diff --git a/Untitled.ipynb b/Untitled.ipynb
index f05859bb38cbefb0db8b6a4a7ae94d302ee60aa1..9c9d32789d52e3a957e860b3394094ed301673fe 100644
--- a/Untitled.ipynb
+++ b/Untitled.ipynb
@@ -43,7 +43,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "[SeqRecord(seq=Seq('ATCCATAAAAAAAAA'), id='Transcript_1_0', name='Transcript copy number: 8.0', description='', dbxrefs=[]), SeqRecord(seq=Seq('CATCTCAAAAAGTCT'), id='Transcript_1_1', name='Transcript copy number: 4.0', description='', dbxrefs=[]), SeqRecord(seq=Seq('AAAAAAAAAAAAAAA'), id='Transcript_2_0', name='Transcript copy number: 11.0', description='', dbxrefs=[])]\n"
+ "[SeqRecord(seq=Seq('TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATACAACCAAGT...AAA'), id='Transcript_1_0', name='Transcript copy number: 8.0', description='', dbxrefs=[]), SeqRecord(seq=Seq('TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATACAACCAAGT...TCT'), id='Transcript_1_1', name='Transcript copy number: 4.0', description='', dbxrefs=[]), SeqRecord(seq=Seq('AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAAATTCTTTC...AAA'), id='Transcript_2_0', name='Transcript copy number: 11.0', description='', dbxrefs=[])]\n"
]
}
],
@@ -213,8 +213,8 @@
" <td>0.705882</td>\n",
" <td>8.0</td>\n",
" <td>Transcript_1_0</td>\n",
- " <td>(T, T, T, T, T, T, T, T, T, A, T, G, G, A, T)</td>\n",
- " <td>ATCCATAAAAAAAAA</td>\n",
+ " <td>(T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ...</td>\n",
+ " <td>TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
@@ -234,8 +234,8 @@
" <td>0.294118</td>\n",
" <td>4.0</td>\n",
" <td>Transcript_1_1</td>\n",
- " <td>(A, G, A, C, T, T, T, T, T, G, A, G, A, T, G)</td>\n",
- " <td>CATCTCAAAAAGTCT</td>\n",
+ " <td>(A, G, A, C, T, T, T, T, T, G, A, G, A, T, G, ...</td>\n",
+ " <td>TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
@@ -255,8 +255,8 @@
" <td>1.000000</td>\n",
" <td>11.0</td>\n",
" <td>Transcript_2_0</td>\n",
- " <td>(T, T, T, T, T, T, T, T, T, T, T, T, T, T, T)</td>\n",
- " <td>AAAAAAAAAAAAAAA</td>\n",
+ " <td>(T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ...</td>\n",
+ " <td>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
@@ -358,13 +358,21 @@
"4 1.000000 11.0 Transcript_4_0 \n",
"5 1.000000 55.0 Transcript_5_0 \n",
"\n",
- " priming_site compliment \n",
- "0 (T, T, T, T, T, T, T, T, T, A, T, G, G, A, T) ATCCATAAAAAAAAA \n",
- "1 (A, G, A, C, T, T, T, T, T, G, A, G, A, T, G) CATCTCAAAAAGTCT \n",
- "2 (T, T, T, T, T, T, T, T, T, T, T, T, T, T, T) AAAAAAAAAAAAAAA \n",
- "3 None None \n",
- "4 None None \n",
- "5 None None "
+ " priming_site \\\n",
+ "0 (T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ... \n",
+ "1 (A, G, A, C, T, T, T, T, T, G, A, G, A, T, G, ... \n",
+ "2 (T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ... \n",
+ "3 None \n",
+ "4 None \n",
+ "5 None \n",
+ "\n",
+ " compliment \n",
+ "0 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
+ "1 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
+ "2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA... \n",
+ "3 None \n",
+ "4 None \n",
+ "5 None "
]
},
"execution_count": 4,
@@ -398,20 +406,235 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 7,
"id": "2eb8f224-0292-4bb0-9e27-ef3bc3676f1d",
"metadata": {},
"outputs": [
{
- "ename": "NameError",
- "evalue": "name 'G' is not defined",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
- "Input \u001b[0;32mIn [3]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mG\u001b[49m\u001b[38;5;241m.\u001b[39mdf_input_GTF\n",
- "\u001b[0;31mNameError\u001b[0m: name 'G' is not defined"
- ]
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>seqname</th>\n",
+ " <th>source</th>\n",
+ " <th>feature</th>\n",
+ " <th>start</th>\n",
+ " <th>end</th>\n",
+ " <th>score</th>\n",
+ " <th>strand</th>\n",
+ " <th>frame</th>\n",
+ " <th>Accessibility_Energy</th>\n",
+ " <th>Hybridization_Energy</th>\n",
+ " <th>Interaction_Energy</th>\n",
