From f6ff40005e9e2c58875dae4455b9dc63c93f4d40 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 30 Oct 2019 17:41:30 +0100
Subject: [PATCH] Trying to use libreads for id conversions.

---
 CLIP/iCLIP.snakefile                  | 5 +++--
 CLIP/requirements.txt                 | 2 ++
 Degradome-seq/Degradome-seq.snakefile | 3 ++-
 Degradome-seq/requirements.txt        | 2 ++
 PRO-seq/PRO-seq.snakefile             | 3 ++-
 PRO-seq/requirements.txt              | 1 +
 RNA_Seq_Cecere/RNA-seq.snakefile      | 3 ++-
 RNA_Seq_Cecere/requirements.txt       | 2 ++
 8 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index b56f154..b52fb5f 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -541,14 +541,15 @@ rule feature_count_reads:
         err = OPJ(log_dir, "{trimmer}", "feature_count_reads", "{lib}_{rep}_{read_type}.err")
     shell:
         """
-        converter="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes_id2name.pickle"
+        # converter="/pasteur/entites/Mhe/Genomes/C_elegans/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes_id2name.pickle"
         tmpdir=$(mktemp -dt "feature_{wildcards.lib}_{wildcards.rep}_{wildcards.read_type}_{wildcards.biotype}_{wildcards.orientation}.XXXXXXXXXX")
         cmd="featureCounts -a {params.annot} -o {output.counts} -t transcript -g "gene_id" -O -M --primary -s {params.stranded} --fracOverlap 0 --tmpDir ${{tmpdir}} {input.sorted_bam}"
         featureCounts -v 2> {log.log}
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py ${{converter}} > {output.counts_converted}
+        cat {output.counts} | wormid2name > {output.counts_converted}
+        # cat {output.counts} | id2name.py ${{converter}} > {output.counts_converted}
         """
 
 
diff --git a/CLIP/requirements.txt b/CLIP/requirements.txt
index f128eab..fc0e8a5 100644
--- a/CLIP/requirements.txt
+++ b/CLIP/requirements.txt
@@ -3,3 +3,5 @@ pandas
 libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+# extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index f91c701..91effc6 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -227,7 +227,8 @@ rule feature_count_reads:
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
+        cat {output.counts} | wormid2name {params.converter} > {output.counts_converted}
+        # cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
         """
 
 
diff --git a/Degradome-seq/requirements.txt b/Degradome-seq/requirements.txt
index 336115a..38c60ce 100644
--- a/Degradome-seq/requirements.txt
+++ b/Degradome-seq/requirements.txt
@@ -2,3 +2,5 @@ numpy
 pandas
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
+# extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index b1d73f0..8e12e5b 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -703,7 +703,8 @@ rule feature_count_reads:
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
+        cat {output.counts} | wormid2name > {output.counts_converted}
+        # cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
         """
 
 
diff --git a/PRO-seq/requirements.txt b/PRO-seq/requirements.txt
index 958e2df..4fa1c4c 100644
--- a/PRO-seq/requirements.txt
+++ b/PRO-seq/requirements.txt
@@ -11,4 +11,5 @@ libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/li
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
 # extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git
 deeptools
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 534c174..6f9b419 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -895,7 +895,8 @@ rule feature_count_reads:
         echo ${{cmd}} 1>> {log.log}
         eval ${{cmd}} 1>> {log.log} 2> {log.err} || error_exit "featureCounts failed"
         rm -rf ${{tmpdir}}
-        cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
+        cat {output.counts} | wormid2name > {output.counts_converted}
+        # cat {output.counts} | id2name.py {params.converter} > {output.counts_converted}
         """
 
 
diff --git a/RNA_Seq_Cecere/requirements.txt b/RNA_Seq_Cecere/requirements.txt
index c63dab2..9258ec0 100644
--- a/RNA_Seq_Cecere/requirements.txt
+++ b/RNA_Seq_Cecere/requirements.txt
@@ -11,3 +11,5 @@ libdeseq @ git+https://bioinfo_utils:uqiFbzWyBtzxYn7br82P@gitlab.pasteur.fr/bli/
 libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
 libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git
 snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+# extra dependencies for some rules
+libcelegans @ git+https://bioinfo_utils:izoZHUvhFJU8689hqM5u@gitlab.pasteur.fr/bli/libcelegans.git
-- 
GitLab