MultiGeneBlastParser
A script to simplify the output of MultiGeneBlast
This script will convert the output of MultiGeneBlast (Medema, M. et al 2013) in to distinct entries for each hit, for easier downstream processing,
It depends on the pandas module as the only non-standard module.
This can be installed as follows:
$ python -m pip install pandas
or
$ conda install pandas
Full Script Options
usage: MGBparser.py [-h] [-v] [-r] [-q] [-s] [-b] [-o OUTFILE] [-m MAX_RESULT]
clusterfile
Parse and extract data from the output of MultiGeneBlast.
positional arguments:
clusterfile The text file of hits output by MGB. By default this
is called 'clusterblast_output.txt'.
optional arguments:
-h, --help show this help message and exit
-v, --verbose Verbose behaviour, printing parameters of the script.
-r, --references Display relevant references. This option cannot be
used with any others.
-q, --query Output the query sequence information (and write a
file). [Boolean]
-s, --sighits Output the table of significant hits (and write a
file). [Boolean]
-b, --blastfile Output the table of BLAST hits for each match (and
write a file). [Boolean]
-o OUTFILE, --outfile OUTFILE
Name stem for all output files (extensions are set
internally).
-m MAX_RESULT, --max_result MAX_RESULT
Return results for just the top n details sections
[Def: 50].
N.B. Python2 only at the present time. Pull requests to port to Py3 are welcome.
A simple invocation may look like:
python MGBparser.py --outfile myclusters clusterblast_output.txt
This would simply return as many hits as are in the input file, but will silently write files with the BLAST infomation and operon locations with the filename prefix myoperon*.
Note, the input file is a positional argument, and must come last. Note also that the output file is a name stem, and not the full filename. Output files will be created where the input file originated.
A more comprehensive invocation might look like:
python MGBparser.py --outfile myclusers -m 10 -qsbv clusterblast_output.txt
Which would run the script as before, but this time only return the top 10 hits (-m 10), whilst
also printing and writing files with the details of the input sequence, BLAST results, operon locations,
significant hit descriptions and would print many more status and information messages.
Output
Here is some example output (as generated from the /test_data/single_clusterblast_output.txt file):
(Note there is no need for the -m flag as there is only a single entry.)
Opening test_data/single_clusterblast_output.txt for reading...
Parsing Query details section...
Parsing Significant hit section...
Parsing Hit details section...
Splitting Hit details section...
Establishing Hit classes...
Writing query details to file: test_data/single_queryinfo.tsv
Query sequence information:
===========================
Input file:PVCcif_ATCC43949.gbk
Locus Start Stop Strand Annotation Comment
0 PAU_01961 8 457 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
1 PAU_01962 521 1618 + major_tail_sheath_protein no_locus_tag
2 PAU_01963 1799 3280 + tail_sheath_protein no_locus_tag
3 PAU_01964 3334 4533 + tail_sheath_protein no_locus_tag
4 PAU_01965 4547 5005 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
5 PAU_01966 5002 5181 + hypothetical_protein no_locus_tag
6 PAU_01967 5168 5851 + hypothetical_protein no_locus_tag
7 PAU_01968 5848 7449 + Rhs_element_Vgr_protein no_locus_tag
8 PAU_01969 7462 7905 + baseplate_wedge_subunit no_locus_tag
9 PAU_01970 7902 8318 + hypothetical_protein no_locus_tag
10 PAU_01971 8527 11253 + hypothetical_protein no_locus_tag
11 PAU_01972 11246 14197 + hypothetical_protein no_locus_tag
12 PAU_01973 14333 15184 + hypothetical_protein no_locus_tag
13 PAU_01974 15247 17145 + hypothetical_protein no_locus_tag
14 PAU_01975 17155 19227 + ATP-dependent_zinc_metalloprotease_FtsH no_locus_tag
15 PAU_01976 19252 20166 + hypothetical_protein no_locus_tag