+ " <th>Number_of_binding_sites</th>\n",
+ " <th>Binding_Probability</th>\n",
+ " <th>Normalized_Binding_Probability</th>\n",
+ " <th>Transcript_Copy_Number</th>\n",
+ " <th>cdna_ID</th>\n",
+ " <th>priming_site</th>\n",
+ " <th>compliment</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>Transcript_1</td>\n",
+ " <td>RIBlast</td>\n",
+ " <td>Priming_site</td>\n",
+ " <td>10</td>\n",
+ " <td>25</td>\n",
+ " <td>NaN</td>\n",
+ " <td>+</td>\n",
+ " <td>0</td>\n",
+ " <td>1.49</td>\n",
+ " <td>-9.76</td>\n",
+ " <td>-8.74</td>\n",
+ " <td>2</td>\n",
+ " <td>0.12</td>\n",
+ " <td>0.705882</td>\n",
+ " <td>8.0</td>\n",
+ " <td>Transcript_1_0</td>\n",
+ " <td>(T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ...</td>\n",
+ " <td>TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>Transcript_1</td>\n",
+ " <td>RIBlast</td>\n",
+ " <td>Priming_site</td>\n",
+ " <td>640</td>\n",
+ " <td>655</td>\n",
+ " <td>NaN</td>\n",
+ " <td>+</td>\n",
+ " <td>0</td>\n",
+ " <td>1.71</td>\n",
+ " <td>-9.12</td>\n",
+ " <td>-8.34</td>\n",
+ " <td>2</td>\n",
+ " <td>0.05</td>\n",
+ " <td>0.294118</td>\n",
+ " <td>4.0</td>\n",
+ " <td>Transcript_1_1</td>\n",
+ " <td>(A, G, A, C, T, T, T, T, T, G, A, G, A, T, G, ...</td>\n",
+ " <td>TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>Transcript_2</td>\n",
+ " <td>RIBlast</td>\n",
+ " <td>Priming_site</td>\n",
+ " <td>3</td>\n",
+ " <td>18</td>\n",
+ " <td>NaN</td>\n",
+ " <td>+</td>\n",
+ " <td>0</td>\n",
+ " <td>1.21</td>\n",
+ " <td>-5.12</td>\n",
+ " <td>-2.34</td>\n",
+ " <td>1</td>\n",
+ " <td>0.15</td>\n",
+ " <td>1.000000</td>\n",
+ " <td>11.0</td>\n",
+ " <td>Transcript_2_0</td>\n",
+ " <td>(T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ...</td>\n",
+ " <td>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>Transcript_3</td>\n",
+ " <td>RIBlast</td>\n",
+ " <td>Priming_site</td>\n",
+ " <td>5</td>\n",
+ " <td>35</td>\n",
+ " <td>NaN</td>\n",
+ " <td>+</td>\n",
+ " <td>0</td>\n",
+ " <td>1.21</td>\n",
+ " <td>-5.12</td>\n",
+ " <td>-2.34</td>\n",
+ " <td>1</td>\n",
+ " <td>0.25</td>\n",
+ " <td>1.000000</td>\n",
+ " <td>33.0</td>\n",
+ " <td>Transcript_3_0</td>\n",
+ " <td>None</td>\n",
+ " <td>None</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>Transcript_4</td>\n",
+ " <td>RIBlast</td>\n",
+ " <td>Priming_site</td>\n",
+ " <td>5</td>\n",
+ " <td>35</td>\n",
+ " <td>NaN</td>\n",
+ " <td>+</td>\n",
+ " <td>0</td>\n",
+ " <td>1.21</td>\n",
+ " <td>-5.12</td>\n",
+ " <td>-2.34</td>\n",
+ " <td>1</td>\n",
+ " <td>0.15</td>\n",
+ " <td>1.000000</td>\n",
+ " <td>11.0</td>\n",
+ " <td>Transcript_4_0</td>\n",
+ " <td>None</td>\n",
+ " <td>None</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>5</th>\n",
+ " <td>Transcript_5</td>\n",
+ " <td>RIBlast</td>\n",
+ " <td>Priming_site</td>\n",
+ " <td>5</td>\n",
+ " <td>35</td>\n",
+ " <td>NaN</td>\n",
+ " <td>+</td>\n",
+ " <td>0</td>\n",
+ " <td>1.21</td>\n",
+ " <td>-5.12</td>\n",
+ " <td>-2.34</td>\n",
+ " <td>1</td>\n",
+ " <td>0.15</td>\n",
+ " <td>1.000000</td>\n",
+ " <td>55.0</td>\n",
+ " <td>Transcript_5_0</td>\n",
+ " <td>None</td>\n",
+ " <td>None</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " seqname source feature start end score strand frame \\\n",
+ "0 Transcript_1 RIBlast Priming_site 10 25 NaN + 0 \n",
+ "1 Transcript_1 RIBlast Priming_site 640 655 NaN + 0 \n",
+ "2 Transcript_2 RIBlast Priming_site 3 18 NaN + 0 \n",
+ "3 Transcript_3 RIBlast Priming_site 5 35 NaN + 0 \n",
+ "4 Transcript_4 RIBlast Priming_site 5 35 NaN + 0 \n",
+ "5 Transcript_5 RIBlast Priming_site 5 35 NaN + 0 \n",
+ "\n",
+ " Accessibility_Energy Hybridization_Energy Interaction_Energy \\\n",
+ "0 1.49 -9.76 -8.74 \n",
+ "1 1.71 -9.12 -8.34 \n",
+ "2 1.21 -5.12 -2.34 \n",
+ "3 1.21 -5.12 -2.34 \n",
+ "4 1.21 -5.12 -2.34 \n",
+ "5 1.21 -5.12 -2.34 \n",
+ "\n",
+ " Number_of_binding_sites Binding_Probability \\\n",
+ "0 2 0.12 \n",
