Mercurial > repos > artbio > repenrich

changeset 14:bf866bedd4b4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5
author artbio
date Sat, 20 Apr 2024 12:13:52 +0000
parents 530626b0757c
children 2e3d976e7d5d
files RepEnrich.py RepEnrich_setup.py macros.xml
diffstat 3 files changed, 1 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/RepEnrich.py	Tue Apr 02 21:16:37 2024 +0000
+++ b/RepEnrich.py	Sat Apr 20 12:13:52 2024 +0000
@@ -1,6 +1,5 @@
 import argparse
 import csv
-import os
 import shlex
 import subprocess
 import sys
@@ -46,18 +45,6 @@
 else:
     paired_end = False
 
-# check that the programs we need are available
-try:
-    subprocess.call(shlex.split("coverageBed -h"),
-                    stdout=open(os.devnull, 'wb'),
-                    stderr=open(os.devnull, 'wb'))
-    subprocess.call(shlex.split("bowtie --version"),
-                    stdout=open(os.devnull, 'wb'),
-                    stderr=open(os.devnull, 'wb'))
-except OSError:
-    print("Error: Bowtie or bedtools not loaded")
-    raise
-
 
 def starts_with_numerical(list):
     try:
--- a/RepEnrich_setup.py	Tue Apr 02 21:16:37 2024 +0000
+++ b/RepEnrich_setup.py	Sat Apr 20 12:13:52 2024 +0000
@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 import argparse
 import csv
-import os
 import shlex
 import subprocess
 import sys
@@ -48,15 +47,6 @@
 genomefasta = args.genomefasta
 cpus = args.cpus
 
-# check that the programs we need are available
-try:
-    subprocess.call(shlex.split("bowtie --version"),
-                    stdout=open(os.devnull, 'wb'),
-                    stderr=open(os.devnull, 'wb'))
-except OSError:
-    print("Error: Bowtie not available in the path")
-    raise
-
 
 def starts_with_numerical(list):
     try:
@@ -115,7 +105,6 @@
     block = 3
     for i in range(0, len(rep_coords[repname]) - block + 1, block):
         batch = rep_coords[repname][i:i+block]
-        print(batch)
         chromosome = batch[0]
         start = max(int(batch[1]) - flankingl, 0)
         end = min(int(batch[2]) + flankingl,
--- a/macros.xml	Tue Apr 02 21:16:37 2024 +0000
+++ b/macros.xml	Sat Apr 20 12:13:52 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.31.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">23.0</token>
 
     <xml name="repenrich_requirements">