find marine

YeoLab · Jul 8, 2024 · 711a516 · 711a516
1 parent 99a882b
commit 711a516
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Showing 18 changed files with 41 additions and 55 deletions.
diff --git a/tests/TESTS_README.txt b/tests/TESTS_README.txt
@@ -1,7 +1,7 @@
 Before running tests, MARINE environment variable must be set from main MARINE directory (i.e. the directory containingg the examples directory). The path to the main MARINE directory should also be appended to the PATH environment variable.
 
-    export MARINE=$(pwd)
-    export PATH=$PATH:$(pwd)
+export MARINE=$(pwd)
+export PATH=$PATH:$(pwd)
 
 
 

diff --git a/tests/integration_tests_run.sh b/tests/integration_tests_run.sh
@@ -21,7 +21,7 @@ do
     rm $MARINE/tests/$tests_folder$t/* -r
 
     echo "Running tests..."
-    bash $MARINE/tests/$tests_folder/scripts/$t.sh 
+    bash $MARINE/tests/$tests_folder/scripts/$t.sh $mypython
 
 done
 
@@ -43,7 +43,7 @@ do
     rm $MARINE/tests/$tests_folder$t/* -r
 
     echo "Running tests..."
-    bash $MARINE/tests/$tests_folder/scripts/$t.sh 
+    bash $MARINE/tests/$tests_folder/scripts/$t.sh $mypython
 
 done
 

diff --git a/tests/singlecell_tests/scripts/long_read_sc_test.sh b/tests/singlecell_tests/scripts/long_read_sc_test.sh
@@ -1,18 +1,19 @@
-python \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/examples/data/LR_single_cell.md.subset.filtered.sorted.bam \
+$MARINE/examples/data/LR_single_cell.md.subset.filtered.sorted.bam \
 --annotation_bedfile_path \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
+$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
 --output_folder \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/tests/singlecell_tests/long_read_sc_test \
+$MARINE/tests/singlecell_tests/long_read_sc_test \
 --min_dist_from_end \
 0 \
 --min_base_quality \
 0 \
 --cores \
 16 \
---barcode_whitelist_file /tscc/projects/ps-yeolab3/ekofman/sailor2/examples/data/sc_lr_barcodes.tsv.gz \
+--barcode_whitelist_file $MARINE/examples/data/sc_lr_barcodes.tsv.gz \
 --strandedness 2 \
 --barcode_tag "IB" \
 --contigs "6" \

diff --git a/tests/singlecell_tests/scripts/only_5_cells_test.sh b/tests/singlecell_tests/scripts/only_5_cells_test.sh
@@ -1,11 +1,12 @@
-python \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
+$MARINE/tests/singlecell_tests/bams/9_3000526_only_5_cells.bam \
 --annotation_bedfile_path \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
+$MARINE/annotations/cellranger-mm10-3.0.0.annotation.genes.bed \
 --output_folder \
-/tscc/projects/ps-yeolab3/ekofman/sailor2/tests/singlecell_tests/only_5_cells_test \
+$MARINE/tests/singlecell_tests/only_5_cells_test \
 --min_dist_from_end \
 0 \
 --min_base_quality \

diff --git a/tests/strandedness_tests/F1R2_pair_test/final_filtered_site_info_annotated.tsv b/tests/strandedness_tests/F1R2_pair_test/final_filtered_site_info_annotated.tsv
diff --git a/tests/strandedness_tests/F2R1_end_second_in_pair_test/final_filtered_site_info_annotated.tsv b/tests/strandedness_tests/F2R1_end_second_in_pair_test/final_filtered_site_info_annotated.tsv
diff --git a/tests/strandedness_tests/pair_test/final_filtered_site_info.tsv b/tests/strandedness_tests/pair_test/final_filtered_site_info.tsv
diff --git a/tests/strandedness_tests/pair_test/final_filtered_site_info_annotated.tsv b/tests/strandedness_tests/pair_test/final_filtered_site_info_annotated.tsv
diff --git a/tests/strandedness_tests/same_pos_dif_reads_test/final_filtered_site_info_annotated.tsv b/tests/strandedness_tests/same_pos_dif_reads_test/final_filtered_site_info_annotated.tsv
diff --git a/tests/strandedness_tests/scripts/.ipynb_checkpoints/F1R2_pair_test-checkpoint.sh b/tests/strandedness_tests/scripts/.ipynb_checkpoints/F1R2_pair_test-checkpoint.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/F1R2_pair.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/F1R2_pair_test-single_end_mode.sh b/tests/strandedness_tests/scripts/F1R2_pair_test-single_end_mode.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/F1R2_pair.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/F1R2_pair_test.sh b/tests/strandedness_tests/scripts/F1R2_pair_test.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/F1R2_pair.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/F2R1_end_second_in_pair_test.sh b/tests/strandedness_tests/scripts/F2R1_end_second_in_pair_test.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/F2R1_end_second_in_pair.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/pair_test.sh b/tests/strandedness_tests/scripts/pair_test.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/pair_example_18_49488551_49590000.sorted.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/same_pos_dif_reads_test.sh b/tests/strandedness_tests/scripts/same_pos_dif_reads_test.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/same_pos_dif_reads.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/tax1bp3_chr17_3665556.sh b/tests/strandedness_tests/scripts/tax1bp3_chr17_3665556.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/tax1bp3_chr17_3665556.bam \
 --annotation_bedfile_path \

diff --git a/tests/strandedness_tests/scripts/tax1bp3_chr17_3665556_read_test.sh b/tests/strandedness_tests/scripts/tax1bp3_chr17_3665556_read_test.sh
@@ -1,4 +1,6 @@
-marine.py \
+mypython=$1
+
+$mypython $MARINE/marine.py \
 --bam_filepath \
 $MARINE/tests/strandedness_tests/bams/tax1bp3_chr17_3665556_read.bam \
 --annotation_bedfile_path \

diff --git a/...strandedness_tests/tax1bp3_chr17_3665556_read_test/final_filtered_site_info_annotated.tsv b/...strandedness_tests/tax1bp3_chr17_3665556_read_test/final_filtered_site_info_annotated.tsv