{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/pulls/comments/40850955","id":40850955,"diff_hunk":"@@ -0,0 +1,287 @@\n+\"\"\"\n+BLAST+6 format (:mod:`skbio.io.format.blast6`)\n+=========================================================================\n+\n+.. currentmodule:: skbio.io.format.blast6\n+\n+The BLAST+6 format (``blast6``) stores strings, integers, and floats relating\n+to the similarities between multiple DNA sequences. These values are stored in\n+a simple tabular format with no labels on individual columns. The values are\n+separated by the tab character.\n+\n+An example BLAST+6-formatted file comparing two protein sequences, taken\n+from [1]_::\n+\n+    moaC    gi|15800534|ref|NP_286546.1|    100.00  161 0   0   1   161 1\n+    161 3e-114  330\n+    moaC    gi|170768970|ref|ZP_02903423.1| 99.38   161 1   0   1   161 1\n+    161 9e-114  329\n+\n+Format Support\n+--------------\n+**Has Sniffer: No**\n+\n++------+------+---------------------------------------------------------------+\n+|Reader|Writer|                          Object Class                         |\n++======+======+===============================================================+\n+|Yes   |No    |:mod:`pandas.DataFrame`                                        |\n++------+------+---------------------------------------------------------------+\n+\n+Format Specification\n+--------------------\n+BLAST+6 format is a tabular text-based format produced by BLAST+ format 6,\n+containing data related to passed sequences, tab-separated, with no column\n+labels or headers of any kind.\n+\n+When blasting sequences using Ubuntu's command line, the user may specify what\n+data is returned.\n+\n+For example::\n+\n+    $ blastp -query queries.fasta -subject subjects.fasta -evalue 0.0001\\\n+    -max_target_seqs 2 -outfmt \"6 qseqid sseqid bitscore qstart sstart\"\n+    $ query1\tsubject2\t16.9\t1\t3\n+\n+In this case, the blastp command returns custom values, which were specified\n+by the user to be qseqid, sseqid, bitscore, qstart, and sstart. These names\n+are retained, but as the returned values show, these names do not mark the\n+columns. The user can also pass ``-outfmt 6`` instead, which will set the\n+columns to their default values.\n+\n+For example::\n+\n+    $ blastp -query queries.fasta -subject subjects.fasta -evalue 0.0001\\\n+    -max_target_seqs 2 -outfmt 6\n+    $ query1\tsubject2\t100.00\t8\t0\t0\t1\t8\t3\t10\t9e-05\t16.9\n+\n+If the user does not pass custom values, the blastp command will use the\n+default columns, which are qseqid, sseqid, pident, length, mismatch, gapopen,\n+qstart, qend, sstart, send, evalue, and bitscore.\n+\n+Types of Data\n+^^^^^^^^^^^^^\n++-----------+------------------------------------+-----+\n+|Name       |Description                         |Type |\n++===========+====================================+=====+\n+|qseqid     |Query Seq-id                        |str  |\n++-----------+------------------------------------+-----+\n+|qgi        |Query GI                            |int  |\n++-----------+------------------------------------+-----+\n+|qacc       |Query accesion                      |str  |\n++-----------+------------------------------------+-----+\n+|qaccver    |Query accesion.version              |str  |\n++-----------+------------------------------------+-----+\n+|qlen       |Query sequence length               |int  |\n++-----------+------------------------------------+-----+\n+|sseqid     |Subject Seq-id                      |str  |\n++-----------+------------------------------------+-----+\n+|sallseqid  |All subject Seq-id(s), separated by\\|str  |\n+|           |a ';'                               |     |\n++-----------+------------------------------------+-----+\n+|sgi        |Subject GI                          |int  |\n++-----------+------------------------------------+-----+\n+|sallgi     |All subject GIs                     |int  |\n++-----------+------------------------------------+-----+\n+|sacc       |Subject accesion                    |str  |\n++-----------+------------------------------------+-----+\n+|saccver    |Subject accesion.version            |str  |\n++-----------+------------------------------------+-----+\n+|sallacc    |All subject accesions               |str  |\n++-----------+------------------------------------+-----+\n+|slen       |Subject sequence length             |int  |\n++-----------+------------------------------------+-----+\n+|qstart     |Start of alignment in query         |int  |\n++-----------+------------------------------------+-----+\n+|qend       |End of alignment in query           |int  |\n++-----------+------------------------------------+-----+\n+|sstart     |Start of alignment in subject       |int  |\n++-----------+------------------------------------+-----+\n+|send       |End of alignment in subject         |int  |\n++-----------+------------------------------------+-----+\n+|qseq       |Aligned part of query sequence      |str  |\n++-----------+------------------------------------+-----+\n+|sseq       |Aligned part of subject sequence    |str  |\n++-----------+------------------------------------+-----+\n+|evalue     |Expect value                        |float|\n++-----------+------------------------------------+-----+\n+|bitscore   |Bit score                           |float|\n++-----------+------------------------------------+-----+\n+|score      |Raw score                           |int  |\n++-----------+------------------------------------+-----+\n+|length     |Alignment length                    |int  |\n++-----------+------------------------------------+-----+\n+|pident     |Percent of identical matches        |float|\n++-----------+------------------------------------+-----+\n+|nident     |Number of identical matches         |int  |\n++-----------+------------------------------------+-----+\n+|mismatch   |Number of mismatches                |int  |\n++-----------+------------------------------------+-----+\n+|positive   |Number of positive-scoring matches  |int  |\n++-----------+------------------------------------+-----+\n+|gapopen    |Number of gap openings              |int  |\n++-----------+------------------------------------+-----+\n+|gaps       |Total number of gaps                |int  |\n++-----------+------------------------------------+-----+\n+|ppos       |Percentage of positive-scoring matc\\|float|\n+|           |hes                                 |     |\n++-----------+------------------------------------+-----+\n+|frames     |Query and subject frames separated \\|str  |\n+|           |by a '/'                            |     |\n++-----------+------------------------------------+-----+\n+|qframe     |Query frame                         |int  |\n++-----------+------------------------------------+-----+\n+|sframe     |Subject frame                       |int  |\n++-----------+------------------------------------+-----+\n+|btop       |Blast traceback operations (BTOP)   |int  |\n++-----------+------------------------------------+-----+\n+|staxids    |Unique Subject Taxonomy ID(s), sepa\\|str  |\n+|           |rated by a ';' (in numerical order) |     |\n++-----------+------------------------------------+-----+\n+|sscinames  |Unique Subject Scientific Name(s), \\|str  |\n+|           |separated by a ';'                  |     |\n++-----------+------------------------------------+-----+\n+|scomnames  |Unique Subject Common Name(s), sepa\\|str  |\n+|           |rated by a ';'                      |     |\n++-----------+------------------------------------+-----+\n+|sblastnames|unique Subject Blast Name(s), separ\\|str  |\n+|           |ated by a ';' (in alphabetical\\     |     |\n+|           |order)                              |     |\n++-----------+------------------------------------+-----+\n+|sskingdoms |unique Subject Super Kingdom(s), se\\|str  |\n+|           |parated by a ';' (in alphabetical\\  |     |\n+|           |order)                              |     |\n++-----------+------------------------------------+-----+\n+|stitle     |Subject Title                       |str  |\n++-----------+------------------------------------+-----+\n+|sstrand    |Subject Strand                      |str  |\n++-----------+------------------------------------+-----+\n+|salltitles |All Subject Title(s), separated by \\|str  |\n+|           |a '<>'                              |     |\n++-----------+------------------------------------+-----+\n+|qcovs      |Query Coverage Per Subject          |int  |\n++-----------+------------------------------------+-----+\n+|qcovhsp    |Query Coverage Per HSP              |int  |\n++-----------+------------------------------------+-----+\n+\n+List of data and descriptions taken from BLAST Command Line Applications User\n+Manual [2]_.\n+\n+Examples\n+--------\n+An example of using _blast6_to_data_frame with default column labels.\n+\n+>>> from io import StringIO\n+>>> from skbio import read\n+>>> import pandas as pd\n+>>> fs = '\\\\n'.join([\n+...     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