plenoi / SAPPHIRE

SAPPHIRE: a stacking-based ensemble learning framework for accurate prediction of thermophilic proteins
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List index out of range #2

Open PaabloFdeez opened 1 year ago

PaabloFdeez commented 1 year ago

Hello,

During the last few days I have been trying to use your code in order to analyze the thermophilicity for a set of proteins, I have followed the instructions proposed both for sapphire and those indicated for sapphire. It is in the last step, at the time of executing sapphire.py when I get the following error:

Traceback (most recent call last): File "sapphire", line 380, in <module> fasta = read_fasta('/home/sie/TFM_pablo/uniref50/uniref50.fasta') File "scriptpssm", line 10, in read_fasta fasta = [[item[0], re.sub('[^ACDEFGHIKLMNPQRSTVWY]', '', ''.join(item[1:]).upper())] for item in line2] File "scriptpssm", line 10, in <listcomp> fasta = [[item[0], re.sub('[^ACDEFGHIKLMNPQRSTVWY]', '', ''.join(item[1:]).upper())] for item in line2] IndexError: list index out of range

I am not sure what may be the problem causing it, thank you in advance.

plenoi commented 1 year ago

Hi,

 

Did you change something in sapphire.py ?   the error tell me like it cannot read fasta file.

is your fasta file has the same format as seq.fasta.  can you send me your input file ?

 

Phasit 

   

Sent: Saturday, August 05, 2023 at 10:40 PM From: "PaabloFdeez" @.> To: "plenoi/SAPPHIRE" @.> Cc: "Subscribed" @.***> Subject: [plenoi/SAPPHIRE] List index out of range (Issue #2)

 

Hello,

During the last few days I have been trying to use your code in order to analyze the thermophilicity for a set of proteins, I have followed the instructions proposed both for sapphire and those indicated for sapphire. It is in the last step, at the time of executing sapphire.py when I get the following error:

Traceback (most recent call last): File "sapphire", line 380, in fasta = read_fasta('/home/sie/TFM_pablo/uniref50/uniref50.fasta') File "scriptpssm", line 10, in read_fasta fasta = [[item[0], re.sub('[^ACDEFGHIKLMNPQRSTVWY]', '', ''.join(item[1:]).upper())] for item in line2] File "scriptpssm", line 10, in fasta = [[item[0], re.sub('[^ACDEFGHIKLMNPQRSTVWY]', '', ''.join(item[1:]).upper())] for item in line2] IndexError: list index out of range

I am not sure what may be the problem causing it, thank you in advance.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: @.***>

PaabloFdeez commented 1 year ago

I think I made a mistake when using the seq.fasta file, in my case, I am using the fasta file provided by pssmpro, I mean the uniref50.fasta file. If this is not the file, which one should I use?

Thanks again.