fixes

sfletc · Apr 26, 2023 · d528441 · d528441
1 parent dd6b040
commit d528441
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Showing 4 changed files with 13 additions and 14 deletions.
diff --git a/cmd/align.go b/cmd/align.go
@@ -61,14 +61,10 @@ scramAligner align -r ref.fa -1 seq1a.fa,seq1b.fa,seq1c.fa -l 21,22,24 -o testAl
 		t0 := time.Now()
 		var a map[string]interface{}
 		var fileOrder []string
-		switch {
-		case !indv:
-			fmt.Println("\nLoading mean and standard errors of replicate reads")
-			a = scramPkg.SeqLoad(strings.Split(fastaSet1, ","), readFileType, adapter, minLen, maxLen, minCount, noNorm)
-		case indv:
-			fmt.Println("\nLoading individual read counts")
-			a, fileOrder = scramPkg.IndvSeqLoad(strings.Split(fastaSet1, ","), readFileType, adapter, minLen, maxLen, minCount, noNorm)
-		}
+
+		fmt.Println("\nLoading individual read counts")
+		a, fileOrder = scramPkg.IndvSeqLoad(strings.Split(fastaSet1, ","), readFileType, adapter, minLen, maxLen, minCount, noNorm)
+
 		fmt.Println("\nLoading reference")
 		c := scramPkg.RefLoad(alignTo)
 		for _, nt := range strings.Split(length, ",") {

diff --git a/cmd/root.go b/cmd/root.go
@@ -38,7 +38,7 @@ import (
 	"github.com/spf13/viper"
 )
 
-const version = "2.0.1"
+const version = "2.0.4"
 
 var cfgFile string
 var fastaSet1 string
@@ -52,7 +52,6 @@ var maxLen int
 var minCount float64
 var adapter string
 var noNorm bool
-var indv bool
 
 var RootCmd = &cobra.Command{
 	Use:   "scram2",

diff --git a/scramScripts/scram2Plot/src/scram2Plot.py b/scramScripts/scram2Plot/src/scram2Plot.py
@@ -265,7 +265,7 @@ def __eq__(self, other): #TODO: update
             and np.array_equal(self.rvs, other.rvs)
         )
 
-def profile_plot(align_prefix, align_lens, header, smoothing_window=1, cov = True, abund=True, se = True, save=True, ylim_set=(0,0)):
+def align_plot(align_prefix, align_lens, header, smoothing_window=1, cov = True, abund=True, se = True, save=True, ylim_set=(0,0)):
     """
     
     """
@@ -284,7 +284,7 @@ def profile_plot(align_prefix, align_lens, header, smoothing_window=1, cov = Tru
     if se:
         plt.legend()
     if save:
-        save_file = align_prefix+header+".png"
+        save_file = align_prefix+"_"+header+".png"
         plt.savefig(save_file)
     plt.show()
 
@@ -354,7 +354,9 @@ def main():
     parser.add_argument("-y", "--ylim", help="Set y-axis limit", type=int, nargs=2, default=(0,0))
     parser.add_argument("-n", "--no_save", help="Do not save plot", action="store_true")
     args = parser.parse_args()
-    profile_plot(
+    if args.abundance:
+        args.coverage = True
+    align_plot(
         args.align_prefix,
         args.align_lens,
         args.header,

diff --git a/scramScripts/scram2Plot/src/setup.py b/scramScripts/scram2Plot/src/setup.py
@@ -11,12 +11,14 @@
         'pandas>=1.4.0',
         'seaborn>=0.12.0',
         'numpy>=1.23.0',
-        # Add more dependencies as needed
     ],
     entry_points={
         'console_scripts': [
             'scram2Plot=scram2Plot:main',
         ],
+        'scram2Plot': [
+            'scram2Plot=scram2Plot',
+        ]
     },
     classifiers=[
         'Development Status :: 3 - Alpha',