16 PAU_01977 20327 21223 + hypothetical_protein no_locus_tag
17 PAU_01978 21308 22291 + hypothetical_protein no_locus_tag
18 PAU_01979 22788 23684 + hypothetical_protein no_locus_tag
19 PAU_01980 23656 24114 + hypothetical_protein no_locus_tag
Writing Significant hit details to file: test_data/single_sighitinfo.tsv
Significant Hit information:
============================
Rank ID Description
0 1 PAU_1 Photorhabdus asymbiotica strain ATCC43949
Writing Hit details for: 1. PAU_1 to test_data/single_PAU_1_locationinfo.tsv (1 of 1)
Hit location information:
============================
Locus Start Stop Strand Annotation Comment
0 PAU_01961 2233799 2234248 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
1 PAU_01962 2234312 2235409 + major_tail_sheath_protein no_locus_tag
2 PAU_01963 2235590 2237071 + tail_sheath_protein no_locus_tag
3 PAU_01964 2237125 2238324 + tail_sheath_protein no_locus_tag
4 PAU_01965 2238338 2238796 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
5 PAU_01966 2238793 2238972 + hypothetical_protein no_locus_tag
6 PAU_01967 2238959 2239642 + hypothetical_protein no_locus_tag
7 PAU_01968 2239639 2241240 + Rhs_element_Vgr_protein no_locus_tag
8 PAU_01969 2241253 2241696 + baseplate_wedge_subunit no_locus_tag
9 PAU_01970 2241693 2242109 + hypothetical_protein no_locus_tag
10 PAU_01971 2242318 2245044 + hypothetical_protein no_locus_tag
11 PAU_01972 2245037 2247988 + hypothetical_protein no_locus_tag
12 PAU_01973 2248124 2248975 + hypothetical_protein no_locus_tag
13 PAU_01974 2249038 2250936 + hypothetical_protein no_locus_tag
14 PAU_01976 2253043 2253957 + hypothetical_protein no_locus_tag
15 PAU_01977 2254118 2255014 + hypothetical_protein no_locus_tag
16 PAU_01978 2255099 2256082 + hypothetical_protein no_locus_tag
17 PAU_01979 2256579 2257475 + hypothetical_protein no_locus_tag
18 PAU_01980 2257447 2257905 + hypothetical_protein no_locus_tag
Writing Hit BLAST details for: 1. PAU_1 to test_data/single_PAU_1_blastinfo.tsv (1 of 50)
Hit location information:
============================
Locus Start Stop Strand Annotation Comment
0 PAU_01961 2233799 2234248 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
1 PAU_01962 2234312 2235409 + major_tail_sheath_protein no_locus_tag
2 PAU_01963 2235590 2237071 + tail_sheath_protein no_locus_tag
3 PAU_01964 2237125 2238324 + tail_sheath_protein no_locus_tag
4 PAU_01965 2238338 2238796 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
5 PAU_01966 2238793 2238972 + hypothetical_protein no_locus_tag
6 PAU_01967 2238959 2239642 + hypothetical_protein no_locus_tag
7 PAU_01968 2239639 2241240 + Rhs_element_Vgr_protein no_locus_tag
8 PAU_01969 2241253 2241696 + baseplate_wedge_subunit no_locus_tag
9 PAU_01970 2241693 2242109 + hypothetical_protein no_locus_tag
10 PAU_01971 2242318 2245044 + hypothetical_protein no_locus_tag
11 PAU_01972 2245037 2247988 + hypothetical_protein no_locus_tag
12 PAU_01973 2248124 2248975 + hypothetical_protein no_locus_tag
13 PAU_01974 2249038 2250936 + hypothetical_protein no_locus_tag
14 PAU_01976 2253043 2253957 + hypothetical_protein no_locus_tag
15 PAU_01977 2254118 2255014 + hypothetical_protein no_locus_tag
16 PAU_01978 2255099 2256082 + hypothetical_protein no_locus_tag
17 PAU_01979 2256579 2257475 + hypothetical_protein no_locus_tag
18 PAU_01980 2257447 2257905 + hypothetical_protein no_locus_tag
Writing Hit coordinates for: 1. PAU_1 to test_data/single_PAU_1_coords.tsv (1 of 1)
Hit coordinate information:
===========================
Hit No ID Start Locus End Locus Start Index End Index Main Strand Source
1 PAU_1 PAU_01961 PAU_01980 2233799 2257905 + Photorhabdus asymbiotica strain ATCC43949
MultiGeneBlast has been previously published here:
Medema MH, Takano E, Breitling R. "Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast." Molecular Biology and Evolution. 2013;30(5):1218-1223. doi:10.1093/molbev/mst025.