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diff --git a/README.md b/README.md
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-# cDNA Generator
-
-Description of the project
-
-
-
-**Input files**
-
-Copy_number_file:
-
-- csv-formatted file ("NewTranscriptID,ID,Count")
-
-- id of generated transcript
-
-- id of original transcript (without intron inclusions)
-count
-
-_Eample_
-
-`[id of generated transcript] [ID] [Count]`
-
-
-transcript_sequences_file:
-
-- fasta-formatted file
-
-- id of generated transcript? (in the header)
-
-_Eample_
-
-`> [id of generated transcript]
-AGUGACGUUAGACCAGAUAGAC....`
-
-
-priming_site_file:
-
-- gtf-formatted file
-
-- id of generated transcript?
-
-- position of priming site and binding likelihood
-
-_Eample_
-
-`[id of generated transcript] ... [position of priming site]... [binding likelihood ]`
-
-
-**Output files**
-
-cDNA_file:
-
-- fasta-formatted file
-
-- Includes all the uniquie "cDNA sequence" and "cDNA sequence ID"
-
-
-
-cDNA_count_file:
-
-- csv-formatted file
-
-- Includes "cDNA sequence ID" and "cDNA count"
-
-
-
-
-
-
diff --git a/Test/.gitkeep b/Test/.gitkeep
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diff --git a/Test/copy_number_file.csv b/Test/copy_number_file.csv
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-NewTranscriptID, ID, Count
-1,1,12
-2,1,11
-3,2,33
-4,3,11
-5,4,55
diff --git a/Test/priming_sites.gtf b/Test/priming_sites.gtf
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-Transcript_1 RIBlast Priming_site 10 25 . + . Accessibility_Energy "1.49"; Hybridization_Energy "-9.76"; Interaction_Energy "-8.74"; Number_of_binding_sites "2"; Binding_Probability "0.12"
-Transcript_1 RIBlast Priming_site 640 655 . + . Accessibility_Energy "1.71"; Hybridization_Energy "-9.12"; Interaction_Energy "-8.34"; Number_of_binding_sites "2"; Binding_Probability "0.05"
-Transcript_2 RIBlast Priming_site 3 18 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.15"
diff --git a/Test/transcript.fasta b/Test/transcript.fasta
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->1
-GAUAGCUAGAGGAUUCUCAGAGGAGAAGCUAGAGGAGCUAGAGGAGCUAGAGGAGCUAGAGGAGCUAGAGG
->2
-AGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAGCUAGAGGAGCUAGAGGAGCUAGAGG
->3
-AGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAGCUAGAGG
->4
-AGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAUAGCUAGAGGAGCUAGAGGAGCUAGAGG
diff --git a/cdna/__init__.py b/cdna/__init__.py
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diff --git a/cdna/cdna.py b/cdna/cdna.py
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-import sys
-
-def translate(res):
- translate_dict = {"A": "T", "U": "A", "G": "C", "C":"G"}
- if res not in translate_dict.keys():
- print("cDNA residue not A,T,U or G ")
- sys.exit(1)
- return translate_dict[res]
-
-class cDNA_Gen:
- def __init__(self,
- fasta,
- gtf,
- cpn,
- output_fasta = "cDNA.fasta",
- output_csv = "cDNA.csv"
- ):
- # inputs
- self.fasta = fasta
- self.gtf = gtf
- self.cpn = cpn
- self.output_fasta = output_fasta
- self.output_csv = output_csv
- # variables
- self.prime_sites = []
- self.fasta_seq = ""
- self.fasta_id = ""
- self.copy_numbers = {}
-
- self.run()
-
- def run(self):
- self.read_fasta()
- self.read_gtf()
-
- def order_priming_sites(self):
- pass
-
- def generate_cdna(self):
- pass
-
-
- def read_fasta(self):
- fasta = open(self.fasta).readlines()
- self.fasta_id = fasta[0]
- print(fasta[0])
- self.fasta_seq = "".join([_.rstrip() for _ in fasta[1:]])
-
-
- def read_gtf(self):
- with open(self.gtf) as gtf_file:
- gtf_lines = gtf_file.readlines()
- for line in gtf_lines[:1000]:
- if not line.startswith("#"):
- temp_gtf = GTF_entry(line)
- temp_gtf.set_sequence(self.fasta_seq)
- self.prime_sites.append(temp_gtf)
-
- def write_fasta(self):
- pass
-
- def read_copy_numbers(self):
- with open(self.cpn) as cpn_file:
- cpn_lines = cpn_file.readlines()
- for line in cpn_lines:
- csv = line.split(",")
- trans_id = csv[0]
- if trans_id:
- gene_id = csv[1]
- count = csv[2]
- self.copy_numbers[gene_id] = count
-
-
- def return_output(self):
- return self.output_fasta, self.output_csv
-
-
-class GTF_entry:
- def __init__(self, string):
- self.string = string
- self.values = self.string.split("\t")
- self.id = self.values[0]
- self.start = int(self.values[3])
- self.end = int(self.values[4])
- self.score = float(0.5) #self.values[5]
- self.sequence = "no sequence set"
- self.length = self.end - self.start
-
- def __repr__(self):
- return self.sequence[:10] + "..." + f" len={self.length} score={self.score}"
-
- def set_sequence(self, full_sequence):
- self.sequence = full_sequence[self.start:self.end]
-
-
-if __name__ == "__main__":
- import argparse
- pass
-
-
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