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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3
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4 import sys
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5 #from galaxy.tools.read_file import *
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6 from Bio import SeqIO
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7 import os
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8 from read_file import *
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9
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10 fasta_file = sys.argv[1]
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11 map_file = sys.argv[2]
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12 result_file = sys.argv[3]
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13
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14 os.system("samtools view -F 0xfff "+map_file+"|cut -f 3,4 > map_info.txt")
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15
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16 fasta_sequences = SeqIO.parse(open(fasta_file),'fasta');
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17 length_seq = {};
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18 for seq in fasta_sequences:
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19 nuc = seq.id;
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20 length_seq[nuc] = len(seq.seq.tostring());
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21
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22
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23
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24 mapping = {}
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25 transcripts = []
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26
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27 f = open("map_info.txt");
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28 for aline in f.readlines():
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29 tline = aline.strip();
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30 tl = tline.split('\t');
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31 if tl[0].strip() not in transcripts:
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32 transcripts.append(tl[0].strip());
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33 mapping[tl[0].strip()] = [];
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34
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35 mapping[tl[0].strip()].append(tl[1].strip());
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36
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37 distribution = {};
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38 coverage = {};
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39 for transcript in length_seq:
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40 distribution[transcript] = [];
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41 for i in range(0, length_seq[transcript]):
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42 distribution[transcript].append(0);
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43 sum_count = float(0);
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44 if transcript in mapping:
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45 for j in range(0, len(mapping[transcript])):
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46 index = mapping[transcript][j];
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47 #count = reads[mapping[transcript][j][0]];
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48 sum_count = sum_count + 1;
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49 distribution[transcript][int(index)-1] = distribution[transcript][int(index)-1] + 1;
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50 coverage[transcript] = float(sum_count)/float(length_seq[transcript]);
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51 else:
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52 coverage[transcript] = 0
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53
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54
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55
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56
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57
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58 h = file(result_file, 'w')
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59 for transcript in length_seq:
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60 h.write(transcript);
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61 h.write('\n')
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62 for i in range(0, length_seq[transcript]):
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63 h.write(str(distribution[transcript][i]))
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64 h.write('\t')
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65 h.write('\n')
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66 h.write('\n')
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67
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68
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69
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70
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71
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72 f.close();
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73 h.close()
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74
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75
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76
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77
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