NAME
====
fastafromGenbank
DEPENDENCIES
============
python-biopython, python3-biopython
DESCRIPTION
===========
The files in this directory allow you to download multiple fasta files from Genbank.
You can also use the same files to download genbank records by subsitituting "rettype=fasta"
with "rettype=gb" in the "*.py" files.
SCRIPTS
=======
clipper.sh - use this script to extract the gi number from a header format
acc2fa.py - run this script using python2 on a list of gi or accession numbers or both. It will use the genbank eutils to download the set of fasta files for the given list of id's.
acc2fa2.py - If the acc2fa.py script outputs "Error! Cannot fetch 'file-with-gi/acc-number' " for some of the ids
then run this script using python3 and it will create a new file with the names of files still to download.
INSTRUCTIONS FOR USE
====================
1. Visually inspect file with list of id's using an editor (vi, vim, gedit, emacs, your favorite editor)
2. The input file should be a list of different id formats. Don't worry about descriptions like "Acintobacteria_..". We'll deal with that shortly
For now if there are full header lines in the list then use the "clipper.sh" script like so.
$ bash clipper.sh inputfile
---------------------------
3. This will create a new file called "clipped" with just gi numbers. You will then use this as the new input when running the python scripts like so
$ cat clipped | python acc2fa.py > out.fasta
--------------------------------------------
4. For files that acc2fa.py cannot download an error message (Error! Cannot fetch:) will indicate what the id/description of this file is.
To get a new list of all these names just run "acc2fa2.py" like so
$ cat clipped | python3 acc2fa2.py > out.fasta
----------------------------------------------
5. Visually inpect this new file called "test.txt". At this point the names of id's will most likely have the id numbers that genbbank requires as the first 8 or 9 digits
in the string. In this case you can just use some simple cut commands followed by sed to replace "_" with empty space like so
$ cat test.txt | cut -c 1-9 | sed -e 's/_/ /g' > retest.txt
-----------------------------------------------------------
6. Run the "acc2fa.py" on the new "retest.txt" file like so
$ cat retest.txt | python acc2fa.py > out2.fasta
------------------------------------------------
7. Now all the fasta are within files out.fasta and out2,fasta so we can conctenate them into one file like so
$ cat out.fasta out2.fasta > all.fasta
--------------------------------------
8. As a check to see if all the fasta files are there you can extract all the header and count them like so
$ grep -e ">" allout.fasta | sort | uniq -c | wc -l
---------------------------------------------------
9. Finally to split the multifasta file into separate fasta files according to each header use the following command
$ seqretsplit allout.fasta
--------------------------