Cutting the sequence into several sequences with the information of a dataframe

Question

I have a fasta file with several 120-concatenation protein sequences. I also have a data frame with 120 names of proteins in column 1 and their length in column 2. Using this dataframe I want to create a new fasta file per sequence in which I get each protein independent with the name of the protein and the bacteria.

Here my fasta file.

Bacteria_1
Seq('GRRKAAVARAYMTAGKGNVTVNKKDYKDFFPVPTLQYKITQPFAITETLGQYDV...IEE', SingleLetterAlphabet())

Bacteria_2
Seq('GRRKDSVARVYLRPGKGEIVVNKRPVEDYFGRETLKMVLRQPLELTESLDKFDI...YK-', SingleLetterAlphabet())

Here my dataframe

      Names  LEN
0     Ribosomal_S9:  121
1     Ribosomal_S8:  129
2    Ribosomal_L10:  100
3             GrpE:  166
4           DUF150:  141
..              ...  ...
115      TIGR03632:  117
116      TIGR03654:  175
117      TIGR03723:  314
118      TIGR03725:  212
119      TIGR03953:  188

[120 rows x 2 columns]

The name of the genes and their length is the same for all my bacteria so this df is applicable for all sequences in my fasta file.

I am trying to get new fasta files like this:

>Bacteria_1 Ribosomal_S9:
GRRKAAVARAYMTAGKGNVTVNKKDYKDFFPVPTLQYKITQPFAITETLGQYDV...

>Bacteria_1 Ribosomal_S8:
KDYKDFFPVPTLAAVARAYMTAGKGNLGQYDVGRRKAAVARAYMTAGKGN...
...

>Bacteria_1 TIGR03953:
AJEFISUBEVFCVALSKDMCFPADNSCF0AISCIABNSCNAISCN...

The second fasta file

>Bacteria_2 Ribosomal_S9:
GRRKAAVARAYMTAGKGNVTVNKKDYKDFFPVPTLQYKITQPFAITETLGQYDV...

>Bacteria_2 Ribosomal_S8:
KDYKDFFPVPTLAAVARAYMTAGKGNLGQYDVGRRKAAVARAYMTAGKGN...
...

>Bacteria_2 TIGR03953:
AJEFISUBEVFCVALSKDMCFPADNSCF0AISCIABNSCNAISCN...

Answer 1

We wouldn't write the code for you from scratch (thats your job), but its an easy problem because in Python any string is an "array" or "dictionary". Thus

bacteria1 = 'GRRKAAVARAYMTAGKGNVTVNKKDYKDFFPVPTLQYKITQPFAITETLGQYDVIEEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'
print (bacteria1[0:120])

This will define the first gene in your list, remembering the array starts at 0 whilst your gene starts at position 1 (so you need to subtract 1). You simply parse the input list so the gene lengths form a dictionary and loop through the dictionary of gene lengths ensuring the last length is added to the current one and then issuing a write command.

You don't really need biopython in this instance, unless it will parse the gene length file you need to open (I'm not aware it can).

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BTW the format you supplied isn't fasta it looks like a Biopython statement, again in this problem I wouldn't bother because Python is perfectly capable of splicing a string.