update version 0.10.2

ChangeLog.md

@@ -1,55 +1,64 @@
 # Changelog
 
+## 0.10.2 (2023-10-07)
+- Omit the creation of PDF files for WG and p-value distributions when no input sample is provided
+
 ## 0.10.1 (2023-10-01)
-- Bug fix when the input sample is not provided
+- Fixed bug occurring when no input sample is provided
 
 ## 0.10.0 (2023-08-04)
-- Add `churros_classheat` function
-- Add [HOMER](http://homer.ucsd.edu/homer/): Motif analysis
+- Added `churros_classheat` function
+- Added [HOMER](http://homer.ucsd.edu/homer/) for Motif analysis
+
+
+0.9.0 (2023-04-25)
+
+Added GenMap for fast genome mappability computation
+Added utility scripts gen_samplelist.sh and gen_samplepairlist.sh for creating sample lists
 
 ## 0.9.3 (2023-07-06)
-- Add Genometable file for S.pombe
-- Modify `ssp.sh` to take a mptable as an argument
-- Modify `churros_mapping` to use the mptable in `Ddir/mappability_Mosaics_kmer`
-- Bug fix in `calculate_mappability_mosaics.sh`
-- Bug fix of `chrros_mapping stats` command when paired-end ChIP-seq data is applied
+- Added Genometable file for S.pombe
+- Modified `ssp.sh` to accept mptable as an argument
+- Modified `churros_mapping` to use mptable in `Ddir/mappability_Mosaics_kmer`
+- Fixed bug in `calculate_mappability_mosaics.sh`
+- Fixed bug in `chrros_mapping stats` command for paired-end ChIP-seq data
 
 ## 0.9.2 (2023-06-23)
-- Update ChromHMM from v1.23 to v1.24
+- Updated ChromHMM from v1.23 to v1.24
 
 ## 0.9.1 (2023-05-11)
-- Remove /root/.cpanm/work directory
+- Removed /root/.cpanm/work directory to avoid the user id error
 
 ## 0.9.0 (2023-04-25)
-- Changed the base image from rnakato/database to rnakato/mapping (to simplify installation)
-- Add [GenMap](https://github.com/cpockrandt/genmap): fast computation of genome mappability
-- Add `gen_samplelist.sh` and `gen_samplepairlist.sh`, utilities to create samplelist.txt and samplepairlist.txt.
+- Changed base image from `rnakato/database` to `rnakato/mapping` for simplified installation
+- Added [GenMap](https://github.com/cpockrandt/genmap) for fast genome mappability computation
+- Added utility scripts `gen_samplelist.sh` and `gen_samplepairlist.sh` for creating sample lists
 
 ## 0.8.0 (2023-02-19)
-- Update gene annotation for T2T genome
-- Update DROMPAplus to v1.17.1
-- Bigfix of calculate_mappability_mosaics.sh
+- Updated gene annotation for T2T genome
+- Updated DROMPAplus to v1.17.1
+- Fixed bug in `calculate_mappability_mosaics.sh`
 
 ## 0.7.1 (2023-02-10)
-- Fix bug in macs2.sh
+- Fixed bug in `macs2.sh`
 
 ## 0.7.0 (2023-02-08)
-- Change default value of peak-calling (MACS2) from `--nomodel` to default
+- Changed default value for peak-calling in MACS2 from `--nomodel` to default settings
 
 ## 0.6.0 (2023-01-30)
-- Add [TOBIAS](https://github.com/loosolab/TOBIAS): differential ATAC-seq analysis
-- Add [STITCHIT](https://github.com/SchulzLab/STITCHIT): link regulatory elements to genes
+- Added [TOBIAS](https://github.com/loosolab/TOBIAS) for differential ATAC-seq analysis
+- Added [STITCHIT](https://github.com/SchulzLab/STITCHIT) for link regulatory elements to genes
 
 ## 0.5.0 (2023-01-07)
-- Add [Bismark](https://github.com/FelixKrueger/Bismark) and Bismark.sh for bisulfite sequencing analysis
-- Add [TrimGalore](https://github.com/FelixKrueger/TrimGalore) for adapter and quality trimming of FastQ files
-- Add [Cutadapt](https://cutadapt.readthedocs.io/en/stable/index.html) for adapter trimming of FastQ files
+- Added [Bismark](https://github.com/FelixKrueger/Bismark) and the custom script `Bismark.sh` for bisulfite sequencing analysis
+- Added [TrimGalore](https://github.com/FelixKrueger/TrimGalore) for adapter and quality trimming of FastQ files
+- Added [Cutadapt](https://cutadapt.readthedocs.io/en/stable/index.html) for adapter trimming of FastQ files
 
 ## 0.4.1 (2022-11-24)
-- Add ChangeLog
-- Bugfix: removed a bug `duplicate 'row.names' are not allowed` in `churros_compare
-- Update DROMPA+ to `v1.17.0`.
+- Added this ChangeLog
+- Fixed bug: removed a bug `duplicate 'row.names' are not allowed` in `churros_compare`
+- Updated DROMPAplus to `v1.17.0`
 
 ## 0.4.0
 - Public release
-- Update manual
+- Updated manual

Dockerfiles/Churros/churros.py

@@ -128,6 +128,24 @@ def ask_to_proceed_with_overwrite(filepath):
         return False
     return True
 