+ "1 2 0.05 \n",
+ "2 1 0.15 \n",
+ "3 1 0.25 \n",
+ "4 1 0.15 \n",
+ "5 1 0.15 \n",
+ "\n",
+ " Normalized_Binding_Probability Transcript_Copy_Number cdna_ID \\\n",
+ "0 0.705882 8.0 Transcript_1_0 \n",
+ "1 0.294118 4.0 Transcript_1_1 \n",
+ "2 1.000000 11.0 Transcript_2_0 \n",
+ "3 1.000000 33.0 Transcript_3_0 \n",
+ "4 1.000000 11.0 Transcript_4_0 \n",
+ "5 1.000000 55.0 Transcript_5_0 \n",
+ "\n",
+ " priming_site \\\n",
+ "0 (T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ... \n",
+ "1 (A, G, A, C, T, T, T, T, T, G, A, G, A, T, G, ... \n",
+ "2 (T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ... \n",
+ "3 None \n",
+ "4 None \n",
+ "5 None \n",
+ "\n",
+ " compliment \n",
+ "0 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
+ "1 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
+ "2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA... \n",
+ "3 None \n",
+ "4 None \n",
+ "5 None "
+ ]
+ },
+ "execution_count": 7,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
@@ -420,30 +643,11 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"id": "4a482960-0e05-4355-b91c-fc7f51c138c2",
"metadata": {},
- "outputs": [
- {
- "ename": "NameError",
- "evalue": "name 'G' is not defined",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
- "Input \u001b[0;32mIn [4]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m G\u001b[38;5;241m.\u001b[39mdf_input_GTF[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mA\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[43mG\u001b[49m\u001b[38;5;241m.\u001b[39mdf_input_GTF\u001b[38;5;241m.\u001b[39mapply(\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mlambda\u001b[39;00m row: foo(row[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mseqname\u001b[39m\u001b[38;5;124m\"\u001b[39m], \n\u001b[1;32m 3\u001b[0m row[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstart\u001b[39m\u001b[38;5;124m\"\u001b[39m], \n\u001b[1;32m 4\u001b[0m row[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mend\u001b[39m\u001b[38;5;124m\"\u001b[39m]), \n\u001b[1;32m 5\u001b[0m axis\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m\n\u001b[1;32m 6\u001b[0m )\n",
- "\u001b[0;31mNameError\u001b[0m: name 'G' is not defined"
- ]
- }
- ],
- "source": [
- "G.df_input_GTF[\"A\"] = G.df_input_GTF.apply(\n",
- " lambda row: foo(row[\"seqname\"], \n",
- " row[\"start\"], \n",
- " row[\"end\"]), \n",
- " axis=1\n",
- ")"
- ]
+ "outputs": [],
+ "source": []
},
{
"cell_type": "code",
diff --git a/cdna/cdna.py b/cdna/cdna.py
index 5615eb5f7887c9a3ab7303842c867d40ac567635..a6025f8f86b5a9634b809e8fa7b6a1f0dd63a041 100644
--- a/cdna/cdna.py
+++ b/cdna/cdna.py
@@ -1,6 +1,8 @@
import sys
import warnings
+import logging
+from cli import parser
import pandas as pd
from Bio import SeqIO
from Bio.Seq import Seq
@@ -8,41 +10,32 @@ from Bio.SeqRecord import SeqRecord
from gtfparse import read_gtf
# ignore warnings from read_gtf
-warnings.filterwarnings(action='ignore', category=FutureWarning)
+warnings.filterwarnings(action="ignore", category=FutureWarning)
-def compliment(res):
+
+def compliment(res: str) -> str:
translate_dict = {"A": "T", "T": "A", "U": "A", "G": "C", "C": "G"}
if res not in translate_dict.keys():
print(f"Unknown character, {res}")
- sys.exit(1)
+ sys.exit(1)
return translate_dict[res]
-def seq_compliment(sequence):
+
+def seq_compliment(sequence: str) -> str:
if sequence is None:
- return None
- _ = "".join([compliment(char) for char in str(sequence)])[::-1] # reverse string
+ return "None"
+ _ = "".join([compliment(char) for char in str(sequence)])[::-1] # reverse string
return _
-class cDNA_Gen:
- def __init__(
- self, fasta, gtf, cpn, output_fasta="cDNA.fasta", output_csv="cDNA.csv"
- ):
- """_summary_
-
- Args:
- fasta (_type_): _description_
- gtf (_type_): _description_
- cpn (_type_): _description_
- output_fasta (str, optional): _description_. Defaults to "cDNA.fasta".
