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POParse a fasta sequence file to retrieve Title and Sequence in Python
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2013-05-25T06:08:19.263
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2013-05-26T09:21:31.640
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2013-05-26T09:21:31.640
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I have to make a generic parser for parsing fasta files using Python. The format is like: <pre><code>>gi|348686675|gb|JH159151.1| Phytophthora sojae unplaced genomic scaffold PHYSOscaffold_1, whole genome shotgun sequence TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCA >gi|348686675|gb|JH159151.1| Phytophthora sojae unplaced genomic scaffold PHYSOscaffold_2, whole genome shotgun sequence CAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGA AGTTTATATATAAATTTCCTTTTTATTGGA >gi|348686675|gb|JH159151.1| Phytophthora sojae unplaced genomic scaffold PHYSOscaffold_3, whole genome shotgun sequence GAACTTAACATTTTCTTATGACGTAAATGAAGTTTATATATAAATTTCCTTTTTATTGGA TAATATGCCTATGCCGCATAATTTTTATATCTTTCTCCTAACAAAACATTCGCTTGTAAA </code></pre> I have to retrieve each title and sequence separately and insert the values in my created MySQL database. <pre><code>eg: title1 = PHYSOscaffold_1 sequence2 = TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCA title2 = PHYSOscaffold_2 sequence1 = CAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGA AGTTTATATATAAATTTCCTTTTTATTGGA </code></pre> and so on... I the insert these values into a MySQL table. The output of my parse should be like: <pre><code>name1 \t sequence1 \t length_of_sequence \t a_count \t t_count \t g_count \t c_count name2 \t sequence2 \t length_of_sequence \t a_count \t t_count \t g_count \t c_count </code></pre> So far, I have written a very basic script like this: <pre><code>infile = open("simple.fasta") line = infile.readline() if not line.startswith(">"): raise TypeError("Not a FASTA file: %r" % line) title = line sequence_lines = [] while 1: line = infile.readline().rstrip() if line == "": break sequence_lines.append(line) </code></pre> I am only getting my first sequence and title. I am a novice and need expert help.
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<python><parsing><fasta>
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Parse a fasta sequence file to retrieve Title and Sequence in Python
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