0.980634 - 572 sp|P06672|PDC_ZYMMO - 568 1.2e-263 874.5 0.0 1 1 6.6e-267 1.4e-263 874.2 0.0 5 562 15 570 12 572 0.98 Uncharacterized protein OS=Lomentospora prolificans OX=41688 GN=jhhlp_005678 PE=3 SV=1
I've asked a similar question before. I have a better understanding of python now and would like to revisit this. Can someone critique my thinking?
I have an HMM output file that contains about 20 fields. There are two sets of IDs, e.g., P006672 and jhhlp_005678
In a separate file are FASTA-formatted sequences linked to these IDs.
a) read in fields containing IDs, lets called them fields 8 and 6; b) store field values in an array or dictionary (whatever the proper data structure is for this). Let's called this Fields_8_and_6
a) read proteome file containing FASTA-formatted sequences
b) Grep and store as ID:sequence key:value pairs; let's call this ID_to_sequence
a) Compare Fields_8_and_6 to ID_to_sequence
b) Write ID1:sequence1 ID2:sequence2 as pairs into one file
send to ClustalO