- output_csv (str, optional): _description_. Defaults to "cDNA.csv".
- """
+class CDNAGen:
+ def __init__(self, ifasta: str, igtf: str, icpn: str, ofasta: str, ocsv: str):
# inputs
- self.fasta = fasta
- self.gtf = gtf
- self.cpn = cpn
- self.output_fasta = output_fasta
- self.output_csv = output_csv
+ self.fasta = ifasta
+ self.gtf = igtf
+ self.cpn = icpn
+ self.output_fasta = ofasta
+ self.output_csv = ocsv
# variables
self.fasta_dict = None
@@ -66,27 +59,28 @@ class cDNA_Gen:
if row["compliment"] is not None:
copy_number = row["Transcript_Copy_Number"]
record = SeqRecord(
- Seq(row["compliment"]),
- row["cdna_ID"],
+ Seq(row["compliment"]),
+ row["cdna_ID"],
f"Transcript copy number: {copy_number}",
- "")
+ "",
+ )
self.fasta_records.append(record)
def add_sequences(self):
self.df_input_GTF["priming_site"] = self.df_input_GTF.apply(
- lambda row: self.read_primingsite(row["seqname"],
- row["start"],
- row["end"]),
- axis=1)
+ lambda row: self.read_primingsite(row["seqname"], row["start"]),
+ axis=1,
+ )
def add_compliment(self):
self.df_input_GTF["compliment"] = self.df_input_GTF["priming_site"].apply(
- lambda x: seq_compliment(x))
+ lambda x: seq_compliment(x)
+ )
- def read_primingsite(self, sequence, start, end):
+ def read_primingsite(self, sequence, start):
if sequence not in self.fasta_dict.keys():
return None
- _ = self.fasta_dict[sequence].seq[start:end]
+ _ = self.fasta_dict[sequence].seq[start:]
return _
def read_fasta(self):
@@ -96,35 +90,48 @@ class cDNA_Gen:
def read_csv(self):
df_input_CSV = pd.read_csv(self.cpn, index_col=False)
- df_input_CSV = df_input_CSV.reset_index() # make sure indexes pair with number of rows
+ df_input_CSV = (
+ df_input_CSV.reset_index()
+ ) # make sure indexes pair with number of rows
self.df_input_CSV = df_input_CSV
-
def read_gtf(self):
# returns GTF with essential columns such as "feature", "seqname", "start", "end"
# alongside the names of any optional keys which appeared in the attribute column
df_input_GTF = read_gtf(self.gtf)
- df_input_GTF['Binding_Probability'] = pd.to_numeric(df_input_GTF['Binding_Probability']) # convert to numeric
- df_normalization_bind_probablility = df_input_GTF.groupby('seqname')['Binding_Probability'].sum() # extract binding probablility
+ df_input_GTF["Binding_Probability"] = pd.to_numeric(
+ df_input_GTF["Binding_Probability"]
+ ) # convert to numeric
+ df_normalization_bind_probablility = df_input_GTF.groupby("seqname")[
+ "Binding_Probability"
+ ].sum() # extract binding probablility
count = 0
prev_id = None
# Adds Normalized_Binding_Probability and Transcript_Copy_Number to each transcript in the dataframe
for index, row in df_input_GTF.iterrows():
- # GTF transcript ID
