected_output.md5 b/tests/test_alfa/expected_output.md5
index 57f9dfd..7b2472f 100644
--- a/tests/test_alfa/expected_output.md5
+++ b/tests/test_alfa/expected_output.md5
@@ -1,5 +1,29 @@
90e42aa46890e9cd0a47800428699fbf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
+c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
+e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/UniqueMultiple/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/UniqueMultiple/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/UniqueMultiple/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense_Signal.Unique.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/Unique/paired_end_R1_on_minus_antisense_Signal.Unique.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense_Signal.Unique.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/Unique/paired_end_R1_on_minus_sense_Signal.Unique.out.plus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense_Signal.Unique.out.minus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/Unique/paired_end_R1_on_plus_antisense_Signal.Unique.out.plus.bg
+5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense_Signal.Unique.out.minus.bg
+8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/Unique/paired_end_R1_on_plus_sense_Signal.Unique.out.plus.bg
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str1.out.bg
8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.str2.out.bg
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/STAR_coverage/paired_end_R1_on_minus_antisense_Signal.Unique.str1.out.bg
@@ -16,15 +40,3 @@ ccc3cf5a57fddb0d469e597d4376b1bf results/alfa_indexes/homo_sapiens/75/ALFA/sort
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.str2.out.bg
8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str1.out.bg
5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/STAR_coverage/paired_end_R1_on_plus_sense_Signal.Unique.str2.out.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.minus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense_Signal.UniqueMultiple.out.plus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense_Signal.UniqueMultiple.out.plus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.minus.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense_Signal.UniqueMultiple.out.plus.bg
-5e90c760710980f4f4866dbe9aa32c6c results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.minus.bg
-8e23d52d7f635d927e292174f33168eb results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense_Signal.UniqueMultiple.out.plus.bg
-e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_minus_antisense/ALFA/paired_end_R1_on_minus_antisense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_minus_sense/ALFA/paired_end_R1_on_minus_sense.ALFA_feature_counts.tsv
-c406c1800d3690dd774aaa7e3c190523 results/paired_end/paired_end_R1_on_plus_antisense/ALFA/paired_end_R1_on_plus_antisense.ALFA_feature_counts.tsv
-e5959524a2daf35da9249fb313920315 results/paired_end/paired_end_R1_on_plus_sense/ALFA/paired_end_R1_on_plus_sense.ALFA_feature_counts.tsv
diff --git a/tests/test_alfa/test.sh b/tests/test_alfa/test.sh
index 280749c..3d5c325 100755
--- a/tests/test_alfa/test.sh
+++ b/tests/test_alfa/test.sh
@@ -33,7 +33,8 @@ snakemake \
--use-singularity \
--singularity-args="--bind ${PWD}/../input_files" \
--verbose \
- results/ALFA/ALFA_plots.Categories.pdf
+ results/ALFA/UniqueMultiple/ALFA_plots.Categories.pdf \
+ results/ALFA/Unique/ALFA_plots.Categories.pdf
# Check md5 sum of some output files
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
diff --git a/tests/test_integration_workflow/expected_output.md5 b/tests/test_integration_workflow/expected_output.md5
index c017ef0..e14eb7e 100644
--- a/tests/test_integration_workflow/expected_output.md5
+++ b/tests/test_integration_workflow/expected_output.md5
@@ -78,6 +78,21 @@ e72f5d798c99272f8c0166dc77247db1 results/single_end/synthetic_10_reads_mate_1_s
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias
92bcd0592d22a6a58d0360fc76103e56 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/observed_bias_3p
d41d8cd98f00b204e9800998ecf8427e results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/salmon_quant/aux_info/unmapped_names.txt
+3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
+6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
+2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
+c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+c1254a0bae19ac3ffc39f73099ffcf2b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.out.minus.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/Unique/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.out.plus.bg
+bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/Unique/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.out.plus.bg
+c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
+c1254a0bae19ac3ffc39f73099ffcf2b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
+c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
+0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/UniqueMultiple/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
+bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
+ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/UniqueMultiple/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str1.out.bg
c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.str2.out.bg
0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/STAR_coverage/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.Unique.str1.out.bg
@@ -86,12 +101,3 @@ ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_s
bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.str2.out.bg
ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str1.out.bg
bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/STAR_coverage/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.Unique.str2.out.bg
-3ce47cb1d62482c5d62337751d7e8552 results/transcriptome/homo_sapiens/transcriptome.fa
-6b44c507f0a1c9f7369db0bb1deef0fd results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.stranded.ALFA_index
-2caebc23faf78fdbbbdbb118d28bd6b5 results/alfa_indexes/homo_sapiens/75/ALFA/sorted_genes.unstranded.ALFA_index
-c1254a0bae19ac3ffc39f73099ffcf2b results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired.ALFA_feature_counts.tsv
-c266d31e0a2ad84975cb9de335891e64 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.minus.bg
-0139e75ddbfe6eb081c2c2d9b9108ab4 results/paired_end/synthetic_10_reads_paired_synthetic_10_reads_paired/ALFA/synthetic_10_reads_paired_synthetic_10_reads_paired_Signal.UniqueMultiple.out.plus.bg
-c1254a0bae19ac3ffc39f73099ffcf2b results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1.ALFA_feature_counts.tsv
-bcccf679a8c083d01527514c9f5680a0 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.minus.bg
-ea91b4f85622561158bff2f7c9c312b3 results/single_end/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1/ALFA/synthetic_10_reads_mate_1_synthetic_10_reads_mate_1_Signal.UniqueMultiple.out.plus.bg
\ No newline at end of file
--
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