From c69d673b2478e9302976556d2a8e7a5c3c28ca45 Mon Sep 17 00:00:00 2001
From: miriambt <miriambarrabes@hotmail.com>
Date: Fri, 15 Nov 2024 17:26:39 -0500
Subject: [PATCH] Change output path names to unphased suffix in SNPObj.ipynb

---
 demos/SNPObj.ipynb | 49 +++++++++++++++++++++++-----------------------
 1 file changed, 24 insertions(+), 25 deletions(-)

diff --git a/demos/SNPObj.ipynb b/demos/SNPObj.ipynb
index 8ae372b..4559d4c 100644
--- a/demos/SNPObj.ipynb
+++ b/demos/SNPObj.ipynb
@@ -790,7 +790,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 29,
    "id": "544b2955",
    "metadata": {},
    "outputs": [
@@ -799,14 +799,14 @@
      "output_type": "stream",
      "text": [
       "SNPObject saved to ../data/output.vcf\n",
-      "SNPObject saved to ../data/output.phased\n"
+      "SNPObject saved to ../data/output.unphased\n"
      ]
     }
    ],
    "source": [
     "# Define the path to save the VCF file\n",
     "output_vcf_path1 = '../data/output.vcf'\n",
-    "output_vcf_path2 = '../data/output.phased'\n",
+    "output_vcf_path2 = '../data/output.unphased'\n",
     "\n",
     "# Save the SNPObject as a VCF file (Option 1)\n",
     "snpobj.save(output_vcf_path1)\n",
@@ -827,7 +827,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 30,
    "id": "08eff0b2",
    "metadata": {},
    "outputs": [
@@ -835,27 +835,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.pvar\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.pvar\n",
       "INFO:snputils.snp.io.write.pgen:Writing ../data/output.psam\n",
       "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.pgen\n",
       "SNPObject saved to ../data/output.pgen\n",
-      "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.phased.pvar\n",
-      "INFO:snputils.snp.io.write.pgen:Writing ../data/output.phased.psam\n",
-      "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.phased.pgen\n",
-      "SNPObject saved to ../data/output.phased\n"
+      "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.unphased.pvar\n",
+      "INFO:snputils.snp.io.write.pgen:Writing ../data/output.unphased.psam\n",
+      "INFO:snputils.snp.io.write.pgen:Writing to ../data/output.unphased.pgen\n",
+      "SNPObject saved to ../data/output.unphased\n"
      ]
     }
    ],
    "source": [
     "# Define the path to save the BED file\n",
     "output_pgen_path1 = '../data/output.pgen'\n",
-    "output_pgen_path2 = '../data/output.phased'\n",
+    "output_pgen_path2 = '../data/output.unphased'\n",
     "\n",
     "# Save the SNPObject as a PGEN file (option 1)\n",
     "snpobj.save(output_pgen_path1)\n",
@@ -876,7 +870,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 31,
    "id": "fbca1fd8",
    "metadata": {},
    "outputs": [
@@ -899,14 +893,14 @@
       "INFO:snputils.snp.io.write.bed:Writing .bim file: ../data/output\n",
       "WARNING:snputils.snp.io.write.bed:The .bim file is being saved with 0 cM values.\n",
       "INFO:snputils.snp.io.write.bed:Finished writing .bim file: ../data/output\n",
-      "SNPObject saved to ../data/output.phased\n"
+      "SNPObject saved to ../data/output.unphased\n"
      ]
     }
    ],
    "source": [
     "# Define the path to save the BED file\n",
     "output_bed_path1 = '../data/output.bed'\n",
-    "output_bed_path2 = '../data/output.phased'\n",
+    "output_bed_path2 = '../data/output.unphased'\n",
     "\n",
     "# Save the SNPObject as a BED file (option 1)\n",
     "snpobj.save(output_bed_path1)\n",
@@ -927,7 +921,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 33,
    "id": "cea856ad",
    "metadata": {},
    "outputs": [
@@ -935,18 +929,23 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "SNPObject saved to ../data/output.pkl\n"
+      "SNPObject saved to ../data/output.pkl\n",
+      "SNPObject saved to ../data/output.unphased\n"
      ]
     }
    ],
    "source": [
     "# Define the path to save the pickle file\n",
-    "output_pkl_path = '../data/output.pkl'\n",
+    "output_pkl_path1 = '../data/output.pkl'\n",
+    "output_pkl_path2 = '../data/output.unphased'\n",
     "\n",
-    "# Save the SNPObject as a pickle file\n",
-    "snpobj.save(output_pkl_path)\n",
+    "# Save the SNPObject as a pickle file (option 1)\n",
+    "snpobj.save(output_pkl_path1)\n",
+    "print(f\"SNPObject saved to {output_pkl_path1}\")\n",
     "\n",
-    "print(f\"SNPObject saved to {output_pkl_path}\")"
+    "# Save the SNPObject as a pickle file (option 2)\n",
+    "snpobj.save_pickle(output_pkl_path2)\n",
+    "print(f\"SNPObject saved to {output_pkl_path2}\")"
    ]
   },
   {