- id_GTF = str(row['seqname'])
+ # GTF transcript ID
+ id_GTF = str(row["seqname"])
if id_GTF == prev_id:
count += 1
else:
prev_id = None
- count = 0
- # CVS transcript ID
- id_CSV = str(row['seqname']).split('_')[1]
+ count = 0
+ # CVS transcript ID
+ id_CSV = str(row["seqname"]).split("_")[1]
# Calculate Normalized_Binding_Probability and add to GTF dataframe
- df_input_GTF.loc[index, 'Normalized_Binding_Probability'] = row['Binding_Probability'] / df_normalization_bind_probablility[id_GTF]
+ df_input_GTF.loc[index, "Normalized_Binding_Probability"] = (
+ row["Binding_Probability"] / df_normalization_bind_probablility[id_GTF]
+ )
# Calculate Normalized_Binding_Probability and add to GTF dataframe
- csv_transcript_copy_number = self.df_input_CSV.loc[self.df_input_CSV['ID of transcript'] == int(id_CSV), 'Transcript copy number'].iloc[0]
- df_input_GTF.loc[index,'Transcript_Copy_Number'] = round(csv_transcript_copy_number * df_input_GTF.loc[index,'Normalized_Binding_Probability'])
- df_input_GTF.loc[index,'cdna_ID'] = f"{id_GTF}_{count}"
+ csv_transcript_copy_number = self.df_input_CSV.loc[
+ self.df_input_CSV["ID of transcript"] == int(id_CSV),
+ "Transcript copy number",
+ ].iloc[0]
+ df_input_GTF.loc[index, "Transcript_Copy_Number"] = round(
+ csv_transcript_copy_number
+ * df_input_GTF.loc[index, "Normalized_Binding_Probability"]
+ )
+ df_input_GTF.loc[index, "cdna_ID"] = f"{id_GTF}_{count}"
prev_id = id_GTF
self.df_input_GTF = df_input_GTF
@@ -134,13 +141,18 @@ class cDNA_Gen:
SeqIO.write(self.fasta_records, self.output_fasta, "fasta")
def write_csv(self):
- self.df_input_GTF[["cdna_ID", "Transcript_Copy_Number"]].to_csv(self.output_csv, index=False)
+ self.df_input_GTF[["cdna_ID", "Transcript_Copy_Number"]].to_csv(
+ self.output_csv, index=False
+ )
def return_output(self):
return self.output_fasta, self.output_csv
-
-if __name__ == "__main__":
- import argparse
- pass
+if __name__ == "main":
+ logging.basicConfig(
+ format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+ level=logging.INFO,
+ )
+ LOG = logging.getLogger(__name__)
+ cnda_object = parser()
diff --git a/cdna/cli.py b/cdna/cli.py
index 8a623693ef8b7df6bfea53c8825d65639ba81a6a..8c533020acc431a65bdf5766a42eb4a94a1c4351 100644
--- a/cdna/cli.py
+++ b/cdna/cli.py
@@ -1 +1,23 @@
import cdna
+import argparse
+
+
+def parser():
+ parser = argparse.ArgumentParser(
+ prog="cDNA generator",
+ description="Generate cDNA sequences based on primer probabilities.",
+ )
+ parser.add_argument("--input_fasta_file", help="genome fasta file")
+ parser.add_argument("--input_gtf", help="gtf file")
+ parser.add_argument("--output_fasta_name", help="output fasta file")
