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minor error in CSV documentation #103

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Docs:
"subject_orf_length (Only the part that's really matched)"

CVS file for bmr10002-GenBank EDM17788.1 (F-spondin TSR 4):
 ...LPEC,false,766,518,CLVT...

Query sequence is 56 characters, "length that's really matched" is 766. 
(766 is the length of entire subject sequence with multiple 50+-character
matches between residues 402 and 766.)

Blast result is in
/big/jurgen/condor/blastio/out/weekly/nr/output/bmrb_seqs.faa.split/bmrb_seqs.fa
a.split.000190.blast,
CSV file is /big/jurgen/condor/blastio/processed/weekly/nr/
bmrb_seqs.faa.split.000190.csv

Original issue reported on code.google.com by dmitri.m...@gmail.com on 14 Aug 2008 at 6:04

GoogleCodeExporter commented 9 years ago 
the csv doc:

This partition contains the conversion programs and the objects specific for
describing the results from Blast, i.e. all the BlastMatch classes.
<BR>
The CSV files put out by Wattos follow the following syntax:

<P>for each query identifier set (usually just 1):
<UL>
<LI>orf_db_name
<LI>orf_db_id
<LI>orf_db_subid
<LI>molecule_name
</UL>

<P>followed by:
<UL>
<LI> bit_score
<LI>  bit_score_maximum
<LI>  expectation_value
<LI>  match_size
<LI>  number_gaps
<LI>  number_identities
<LI>  number_positives
<LI>  query_orf_length (full length query)
<LI>  query_orf_match_start
<LI>  query_orf_sequence (Only the part that's matched)
<LI>  query_is_positive_strand (only significant for nucleotides; true/false)
<LI>  subject_orf_length (Only the part that's really matched)
<LI>  subject_orf_match_start
<LI>  subject_orf_sequence (Only the part that's matched)
<LI>  subject_is_positive_strand (only significant for nucleotides; true/false)
</UL>

<P>and then for each subject identifier set (usually just 1)
<UL>
<LI>orf_db_name
<LI>orf_db_id
<LI>orf_db_subid
<LI>molecule_name
</UL>

Original comment by jurge...@gmail.com on 14 Aug 2008 at 6:29

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 14 Aug 2008 at 6:33