+def is_exist_input(samplepairlist):
+    df = pd.read_csv(samplepairlist, sep=",", header=None)
+    df.fillna("", inplace=True)
+
+    nInput = 0
+    for index, row in df.iterrows():
+        chip  = row[0]
+        input = row[1]
+        label = row[2]
+
+        if input != "":
+            nInput += 1
+
+    if nInput == 0:
+        return False
+    else:
+        return True
+
 def exec_churros(args):
     samplelist = args.samplelist
     samplepairlist = args.samplepairlist
@@ -206,10 +224,16 @@ def exec_churros(args):
         print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' --preset scer --enrich ' + str(samplepairlist) + ' drompa+.macspeak ' + build + ' ' + Ddir)
         print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' --preset scer --enrich --logratio ' + str(samplepairlist) + ' drompa+.macspeak ' + build + ' ' + Ddir)
     else:
+        df = pd.read_csv(samplepairlist, sep=",", header=None)
+        df.fillna("", inplace=True)
+
+        if is_exist_input(samplepairlist):
+            print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' -b 5000 -l 8000 --pvalue -P "--pthre_enrich 3 --scale_pvalue 3" ' + str(samplepairlist) + ' drompa+.pval.bin5M ' + build + ' ' + Ddir)
+            print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' -G ' + str(samplepairlist) + ' ' + 'drompa+ ' + build + ' ' + Ddir)
+
         print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' ' + chdir + '/' + args.macsdir + '/samplepairlist.txt drompa+.macspeak ' + build + ' ' + Ddir)
         print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' -b 5000 -l 8000 -P "--scale_tag 100" ' + str(samplepairlist) + ' drompa+.bin5M ' + build + ' ' + Ddir)
-        print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' -b 5000 -l 8000 --pvalue -P "--pthre_enrich 3 --scale_pvalue 3" ' + str(samplepairlist) + ' drompa+.pval.bin5M ' + build + ' ' + Ddir)
-        print_and_exec_shell('churros_visualize '+ param_churros_visualize + ' -G ' + str(samplepairlist) + ' ' + 'drompa+ ' + build + ' ' + Ddir)
+
 
 if(__name__ == '__main__'):
     parser = argparse.ArgumentParser()

Dockerfiles/Churros/churros_visualize.py

@@ -111,6 +111,23 @@ def do_churros_visualize(args):
     else:
         visualize_PCSHARP(args, param, samplepairlist, pdir, pdfdir, logdir, fileext, post, Ddir, chdir)
 
+def is_exist_input(samplepairlist):
+    df = pd.read_csv(samplepairlist, sep=",", header=None)
+    df.fillna("", inplace=True)
+
+    nInput = 0
+    for index, row in df.iterrows():
+        chip  = row[0]
+        input = row[1]
+        label = row[2]
+
+        if input != "":
+            nInput += 1
+
+    if nInput == 0:
+        return False
+    else:
+        return True
 
 def visualize_GV(args, samplepairlist, pdir, pdfdir, logdir, fileext, post, Ddir, build):
     param = " " + args.drompaparam + " "
@@ -139,6 +156,11 @@ def visualize_GV(args, samplepairlist, pdir, pdfdir, logdir, fileext, post, Ddir
 
     df = pd.read_csv(samplepairlist, sep=",", header=None)
     df.fillna("", inplace=True)
+
+    if not is_exist_input(samplepairlist):
+        print ("No ChIP sample with the input sample. Skipped.")
+        return
+
     sGV = ""
     for index, row in df.iterrows():
         chip  = row[0]
@@ -170,6 +192,11 @@ def visualize_PCENRICH(args, param, samplepairlist, pdir, pdfdir, logdir, fileex
 
     df = pd.read_csv(samplepairlist, sep=",", header=None)
     df.fillna("", inplace=True)
+
+    if not is_exist_input(samplepairlist):
+        print ("No ChIP sample with the input sample. Skipped.")
+        return
+
     s = ""
     for index, row in df.iterrows():
         chip  = row[0]
@@ -239,6 +266,7 @@ def visualize_PCSHARP(args, param, samplepairlist, pdir, pdfdir, logdir, fileext
         os.remove(outputprefix + ".pdf")
     print_and_exec_shell("rm " + outputprefix + "*.peak.bed " + outputprefix + "*.peak.tsv")
 
+
 if(__name__ == '__main__'):
     parser = argparse.ArgumentParser()
     parser.add_argument("samplepairlist", help="ChIP/Input pair list", type=str)

Dockerfiles/build.sh

@@ -1,8 +1,8 @@
-tag=0.10.1
+tag=0.10.2
 docker build -f Dockerfile.$tag -t rnakato/churros:$tag . #--no-cache
-#docker save -o churros-$tag.tar rnakato/churros:$tag
-#singularity build -F churros.$tag.sif docker-archive://churros-$tag.tar
-#exit
+docker save -o churros-$tag.tar rnakato/churros:$tag
+singularity build -F churros.$tag.sif docker-archive://churros-$tag.tar
+exit
 
 docker push rnakato/churros:$tag
 docker tag rnakato/churros:$tag rnakato/churros:latest