+ parser.add_argument("--input_copy_number", help="input copy number (csv) file")
+ parser.add_argument("--output_csv_name", help="output fasta file")
+ args = parser.parse_args()
+ CDNA = cdna.cdna.CDNAGen(
+ ifasta=args["input_fasta_file"],
+ igtf=args["input_gtf_file"],
+ icpn=args["input_copy_number"],
+ ocsv=args["output_csv_name"],
+ ofasta=args["output_fasta_name"],
+ )
+ return CDNA
diff --git a/test_files/cDNA.fasta b/test_files/cDNA.fasta
index 18bd991775a765df6bad34d73d75e47e94aedf4b..2168d9f9c386c2bf4ef6db01ea350623b1a055ef 100644
--- a/test_files/cDNA.fasta
+++ b/test_files/cDNA.fasta
@@ -1,6 +1,123 @@
>Transcript_1_0
-ATCCATAAAAAAAAA
+TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATACAACCAAGTGTTCCC
+AGAAATTTTCTTAAAATGCACACCGGCTAAACCAACAATACGAACCTTGACGATATGAAT
+TTCGAATTTGATGGGCTCTTTTTCTGTTGTAGTCATGCCTTCGCTACCGTCACCTTGTTG
+GTGGATGTTCTCCAAAGATGTTCCCGAATGCTTATCATCTCCATAGGTTTCGGTAATAGA
+AAAAAAAAAAAAAAAAAAATGTTTTTCTCTGGTGAATGGAATTAGTTGTCAAAGGAGAAG
+AAGGTGAGTATTTATTAGAGCCTTGACGTCTAATGGATTCGTGGTGCGAAAGTGGCATGA
+TCGATCTTGGAGTCCCTTCTCTCTTCGCTGCCACATTATTGGAAGAGAACCTTTGCATAC
+AAACAAAACCACCCTTAACCTCCTTGAACTCTATATTCATTTTCCTCAGAACAAACATAA
+TCTTGTATCTAACAATTGGCAAAGGCTTCGATGAAGTTGTCTGAACAGAAAAGAAACCCT
+TCAAAAATAAAGAACGGGGGAAATCGATGGATGGCATAGAACCGGCTGGAGCTCTAGAAG
+CTTCCTGCAATATCTCTTCATCTGTTAATTCCTTCTCCACAGATGGCGAGTTTATGTGTG
+CGTTCACAGAATGCACGCTGACGCTATCATTCGTCTGTGAAGTAACATTTCCCAAACTAT
+CGGATTTGTTATCGTCACTTGATTCTAAGAACCCAGTATCTATAAGCTCTTGCTGAGGAT
+AGGCAGATGAAGGCATTGGGGGTCTCATATATTTGAGTGATTCACGACGAGCATGACCAA
+CTGATTTAGCTCTTGCGCTTGGATGTAGTTTTCGACCTTTTGCAACATTGAGAGGTGGTA
+AGGGATGATTCTCGTCGTCGTCGCTTCCTTCAAACTTCTGTGCAGCGTAAGCTTCCCGCC
+CGCTTCCTTTTGCAACTTCATTATTCTGTTTATTAATATCATGCAATTTCATTATATCTT
+CTTCAATTTGCTTCTCCCTTTGCTTCTCTACCATATTTTCTGCATCCGCAGGCAATGCTG
+GAAAGTCACCTTTATTGCCACCTCTGCTATCGTTTGTCTTGACAGGCTCATTCATGGTAT
+AATTTGAATCATAACTCGGTTTAGCAAAACCAGGGACAAAGTCTGAAACAGCGCGAGAAT
+GCGTCTTTTGCACAGGTTTATTGATACTATTATTACTATTAACAGATGTCTGTTCAATGG
+TCTTTTTACGGCGCTGTGATAATTTTCTAAATATATTCCCAAACTTCGCCTTTTCTGAGG
+GATCGCCAGTAGTTGAAGGTACCCTAAATTGTTGATAGTCATTTCCCTGAGGAGTTGGAG
+AGAGAGCATATTCCATTTCACGGCGTTGATTATCAGAACTTTTTCTACTCGTTGGTGACG
+TATGCGCTTGTTCTGGCATTGCTAACCTCGGTGGAATTAAGACATGTAAGGGGGGCTCTG
+TGCCATCGCTATTCTTTGGAGTGAATGGCACAGAGGTATCTTTTGTCGCCAACGTGGCTT
+CTGGCTCTGATTTCATAGCGGTTGTATTGACCTCTACGTCCCTTTGCTTCACACTTTCCG
+GTATTTCAGAAAGCTTTTCTATATTTTCGTGGCTCTGTCGCTGTTGTTGATTCCGAATTT
+TCGCATGTTTCCTATCAAGCATCTCAGAAGTCAAGTAATATATGGAAATCATTGGATGAT
+ATGCCCGAGTTGGGTCTTCAAAACTCTCTGTTATGTTTGGCGCGTTTCCGTTATCACTGG
+ATTCTGCGTTCATTTTGGCCGCTAAAGTCCAGTATTGTCTAGAGAGAAGAACGTAAGTAG
+GATCTGTGATTATACTGACCAAAACACTTCTTGTTTCCTCTACATCGTCAATAAATTCTA
+AACGGTACATTTCTTTTAAGACATTTATATCAAGCATTTCGATAGTTAGGGGAACTCTTT
