Mercurial > repos > chrisd > testing
comparison gene_fraction/src/Fasta.cpp @ 0:f95150c37d38 draft default tip
planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
| author | chrisd |
|---|---|
| date | Sun, 21 Feb 2016 23:31:55 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:f95150c37d38 |
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| 1 #include "Fasta.h" | |
| 2 #include "args.h" | |
| 3 | |
| 4 #include <iostream> | |
| 5 #include <fstream> | |
| 6 #include <vector> | |
| 7 #include <string> | |
| 8 | |
| 9 Fasta::Fasta(std::string amr_fp) : _amr_fp(amr_fp) {} | |
| 10 | |
| 11 void Fasta::read_fasta(const std::string &amr_fp) { | |
| 12 std::ifstream in(amr_fp.c_str()); | |
| 13 if(!in) { | |
| 14 usage(); | |
| 15 exit(EXIT_FAILURE); | |
| 16 } | |
| 17 | |
| 18 std::string gene_id, gene, line; | |
| 19 while(std::getline(in, line)) { | |
| 20 std::size_t gene_idx = line.find(" "); | |
| 21 | |
| 22 if(gene_idx != std::string::npos) | |
| 23 gene_id = line.substr(1, gene_idx-1); | |
| 24 else | |
| 25 gene_id = line.substr(1, line.length()); | |
| 26 | |
| 27 std::getline(in, gene); | |
| 28 records.push_back(FastaRecord(gene_id, gene)); | |
| 29 } | |
| 30 in.close(); | |
| 31 | |
| 32 FastaRecord::sort_by_gene_id(records); | |
| 33 } | |
| 34 | |
| 35 | |
| 36 | |
| 37 | |
| 38 | |
| 39 |