pytest / ci

Author: Fxe

.travis.yml

@@ -0,0 +1,15 @@
+language: python
+python:
+  - 3.6
+  - 3.7
+  - 3.8
+before_install:
+  - python --version
+  - pip install -U pip
+  - pip install -U pytest
+  - pip install codecov
+install:
+  - pip install ".[test]" . # install package + test dependencies
+script: pytest # run tests
+after_success:
+  - codecov # submit coverage

examples/GCF_000005845.2.faa

@@ -0,0 +1,24 @@
+>NP_414543.1 fused aspartate kinase/homoserine dehydrogenase 1 [Escherichia coli str. K-12 substr. MG1655]
+MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAA
+AQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY
+LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV
+PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSV
+SGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIIS
+VVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGAL
+LEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAV
+ADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSL
+SYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMA
+NLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGND
+VTAAGVFADLLRTLSWKLGV
+>NP_414544.1 homoserine kinase [Escherichia coli str. K-12 substr. MG1655]
+MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQI
+PVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI
+ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLP
+GFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN
+>NP_414545.1 threonine synthase [Escherichia coli str. K-12 substr. MG1655]
+MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAF
+AFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRG
+KISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQ
+LVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKI
+WQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKEL
+AERADLPLLSHNLPADFAALRKLMMNHQ

examples/Genomes.ipynb

@@ -22,30 +22,57 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
-    "genome = MSGenome.from_fasta('GCF_000005845.2_ASM584v2_protein.faa', split=' ')"
+    "genome = MSGenome.from_fasta('GCF_000005845.2.faa', split=' ')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Number of features: 4284\n"
+      "Number of features: 3\n"
      ]
     }
    ],
    "source": [
     "print('Number of features:', len(genome.features))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "NP_414543.1 820 fused aspartate kinase/homoserine dehydrogenase 1 [Escherichia coli str. K-12 substr. MG1655]\n",
+      "NP_414544.1 310 homoserine kinase [Escherichia coli str. K-12 substr. MG1655]\n",
+      "NP_414545.1 428 threonine synthase [Escherichia coli str. K-12 substr. MG1655]\n"
+     ]
+    }
+   ],
+   "source": [
+    "for f in genome.features:\n",
+    "    print(f.id, len(f.seq), f.description)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": 14,

examples/ModelSEED.ipynb

@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import modelseedpy\n",
+    "modelseed = modelseedpy.biochem.from_local('/Users/fliu/workspace/jupyter/ModelSEEDDatabase/')\n",
+    "rxn = modelseed.get_seed_reaction('rxn00002')\n",
+    "print(rxn)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{('cpd00001', '0'): -1.0,\n",
+       " ('cpd00067', '0'): -3.0,\n",
+       " ('cpd00742', '0'): -1.0,\n",
+       " ('cpd00011', '0'): 2.0,\n",
+       " ('cpd00013', '0'): 2.0}"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rxn.cstoichiometry"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<modelseedpy.biochem.modelseed_compound.ModelSEEDCompound at 0x7fb8d2fb8450>"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cpd = modelseed.get_seed_compound('cpd00742')\n",
+    "cpd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "rxn00002: cpd00001 [0] + 3.0 cpd00067 [0] + cpd00742 [0] --> 2.0 cpd00011 [0] + 2.0 cpd00013 [0]\n"
+     ]
+    }
+   ],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}