+TCGGTAAGTAAGAAGGAGGGGGACCATTGAACCCTCTTACCATCCAGTGGTGCTCCACAA
+CCTGTTTAAGTGTGGCTCTTCTTTTCGGATCTACTACCAACATTTTGGATAACAGTGATA
+TTACTTCGATAGATAAATGTTGGGGATATTCAACCTTACCTTGCTTGATCTTTTCATGTA
+AAACGCTCGAATTTTCGTCGTCAAATGGCACTTTACCGCATACCAAAACAAATAAAACTA
+CACCAAATGACCAGACATCTACTTCAGGTCCTGTATAAGGATTCGCTTTTAACAGCTCGG
+GAGCGGCAAAATACAGAGAGCCACAGAATGTATGAAGCTGCTTCCTAGAATCATAAATAT
+TTGAAAGTCCAAAATCAATTATCTTGATTTCACTGGAATCTGAAATCATTATATTTTCTA
+TCTTCAAATCTCTATGGACGATGTTGTTAGCATGCAAATATATTAAGGCGCTCGCGATAC
+CCCTAGCAAACTTTCTCGCTTGGTGTTCTCGTATTGACCCATGTTGGATGATATAGTCTA
+ACAGCTGACCACCTGAAACATATTCAAACAACATATAGAAATGATTTGACAACGTGCACA
+TCTCAAAAAGTCTACATATGTGTGGATGATATAAGATTTGTCCCAAGGACGCTTCTCGAA
+TAGTTCTTTTGTCCCTAGATATTTCCTTCTCTAATTTCTTCTGTCTCTCCAAAACATCTT
+GTTCATTTTTGGGTGGTGGCAGCATTTGTTCTTTATGTAGGAAAGCCTTTGTAGCACGGT
+TTACAATTTTTACTGCACAAACCTCATTAGTGTAACGATGTTTTGCCAGCTTCACTTTAC
+CCATAGAACCTGCACCAACTGTTTCAACAAACTCCCAATCTCCTAACGATTTTCGATGAA
+ACTGCTTAGGCATGCCCTGAGAAGACGAAACTCGACTCTGGCTGGTAGTATTTGGCTTTG
+GTGCATTCTCTCTCGATTTACCTTCAAGTTCTACTTGTCTCTCCTTTTGCTCTGCTTGAT
+GTGAGTTACCATTATTGGCGTATTTGATATCCGCCGGGGGCATTAGCGGTGTGTTCTGCT
+GCTGCTGCTGCTGTGGACTTTTTCCCATCATTCTCAGCGTAGCGGGCGCCATAGTGCTTG
+GTTGTGTATGCATGCTGTTGCTTTCACTATTGCCATCATCCTGCTGGTTACCTCTGCCCA
+TTGAGAAGGCAGTATTTACGTGATAATCATCCATAAAAAAAAA
>Transcript_1_1
-CATCTCAAAAAGTCT
+TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATACAACCAAGTGTTCCC
+AGAAATTTTCTTAAAATGCACACCGGCTAAACCAACAATACGAACCTTGACGATATGAAT
+TTCGAATTTGATGGGCTCTTTTTCTGTTGTAGTCATGCCTTCGCTACCGTCACCTTGTTG
+GTGGATGTTCTCCAAAGATGTTCCCGAATGCTTATCATCTCCATAGGTTTCGGTAATAGA
+AAAAAAAAAAAAAAAAAAATGTTTTTCTCTGGTGAATGGAATTAGTTGTCAAAGGAGAAG
+AAGGTGAGTATTTATTAGAGCCTTGACGTCTAATGGATTCGTGGTGCGAAAGTGGCATGA
+TCGATCTTGGAGTCCCTTCTCTCTTCGCTGCCACATTATTGGAAGAGAACCTTTGCATAC
+AAACAAAACCACCCTTAACCTCCTTGAACTCTATATTCATTTTCCTCAGAACAAACATAA
+TCTTGTATCTAACAATTGGCAAAGGCTTCGATGAAGTTGTCTGAACAGAAAAGAAACCCT
+TCAAAAATAAAGAACGGGGGAAATCGATGGATGGCATAGAACCGGCTGGAGCTCTAGAAG
+CTTCCTGCAATATCTCTTCATCTGTTAATTCCTTCTCCACAGATGGCGAGTTTATGTGTG
+CGTTCACAGAATGCACGCTGACGCTATCATTCGTCTGTGAAGTAACATTTCCCAAACTAT
+CGGATTTGTTATCGTCACTTGATTCTAAGAACCCAGTATCTATAAGCTCTTGCTGAGGAT
+AGGCAGATGAAGGCATTGGGGGTCTCATATATTTGAGTGATTCACGACGAGCATGACCAA
+CTGATTTAGCTCTTGCGCTTGGATGTAGTTTTCGACCTTTTGCAACATTGAGAGGTGGTA
+AGGGATGATTCTCGTCGTCGTCGCTTCCTTCAAACTTCTGTGCAGCGTAAGCTTCCCGCC
+CGCTTCCTTTTGCAACTTCATTATTCTGTTTATTAATATCATGCAATTTCATTATATCTT
+CTTCAATTTGCTTCTCCCTTTGCTTCTCTACCATATTTTCTGCATCCGCAGGCAATGCTG
+GAAAGTCACCTTTATTGCCACCTCTGCTATCGTTTGTCTTGACAGGCTCATTCATGGTAT
+AATTTGAATCATAACTCGGTTTAGCAAAACCAGGGACAAAGTCTGAAACAGCGCGAGAAT
+GCGTCTTTTGCACAGGTTTATTGATACTATTATTACTATTAACAGATGTCTGTTCAATGG
+TCTTTTTACGGCGCTGTGATAATTTTCTAAATATATTCCCAAACTTCGCCTTTTCTGAGG
