From 345111630ebd32af2b0d6f1bb057d651a65cc050 Mon Sep 17 00:00:00 2001
From: Migun Shakya <microbeatic@gmail.com>
Date: Fri, 20 Jul 2018 14:44:44 -0600
Subject: [PATCH] removing gff file name from file names

---
 pypiret/Runs/Summ.py         | 11 +++++------
 tests/test_pipeline_linux.sh |  4 ++--
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/pypiret/Runs/Summ.py b/pypiret/Runs/Summ.py
index b4375a8..c1f67e8 100644
--- a/pypiret/Runs/Summ.py
+++ b/pypiret/Runs/Summ.py
@@ -42,18 +42,17 @@ def output(self):
         if ',' in self.gff:
             gff_list = self.gff.split(",")
             gff_full_path = [os.path.abspath(gff) for gff in gff_list]
-            gtfs = [self.workdir + "/" + gff.split("/")[-1].split(".gff")[0] + ".gtf" for gff in gff_full_path]
             all_target = []
             for gffs in gff_full_path:
                 feature = list(set(pd.read_csv(gffs, sep="\t", header=None, comment='#')[2].tolist()))
-                loc_target = [LocalTarget(counts_dir +  os.path.basename(gffs) + "_" + feat + "_count.tsv") for feat in feature]
+                loc_target = [LocalTarget(counts_dir + feat + "_count.tsv") for feat in feature]
                 all_target = loc_target + all_target
                 return all_target
         else:
             gff_fp = os.path.abspath(self.gff)
             features = list(set(pd.read_csv(gff_fp, sep="\t", header=None, comment='#')[2].tolist()))
             features = [feat for feat in features if feat in ['CDS', 'rRNA', 'tRNA', 'exon', 'gene', 'transcript']]
-            loc_target = LocalTarget(counts_dir + "/" + os.path.basename(self.gff).split(".gff")[0] + "_" + features[-1] + "_count.tsv")
+            loc_target = LocalTarget(counts_dir + "/" + features[-1] + "_count.tsv")
             return loc_target
 
     def run(self):
@@ -83,12 +82,12 @@ def run(self):
                                           "-g", self.fid,
                                           "-t", feat,
                                           "-T", self.num_cpus,
-                                          "-o", counts_dir + "/" + gffs.split("/")[-1].split("gff")[0] + "_" + feat + "_count.tsv"] + in_srtbam_list
+                                          "-o", counts_dir + "/" + feat + "_count.tsv"] + in_srtbam_list
                         fcount_cmd = featureCounts[fcount_cmd_opt]
                         fcount_cmd()
         else:
             feature = list(set(pd.read_csv(self.gff, sep="\t", header=None,
-                                            comment='#')[2].tolist()))
+                                           comment='#')[2].tolist()))
             for feat in feature:
                 if feat in ['CDS', 'rRNA', 'tRNA', 'exon', 'gene', 'transcript',
                             'novel_region']:
@@ -99,7 +98,7 @@ def run(self):
                                       "-g", self.fid,
                                       "-t", feat,
                                       "-T", self.num_cpus,
-                                      "-o", counts_dir + "/" + self.gff.split("/")[-1].split(".gff")[0] + "_" + feat + "_count.tsv"] + in_srtbam_list
+                                      "-o", counts_dir + "/" + feat + "_count.tsv"] + in_srtbam_list
                     fcount_cmd = featureCounts[fcount_cmd_opt]
                     fcount_cmd()
 
diff --git a/tests/test_pipeline_linux.sh b/tests/test_pipeline_linux.sh
index d50a10f..b35eeb5 100644
--- a/tests/test_pipeline_linux.sh
+++ b/tests/test_pipeline_linux.sh
@@ -18,12 +18,12 @@ printf "${blue}testing pipeline with prokarya only\n${normal}"
 
 printf "bin/runPiReT -d tests/test_prok -e test_prok.txt \
 -gp tests/data/test_prok.gff \
--i tests/test_prok/prok_index -k prokarya -m all \
+-i tests/test_prok/prok_index -k prokarya -m DEedge \
 -fp tests/data/test_prok.fa --config luigi.cfg"
 
 bin/runPiReT -d tests/test_prok -e test_prok.txt \
 -gp tests/data/test_prok.gff \
--i tests/test_prok/prok_index -k prokarya -m all \
+-i tests/test_prok/prok_index -k prokarya -m DEedge \
 -fp tests/data/test_prok.fa --config luigi.cfg
 
 printf "${blue}fininshed testing pipeline for prokarya only\n${normal}"