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annotate snp_caller/src/Fasta.cpp @ 0:0fd352f62446 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
author chrisd
date Sun, 21 Feb 2016 06:05:24 -0500
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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1 #include "Fasta.h"
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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3 #include <string>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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4 #include <fstream>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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5 #include <vector>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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6 #include <iostream>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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9 Fasta::Fasta(std::string amr_fp) : _amr_fp(amr_fp) {}
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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11 void Fasta::read_fasta(const std::string &amr_fp) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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12 std::ifstream in(amr_fp.c_str());
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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13 if(!in) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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14 std::cerr << "Could not open fasta file " << amr_fp << std::endl;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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15 exit(EXIT_FAILURE);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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16 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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18 std::string gene_id, gene, line;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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19 while(std::getline(in, line)) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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20 std::size_t gene_idx = line.find(" ");
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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22 if(gene_idx != std::string::npos)
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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23 gene_id = line.substr(1, gene_idx-1);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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24 else
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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25 gene_id = line.substr(1, line.length());
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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27 std::getline(in, gene);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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28 records.push_back(FastaRecord(gene_id, gene));
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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29 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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30 in.close();
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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32 FastaRecord::sort_by_gene_id(records);
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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33 }