+GATCGCCAGTAGTTGAAGGTACCCTAAATTGTTGATAGTCATTTCCCTGAGGAGTTGGAG
+AGAGAGCATATTCCATTTCACGGCGTTGATTATCAGAACTTTTTCTACTCGTTGGTGACG
+TATGCGCTTGTTCTGGCATTGCTAACCTCGGTGGAATTAAGACATGTAAGGGGGGCTCTG
+TGCCATCGCTATTCTTTGGAGTGAATGGCACAGAGGTATCTTTTGTCGCCAACGTGGCTT
+CTGGCTCTGATTTCATAGCGGTTGTATTGACCTCTACGTCCCTTTGCTTCACACTTTCCG
+GTATTTCAGAAAGCTTTTCTATATTTTCGTGGCTCTGTCGCTGTTGTTGATTCCGAATTT
+TCGCATGTTTCCTATCAAGCATCTCAGAAGTCAAGTAATATATGGAAATCATTGGATGAT
+ATGCCCGAGTTGGGTCTTCAAAACTCTCTGTTATGTTTGGCGCGTTTCCGTTATCACTGG
+ATTCTGCGTTCATTTTGGCCGCTAAAGTCCAGTATTGTCTAGAGAGAAGAACGTAAGTAG
+GATCTGTGATTATACTGACCAAAACACTTCTTGTTTCCTCTACATCGTCAATAAATTCTA
+AACGGTACATTTCTTTTAAGACATTTATATCAAGCATTTCGATAGTTAGGGGAACTCTTT
+TCGGTAAGTAAGAAGGAGGGGGACCATTGAACCCTCTTACCATCCAGTGGTGCTCCACAA
+CCTGTTTAAGTGTGGCTCTTCTTTTCGGATCTACTACCAACATTTTGGATAACAGTGATA
+TTACTTCGATAGATAAATGTTGGGGATATTCAACCTTACCTTGCTTGATCTTTTCATGTA
+AAACGCTCGAATTTTCGTCGTCAAATGGCACTTTACCGCATACCAAAACAAATAAAACTA
+CACCAAATGACCAGACATCTACTTCAGGTCCTGTATAAGGATTCGCTTTTAACAGCTCGG
+GAGCGGCAAAATACAGAGAGCCACAGAATGTATGAAGCTGCTTCCTAGAATCATAAATAT
+TTGAAAGTCCAAAATCAATTATCTTGATTTCACTGGAATCTGAAATCATTATATTTTCTA
+TCTTCAAATCTCTATGGACGATGTTGTTAGCATGCAAATATATTAAGGCGCTCGCGATAC
+CCCTAGCAAACTTTCTCGCTTGGTGTTCTCGTATTGACCCATGTTGGATGATATAGTCTA
+ACAGCTGACCACCTGAAACATATTCAAACAACATATAGAAATGATTTGACAACGTGCACA
+TCTCAAAAAGTCT
>Transcript_2_0
-AAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAAATTCTTTCATTAAA
+TCCATATATGGATCCTCCCCTTGAATTCCATAGTTGAATTCCTCTTCAGGGTATCTGTCA
+AATTGAGAAGTGTCACCTTGGCCCTGTTGGATTGGTGGTTCGTACGGCGTTTCTATGTAT
+CTTGCTAACAATTTCTCCCATATCACTTCGTTAAACCACGGATGGTTCTTGACATCTTCA
+CTTCCATTTTGTAAGTTACCCAACCTTTCACTTAAGTCTCTGGTAATTAGCTTCTTCAAT
+AAGTCCTGCGCGTCTGGATGGAAAAATGGTGGGAACTTCAATTCGGCGTTCAGTATATTT
+TCGTAAGTTTTCATGGTGTTCGAATTGTAAAATGGAGTGTATCCGGCAAGCATTTCATAG
+ATTAGCACACCAAAACTCCACCAATCCACTGATTTATTATACGGTTTTGTACTGACCACT
+TCCGGCGCTATGTAATCTGGTGTGCCACATAATGTGTATGTGACATCGGGAACGTATTTT
+GCGAAGCCAAAGTCGGTTATCTTGATATGGCCGTTTTTATCTAGAAGGATATTTTCTGGT
+TTCAAGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAATATATATTATATCCTTACTGTGCA
+AATATTCCAACGCTAAGCATACCTCTGCGGCATAAAATTTGGCTACTGGGTTGGGAAATC
+TTTGAGATTTACGTAGTAAAGAAAATAATTCACCACCTTCAATGTAGTCCATTACCATGA
+AAACTTGCTGAGAATCTTGGAACGTTCCCCACATTCGAATGATGAATGGATGTGAAACAA
+TTGAAAGCATTCGGCGTTCGTCATTGGTGTGTTCAACCTGCTTCAGCTTCACTATAGTGT
+GCTTTTTCAATGTCTTCAAAGCGTAAAACCTCCCATTGTGATTGGAACGAATTAGGTGAA
+CTCTCCCAAATGAGCCAGTTCCCAAAGTTCTTAAAATCTGAAAGTCACTTAGGGAATACT
+TTCCTGAGGTATCTCTATATTGTAGCATTGGTTTTTTAACCAAACAAATACCTGCAGACG
+CTTCTTCTTTCAACTTTCCGCTGTTTCTTCCATTTATCTCCACGGGTGTGTTGGAAGAAC
+ATTCCTCATGCACCGAATGTGCGTTTACAGGAATGTCTTGTCCAACGTTATCTGGAGTTG
+TTTCTGTCTTGGCAGTAATGCTTAATTTCCTGATTTCATTGTTGTTCATCGGATCAACAT
+ACATAAAAAAAAAAAAAAAAAA