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