pssm_info reads a series of query strings from the command line or from standard input, and returns full information about each entry in the pssm table matching those queries. Queried fields are pssmID, accession, shortname, family, and length.
$ pssm_info 9831 1221 12345
query pssmid accession shortname family length
========================================================================
9831 9831 pfam04272 Phospholamban 1 51
1221 16405 pfam05110 AF-4 1 1221
12345 12345 COG3002 COG3002 0 880
$ cat pssmfile
5392 14924 15108 5308 14925 10386 15093 14938 16538 7409 14964 16539
$ pssm_info < pssmfile
query pssmid accession shortname family length
========================================================================
5392 5392 cd00192 TyrKc 0 269
14924 14924 smart00219 TyrKc 0 255
15108 15108 pfam00069 pkinase 0 253
5308 5308 cd00180 S_TKc 0 257
14925 14925 smart00220 S_TKc 0 256
10386 10386 COG0515 SPS1 0 384
15093 15093 pfam00017 SH2 0 77
14938 14938 smart00252 SH2 0 85
16538 16538 cd00173 SH2 0 94
7409 7409 pfam00018 SH3 0 56
14964 14964 smart00326 SH3 0 58
16539 16539 cd00174 SH3 0 54
If your query returns a unique pssmid, you can use the '-a' flag to retrieve additional information from other tables about the pssmid.
bash-2.04$ pssm_info -a smart00014
query pssmid accession shortname family length
========================================================================
smart00014 8 smart00014 acidPPc 0 122
Connected to pssmIDs: 10540 16995 13219
Hits on PIGs: 48895 81097 130122 130123 130736 322157 409159 532976 ....
You can also provide more specific queries with the '-w select * from pssm where querystring.
$ pssm_info -w "length > 50 and length < 52 and INSTR(accession,'pfam'sh-2.04$ pssm_info -w "length > 50 and length < 52 and family = 1"
query pssmid accession shortname family length
========================================================================
length > 50 an% 9831 pfam04272 Phospholamban 1 51
length > 50 an% 9831 pfam04272 Phospholamban 1 51
You can also use a querystring with a list of queries to insert multiple values into a querystring. Leave a place for insertion (%s or %r) in your querystring, and follow with a list of queries.
$ pssm_info -w "shortname = %r" Phospholamban PyrI_C
query pssmid accession shortname family length
========================================================================
Phospholamban 9831 pfam04272 Phospholamban 1 51
PyrI_C 3255 pfam02748 PyrI_C 0 51
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