Output a query alignment of domain family from the Pfam Stockholm Alignment files
In Pfam website, some domain family alignments are not downloadable. e.g The FN3 domain using NCBI sequence database . Thus we need to retrieve this data from the big files from the Pfam ftp site (ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/database_files/).
However, there is not such an existing tool to extract all the alignments given a domain ID from the Pfam multiple concatenated alignments files. The most relevant tool Biopython supports parsing Stockholm alignment format but does not support output alignment given a query domain accession ID.
Here, a handy script is written to extract alignments from Pfam file in Stockholm format given a domain ID from Pfam.
Example:
Python parse_pfam_stockholm.py Pfam-A.full.ncbi.gz PF00041 > output.file
Input 1: The Pfam file that contains full alignments of all Pfam-A families e.g. Pfam-A.full.ncbi.gz
Input 2: Pfam Domain ID e.g PF00041
Output: lines of sequences belong to that domain family with IDs and aligned sequences (including gaps)
| Sequence_ID_1 | Aligned_Sequence_1 |
|---|---|
| Sequence_ID_2 | Aligned_Sequence_2 |
